WorldWideScience

Sample records for n-15 nmr assignments

  1. Structural NMR assignment

    International Nuclear Information System (INIS)

    Procter, J.B.; Torda, A.E.

    1999-01-01

    Full text: General automated NMR assignment approaches are aimed at full heteronuclear assignment, which is needed for structure determination. Usually, full assignment requires at least as much spectral information as is used for structure generation. For large proteins, obtaining sufficient spectral information may require a number of sample preparations and many spectra, resulting in a significant overhead for the use of NMR in biochemical investigation. For a protein of biochemical interest one may already have an x-ray crystal structure, but spectral assignment is still needed to use NMR as a structural probe for ligand binding studies. In this situation it may be possible to use much less spectral information to make an assignment based purely on the correspondence of structural data to the measurements contained in a few simple spectra. We introduce a framework to accomplish this 'structural assignment', and give some observations on the practical requirements for a structural assignment to succeed

  2. H-1, C-13, and N-15 resonance assignment of photoactive yellow protein

    NARCIS (Netherlands)

    Pool, Trijntje J.; Oktaviani, Nur Alia; Kamikubo, Hironari; Kataoka, Mikio; Mulder, Frans A. A.

    Photoactive yellow protein (PYP) is involved in the negative phototactic response towards blue light of the bacterium Halorhodospira halophila. Here, we report nearly complete backbone and side chain H-1, C-13 and N-15 resonance assignments at pH 5.8 and 20 A degrees C of PYP in its electronic

  3. H-1 and N-15 resonance assignment of the second fibronectin type III module of the neural cell adhesion molecule

    DEFF Research Database (Denmark)

    Kiselyov, Vladislav V; Berezin, Vladimir; Bock, Elisabeth

    2008-01-01

    We report here the NMR assignment of the second fibronectin type III module of the neural cell adhesion molecule (NCAM). This module has previously been shown to interact with the fibroblast growth factor receptor (FGFR), and the FGFR-binding site was mapped by NMR to the FG-loop region of the mo......We report here the NMR assignment of the second fibronectin type III module of the neural cell adhesion molecule (NCAM). This module has previously been shown to interact with the fibroblast growth factor receptor (FGFR), and the FGFR-binding site was mapped by NMR to the FG-loop region...... of the module. The FG-loop region also contains a putative nucleotide-binding motif, which was shown by NMR to interact with ATP. Furthermore, ATP was demonstrated to inhibit binding of the second F3 module of NCAM to FGFR....

  4. An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments

    International Nuclear Information System (INIS)

    Langmead, Christopher James; Donald, Bruce Randall

    2004-01-01

    We report an automated procedure for high-throughput NMR resonance assignment for a protein of known structure, or of an homologous structure. Our algorithm performs Nuclear Vector Replacement (NVR) by Expectation/Maximization (EM) to compute assignments. NVR correlates experimentally-measured NH residual dipolar couplings (RDCs) and chemical shifts to a given a priori whole-protein 3D structural model. The algorithm requires only uniform 15 N-labelling of the protein, and processes unassigned H N - 15 N HSQC spectra, H N - 15 N RDCs, and sparse H N -H N NOE's (d NN s). NVR runs in minutes and efficiently assigns the (H N , 15 N) backbone resonances as well as the sparse d NN s from the 3D 15 N-NOESY spectrum, in O(n 3 ) time. The algorithm is demonstrated on NMR data from a 76-residue protein, human ubiquitin, matched to four structures, including one mutant (homolog), determined either by X-ray crystallography or by different NMR experiments (without RDCs). NVR achieves an average assignment accuracy of over 99%. We further demonstrate the feasibility of our algorithm for different and larger proteins, using different combinations of real and simulated NMR data for hen lysozyme (129 residues) and streptococcal protein G (56 residues), matched to a variety of 3D structural models. Abbreviations: NMR, nuclear magnetic resonance; NVR, nuclear vector replacement; RDC, residual dipolar coupling; 3D, three-dimensional; HSQC, heteronuclear single-quantum coherence; H N , amide proton; NOE, nuclear Overhauser effect; NOESY, nuclear Overhauser effect spectroscopy; d NN , nuclear Overhauser effect between two amide protons; MR, molecular replacement; SAR, structure activity relation; DOF, degrees of freedom; nt., nucleotides; SPG, Streptococcal protein G; SO(3), special orthogonal (rotation) group in 3D; EM, Expectation/Maximization; SVD, singular value decomposition

  5. Benchmark Theoretical and Experimental Study on N-15 NMR Shifts of Oxidatively Damaged Guanine

    Czech Academy of Sciences Publication Activity Database

    Dračínský, Martin; Šála, Michal; Klepetářová, Blanka; Šebera, Jakub; Fukal, Jiří; Holečková, Veronika; Tanaka, Y.; Nencka, Radim; Sychrovský, Vladimír

    2016-01-01

    Roč. 120, č. 5 (2016), s. 915-925 ISSN 1520-6106 R&D Projects: GA ČR GA13-27676S; GA ČR GA15-11223S Institutional support: RVO:61388963 Keywords : NMR spectroscopy * DFT calculations * oxidatively damaged guanine * hOGG1 Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.177, year: 2016

  6. A probabilistic approach for validating protein NMR chemical shift assignments

    International Nuclear Information System (INIS)

    Wang Bowei; Wang, Yunjun; Wishart, David S.

    2010-01-01

    It has been estimated that more than 20% of the proteins in the BMRB are improperly referenced and that about 1% of all chemical shift assignments are mis-assigned. These statistics also reflect the likelihood that any newly assigned protein will have shift assignment or shift referencing errors. The relatively high frequency of these errors continues to be a concern for the biomolecular NMR community. While several programs do exist to detect and/or correct chemical shift mis-referencing or chemical shift mis-assignments, most can only do one, or the other. The one program (SHIFTCOR) that is capable of handling both chemical shift mis-referencing and mis-assignments, requires the 3D structure coordinates of the target protein. Given that chemical shift mis-assignments and chemical shift re-referencing issues should ideally be addressed prior to 3D structure determination, there is a clear need to develop a structure-independent approach. Here, we present a new structure-independent protocol, which is based on using residue-specific and secondary structure-specific chemical shift distributions calculated over small (3-6 residue) fragments to identify mis-assigned resonances. The method is also able to identify and re-reference mis-referenced chemical shift assignments. Comparisons against existing re-referencing or mis-assignment detection programs show that the method is as good or superior to existing approaches. The protocol described here has been implemented into a freely available Java program called 'Probabilistic Approach for protein Nmr Assignment Validation (PANAV)' and as a web server (http://redpoll.pharmacy.ualberta.ca/PANAVhttp://redpoll.pharmacy.ualberta.ca/PANAV) which can be used to validate and/or correct as well as re-reference assigned protein chemical shifts.

  7. CISA: combined NMR resonance connectivity information determination and sequential assignment.

    Science.gov (United States)

    Wan, Xiang; Lin, Guohui

    2007-01-01

    A nearly complete sequential resonance assignment is a key factor leading to successful protein structure determination via NMR spectroscopy. Assuming the availability of a set of NMR spectral peak lists, most of the existing assignment algorithms first use the differences between chemical shift values for common nuclei across multiple spectra to provide the evidence that some pairs of peaks should be assigned to sequentially adjacent amino acid residues in the target protein. They then use these connectivities as constraints to produce a sequential assignment. At various levels of success, these algorithms typically generate a large number of potential connectivity constraints, and it grows exponentially as the quality of spectral data decreases. A key observation used in our sequential assignment program, CISA, is that chemical shift residual signature information can be used to improve the connectivity determination, and thus to dramatically decrease the number of predicted connectivity constraints. Fewer connectivity constraints lead to less ambiguities in the sequential assignment. Extensive simulation studies on several large test datasets demonstrated that CISA is efficient and effective, compared to three most recently proposed sequential resonance assignment programs RANDOM, PACES, and MARS.

  8. Automated Pre-processing for NMR Assignments with Reduced Tedium

    Energy Technology Data Exchange (ETDEWEB)

    2004-05-11

    An important rate-limiting step in the reasonance asignment process is accurate identification of resonance peaks in MNR spectra. NMR spectra are noisy. Hence, automatic peak-picking programs must navigate between the Scylla of reliable but incomplete picking, and the Charybdis of noisy but complete picking. Each of these extremes complicates the assignment process: incomplete peak-picking results in the loss of essential connectivities, while noisy picking conceals the true connectivities under a combinatiorial explosion of false positives. Intermediate processing can simplify the assignment process by preferentially removing false peaks from noisy peak lists. This is accomplished by requiring consensus between multiple NMR experiments, exploiting a priori information about NMR spectra, and drawing on empirical statistical distributions of chemical shift extracted from the BioMagResBank. Experienced NMR practitioners currently apply many of these techniques "by hand", which is tedious, and may appear arbitrary to the novice. To increase efficiency, we have created a systematic and automated approach to this process, known as APART. Automated pre-processing has three main advantages: reduced tedium, standardization, and pedagogy. In the hands of experienced spectroscopists, the main advantage is reduced tedium (a rapid increase in the ratio of true peaks to false peaks with minimal effort). When a project is passed from hand to hand, the main advantage is standardization. APART automatically documents the peak filtering process by archiving its original recommendations, the accompanying justifications, and whether a user accepted or overrode a given filtering recommendation. In the hands of a novice, this tool can reduce the stumbling block of learning to differentiate between real peaks and noise, by providing real-time examples of how such decisions are made.

  9. CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis

    Energy Technology Data Exchange (ETDEWEB)

    Skinner, Simon P.; Fogh, Rasmus H. [University of Leicester, Department of Molecular and Cell Biology, Leicester Institute for Structural- and Chemical Biology (United Kingdom); Boucher, Wayne [University of Cambridge, Department of Biochemistry (United Kingdom); Ragan, Timothy J.; Mureddu, Luca G.; Vuister, Geerten W., E-mail: gv29@le.ac.uk [University of Leicester, Department of Molecular and Cell Biology, Leicester Institute for Structural- and Chemical Biology (United Kingdom)

    2016-10-15

    NMR spectroscopy is an indispensably powerful technique for the analysis of biomolecules under ambient conditions, both for structural- and functional studies. However, in practice the complexity of the technique has often frustrated its application by non-specialists. In this paper, we present CcpNmr version-3, the latest software release from the Collaborative Computational Project for NMR, for all aspects of NMR data analysis, including liquid- and solid-state NMR data. This software has been designed to be simple, functional and flexible, and aims to ensure that routine tasks can be performed in a straightforward manner. We have designed the software according to modern software engineering principles and leveraged the capabilities of modern graphics libraries to simplify a variety of data analysis tasks. We describe the process of backbone assignment as an example of the flexibility and simplicity of implementing workflows, as well as the toolkit used to create the necessary graphics for this workflow. The package can be downloaded from www.ccpn.ac.uk/v3-software/downloads http://www.ccpn.ac.uk/v3-software/downloads and is freely available to all non-profit organisations.

  10. A tracked approach for automated NMR assignments in proteins (TATAPRO)

    Energy Technology Data Exchange (ETDEWEB)

    Atreya, H.S.; Sahu, S.C.; Chary, K.V.R.; Govil, Girjesh [Tata Institute of Fundamental Research, Department of Chemical Sciences (India)

    2000-06-15

    A novel automated approach for the sequence specific NMR assignments of {sup 1}H{sup N}, {sup 13}C{sup {alpha}}, {sup 13}C{sup {beta}}, {sup 13}C'/{sup 1}H{sup {alpha}} and {sup 15}N spins in proteins, using triple resonance experimental data, is presented. The algorithm, TATAPRO (Tracked AuTomated Assignments in Proteins) utilizes the protein primary sequence and peak lists from a set of triple resonance spectra which correlate {sup 1}H{sup N} and {sup 15}N chemical shifts with those of {sup 13}C{sup {alpha}}, {sup 13}C{sup {beta}} and {sup 13}C'/{sup 1}H{sup {alpha}}. The information derived from such correlations is used to create a 'master{sub l}ist' consisting of all possible sets of {sup 1}H{sup N}{sub i}, {sup 15}N{sub i}, {sup 13}C{sup {alpha}}{sub i}, {sup 13}C{sup {beta}}{sub i}, {sup 13}C'{sub i}/{sup 1}H{sup {alpha}}{sub i}, {sup 13}C{sup {alpha}}{sub i-1}, {sup 13}C{sup {beta}}{sub i-1} and {sup 13}C'{sub i-1}/ {sup 1}H{sup {alpha}}{sub i-1} chemical shifts. On the basis of an extensive statistical analysis of {sup 13}C{sup {alpha}} and {sup 13}C{sup {beta}} chemical shift data of proteins derived from the BioMagResBank (BMRB), it is shown that the 20 amino acid residues can be grouped into eight distinct categories, each of which is assigned a unique two-digit code. Such a code is used to tag individual sets of chemical shifts in the master{sub l}ist and also to translate the protein primary sequence into an array called pps{sub a}rray. The program then uses the master{sub l}ist to search for neighbouring partners of a given amino acid residue along the polypeptide chain and sequentially assigns a maximum possible stretch of residues on either side. While doing so, each assigned residue is tracked in an array called assig{sub a}rray, with the two-digit code assigned earlier. The assig{sub a}rray is then mapped onto the pps{sub a}rray for sequence specific resonance assignment. The program has been tested using

  11. H-1, C-13 and N-15 resonance assignments of human DCL-1 (CD302) extracellular domain

    Czech Academy of Sciences Publication Activity Database

    Pospíšilová, Eliška; Kavan, Daniel; Novák, Petr; Chmelík, Josef

    2016-01-01

    Roč. 10, č. 1 (2016), s. 189-192 ISSN 1874-2718 R&D Projects: GA MŠk(CZ) LO1509; GA MŠk(CZ) EE2.3.20.0055; GA MŠk(CZ) EE2.3.30.0003; GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:61388971 Keywords : DCL-1 (CD302) * C-type lectin like receptor * Protein NMR Subject RIV: EE - Microbiology, Virology Impact factor: 0.459, year: 2016

  12. Structural characterization of homogalacturonan by NMR spectroscopy - assignment of reference compounds

    DEFF Research Database (Denmark)

    Petersen, Bent O.; Meier, Sebastian; Duus, Jens Øllgaard

    2008-01-01

    Complete assignment of 1H and 13C NMR of six hexagalactopyranuronic acids with varying degree and pattern of methyl esterification is reported. The NMR experiments were run at room temperature using approximately 2 mg of sample making this method convenient for studying the structure of homogalac......Complete assignment of 1H and 13C NMR of six hexagalactopyranuronic acids with varying degree and pattern of methyl esterification is reported. The NMR experiments were run at room temperature using approximately 2 mg of sample making this method convenient for studying the structure...

  13. 13C-NMR assignments and cytotoxicity assessment of zoanthoxanthin alkaloids from zoanthid corals.

    Science.gov (United States)

    Jiménez, C; Crews, P

    1993-01-01

    Zoanthoxanthin alkaloids can vary among skeletal types A, B, and C. Three type C zoanthoxanthins were examined, including a new compound 1, previously reported paragracine [2], and zoanthoxanthin 3. Their nmr and cytotoxic properties are reported. We have used 2D nmr data to complete the assignments for 1 and suggest that these benchmark nmr assignments will allow future investigators to establish new metabolites of this class as a member of families A, B, or C with only a 13C APT and a 1H-1H nmr spectra.

  14. H-1-, C-13-, and N-15-NMR chemical shifts for selected glucosides and ribosides of aromatic cytokinins

    Czech Academy of Sciences Publication Activity Database

    Vícha, J.; Maloň, Michal; Veselá, P.; Humpa, O.; Strnad, Miroslav; Marek, R.

    2010-01-01

    Roč. 48, č. 4 (2010), s. 318-322 ISSN 0749-1581 R&D Projects: GA ČR GA301/08/1649 Institutional research plan: CEZ:AV0Z50380511 Keywords : NMR * H-1 * C-13 Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.247, year: 2010

  15. N-15 NMR study of the immobilization of 2,4- and 2,6-dinitrotoluene in aerobic compost

    Science.gov (United States)

    Thorn, K.A.; Pennington, J.C.; Kennedy, K.R.; Cox, L.G.; Hayes, C.A.; Porter, B.E.

    2008-01-01

    Large-scale aerobic windrow composting has been used to bioremediate washout lagoon soils contaminated with the explosives TNT (2,4,6- trinitrotoluene) and RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) at several sites within the United States. We previously used 15N NMR to investigate the reduction and binding of T15NT in aerobic bench -scale reactors simulating the conditions of windrow composting. These studies have been extended to 2,4-dinitrotoluene (2,4DNT) and 2,6-dinitrotoluene (2,6DNT), which, as impurities in TNT, are usually present wherever soils have been contaminated with TNT. Liquid-state 15N NMR analyses of laboratory reactions between 4-methyl-3-nitroaniline-15N, the major monoamine reduction product of 2,4DNT, and the Elliot soil humic acid, both in the presence and absence of horseradish peroxidase, indicated that the amine underwent covalent binding with quinone and other carbonyl groups in the soil humic acid to form both heterocyclic and non-heterocyclic condensation products. Liquid-state 15N NMR analyses of the methanol extracts of 20 day aerobic bench-scale composts of 2,4-di-15N-nitrotoluene and 2,6-di-15N-nitrotoluene revealed the presence of nitrite and monoamine, but not diamine, reduction products, indicating the occurrence of both dioxygenase enzyme and reductive degradation pathways. Solid-state CP/MAS 15N NMR analyses of the whole composts, however, suggested that reduction to monoamines followed by covalent binding of the amines to organic matter was the predominant pathway. ?? 2008 American Chemical Society.

  16. Backbone NMR assignment of a hypothetical protein MJ0754 from Methanococcus jannaschii DSM 2661

    Directory of Open Access Journals (Sweden)

    Kwang Yeon Hwang

    2011-06-01

    Full Text Available MJ0754 is an unknown hypothetical protein from hyperthermophilic archaeon Methanococcus jannaschii DSM 2661. Here we report the protein purification and NMR spectroscopic study of the N-terminal deleted truncated form of recombinant MJ0754 protein (Δ10-MJ0754. We aquired 3D NMR spectra and assigned all the backbone chemical shifts including Cα, Cβ, CO, HN, and N of Δ10-MJ0754. The secondary structure of Δ10-MJ0754 was estimated from the assigned backbone chemical shifts. This NMR result is very useful for further structural and functional study of MJ0754 protein.

  17. NVR-BIP: Nuclear Vector Replacement using Binary Integer Programming for NMR Structure-Based Assignments.

    Science.gov (United States)

    Apaydin, Mehmet Serkan; Çatay, Bülent; Patrick, Nicholas; Donald, Bruce R

    2011-05-01

    Nuclear magnetic resonance (NMR) spectroscopy is an important experimental technique that allows one to study protein structure and dynamics in solution. An important bottleneck in NMR protein structure determination is the assignment of NMR peaks to the corresponding nuclei. Structure-based assignment (SBA) aims to solve this problem with the help of a template protein which is homologous to the target and has applications in the study of structure-activity relationship, protein-protein and protein-ligand interactions. We formulate SBA as a linear assignment problem with additional nuclear overhauser effect constraints, which can be solved within nuclear vector replacement's (NVR) framework (Langmead, C., Yan, A., Lilien, R., Wang, L. and Donald, B. (2003) A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments. Proc. the 7th Annual Int. Conf. Research in Computational Molecular Biology (RECOMB) , Berlin, Germany, April 10-13, pp. 176-187. ACM Press, New York, NY. J. Comp. Bio. , (2004), 11, pp. 277-298; Langmead, C. and Donald, B. (2004) An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments. J. Biomol. NMR , 29, 111-138). Our approach uses NVR's scoring function and data types and also gives the option of using CH and NH residual dipolar coupling (RDCs), instead of NH RDCs which NVR requires. We test our technique on NVR's data set as well as on four new proteins. Our results are comparable to NVR's assignment accuracy on NVR's test set, but higher on novel proteins. Our approach allows partial assignments. It is also complete and can return the optimum as well as near-optimum assignments. Furthermore, it allows us to analyze the information content of each data type and is easily extendable to accept new forms of input data, such as additional RDCs.

  18. Practical aspects of NMR signal assignment in larger and challenging proteins

    Science.gov (United States)

    Frueh, Dominique P.

    2014-01-01

    NMR has matured into a technique routinely employed for studying proteins in near physiological conditions. However, applications to larger proteins are impeded by the complexity of the various correlation maps necessary to assign NMR signals. This article reviews the data analysis techniques traditionally employed for resonance assignment and describes alternative protocols necessary for overcoming challenges in large protein spectra. In particular, simultaneous analysis of multiple spectra may help overcome ambiguities or may reveal correlations in an indirect manner. Similarly, visualization of orthogonal planes in a multidimensional spectrum can provide alternative assignment procedures. We describe examples of such strategies for assignment of backbone, methyl, and nOe resonances. We describe experimental aspects of data acquisition for the related experiments and provide guidelines for preliminary studies. Focus is placed on large folded monomeric proteins and examples are provided for 37, 48, 53, and 81 kDa proteins. PMID:24534088

  19. More reliable protein NMR peak assignment via improved 2-interval scheduling.

    Science.gov (United States)

    Chen, Zhi-Zhong; Lin, Guohui; Rizzi, Romeo; Wen, Jianjun; Xu, Dong; Xu, Ying; Jiang, Tao

    2005-03-01

    Protein NMR peak assignment refers to the process of assigning a group of "spin systems" obtained experimentally to a protein sequence of amino acids. The automation of this process is still an unsolved and challenging problem in NMR protein structure determination. Recently, protein NMR peak assignment has been formulated as an interval scheduling problem (ISP), where a protein sequence P of amino acids is viewed as a discrete time interval I (the amino acids on P one-to-one correspond to the time units of I), each subset S of spin systems that are known to originate from consecutive amino acids from P is viewed as a "job" j(s), the preference of assigning S to a subsequence P of consecutive amino acids on P is viewed as the profit of executing job j(s) in the subinterval of I corresponding to P, and the goal is to maximize the total profit of executing the jobs (on a single machine) during I. The interval scheduling problem is max SNP-hard in general; but in the real practice of protein NMR peak assignment, each job j(s) usually requires at most 10 consecutive time units, and typically the jobs that require one or two consecutive time units are the most difficult to assign/schedule. In order to solve these most difficult assignments, we present an efficient 13/7-approximation algorithm for the special case of the interval scheduling problem where each job takes one or two consecutive time units. Combining this algorithm with a greedy filtering strategy for handling long jobs (i.e., jobs that need more than two consecutive time units), we obtain a new efficient heuristic for protein NMR peak assignment. Our experimental study shows that the new heuristic produces the best peak assignment in most of the cases, compared with the NMR peak assignment algorithms in the recent literature. The above algorithm is also the first approximation algorithm for a nontrivial case of the well-known interval scheduling problem that breaks the ratio 2 barrier.

  20. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Volk, Jochen [ETH Zuerich, Institut fuer Molekularbiologie und Biophysik (Switzerland); Herrmann, Torsten [Universite de Lyon, CNRS/ENS Lyon/UCB-Lyon 1 (France); Wuethrich, Kurt [ETH Zuerich, Institut fuer Molekularbiologie und Biophysik (Switzerland)], E-mail: wuthrich@mol.biol.ethz.ch

    2008-07-15

    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.

  2. 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

  3. 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.

  4. A novel strategy for NMR resonance assignment and protein structure determination.

    Science.gov (United States)

    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.

  5. 1H HR-MAS NMR and S180 cells: metabolite assignment and evaluation of pulse sequence

    International Nuclear Information System (INIS)

    Oliveira, Aline L. de; Martinelli, Bruno César B.; Lião, Luciano M.; Pereira, Flávia C.; Silveira-Lacerda, Elisangela P.; Alcantara, Glaucia B.

    2014-01-01

    High resolution magic angle spinning 1 H nuclear magnetic resonance spectroscopy (HR-MAS NMR) is a useful technique for evaluation of intact cells and tissues. However, optimal NMR parameters are crucial in obtaining reliable results. To identify the key steps for the optimization of HR-MAS NMR parameters, we assessed different pulse sequences and NMR parameters using sarcoma 180 (S180) cells. A complete assignment of the metabolites of S180 is given to assist future studies. (author)

  6. {sup 1}H HR-MAS NMR and S180 cells: metabolite assignment and evaluation of pulse sequence

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, Aline L. de; Martinelli, Bruno César B.; Lião, Luciano M. [Universidade Federal de Goiás (UFG), Goiânia, GO (Brazil). Instituto de Química. Lab. de RMN; Pereira, Flávia C.; Silveira-Lacerda, Elisangela P. [Universidade Federal de Goiás (UFG), Goiânia, GO (Brazil). Instituto de Ciências Biológicas. Laboratório Genética Molecular e Citogenética; Alcantara, Glaucia B., E-mail: glaucia.alcantara@ufms.br [Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, MS (Brazil). Inst. de Química

    2014-07-01

    High resolution magic angle spinning {sup 1}H nuclear magnetic resonance spectroscopy (HR-MAS NMR) is a useful technique for evaluation of intact cells and tissues. However, optimal NMR parameters are crucial in obtaining reliable results. To identify the key steps for the optimization of HR-MAS NMR parameters, we assessed different pulse sequences and NMR parameters using sarcoma 180 (S180) cells. A complete assignment of the metabolites of S180 is given to assist future studies. (author)

  7. Detailed 1H and 13C NMR spectral data assignment for two dihydrobenzofuran neolignans

    International Nuclear Information System (INIS)

    Medeiros, Talita C.T.; Dias, Herbert J.; Crotti, Antônio E.M.

    2016-01-01

    In this work we present a complete proton ( 1 H) and carbon 13 ( 13 C) nuclear magnetic resonance (NMR) spectral analysis of two synthetic dihydrofuran neolignans (±)-trans-dehydrodicoumarate dimethyl ester and (±)-trans-dehydrodiferulate dimethyl ester. Unequivocal assignments were achieved by 1 H NMR, proton decoupled 13 C ( 13 C{ 1 H}) NMR spectra, gradient-selected correlation spectroscopy (gCOSY), J-resolved, gradient-selected heteronuclear multiple quantum coherence (gHMQC), gradient-selected heteronuclear multiple bond coherence (gHMBC) and nuclear Overhauser effect spectroscopy (NOESY) experiments. All hydrogen coupling constants were measured, clarifying all the hydrogen signals multiplicities. Computational methods were also used to simulate the 1 H and 13 C chemical shifts and showed good agreement with the trans configuration of the substituents at C 7 and C 8 . (author)

  8. Complete 1H NMR assignments of pyrrolizidine alkaloids and a new eudesmanoid from Senecio polypodioides.

    Science.gov (United States)

    Villanueva-Cañongo, Claudia; Pérez-Hernández, Nury; Hernández-Carlos, Beatriz; Cedillo-Portugal, Ernestina; Joseph-Nathan, Pedro; Burgueño-Tapia, Eleuterio

    2014-05-01

    Chemical investigation of the aerial parts of Senecio polypodioides lead to the isolation of the new eudesmanoid 1β-angeloyloxyeudesm-7-ene-4β,9α-diol (1) and the known dirhamnosyl flavonoid lespidin (3), while from roots, the known 7β-angeloyloxy-1-methylene-8α-pyrrolizidine (5) and sarracine N-oxide (6), as well as the new neosarracine N-oxide (8), were obtained. The structure of 1 and 8 was elucidated by spectral means. Complete assignments of the (1)H NMR data for 5, 6, sarracine (7), and 8 were made using one-dimensional and two-dimensional NMR experiments and by application of the iterative full spin analysis of the PERCH NMR software. Copyright © 2014 John Wiley & Sons, Ltd.

  9. Detailed {sup 1}H and {sup 13}C NMR spectral data assignment for two dihydrobenzofuran neolignans

    Energy Technology Data Exchange (ETDEWEB)

    Medeiros, Talita C.T.; Dias, Herbert J.; Crotti, Antônio E.M., E-mail: millercrotti@ffclrp.usp.br [Universidade de São Paulo (USP), Ribeirão Preto, SP (Brazil). Faculdade de Filosofia, Ciências e Letras. Departamento de Química

    2016-07-01

    In this work we present a complete proton ({sup 1}H) and carbon 13 ({sup 13}C) nuclear magnetic resonance (NMR) spectral analysis of two synthetic dihydrofuran neolignans (±)-trans-dehydrodicoumarate dimethyl ester and (±)-trans-dehydrodiferulate dimethyl ester. Unequivocal assignments were achieved by 1 H NMR, proton decoupled {sup 13}C ({sup 13}C{"1H}) NMR spectra, gradient-selected correlation spectroscopy (gCOSY), J-resolved, gradient-selected heteronuclear multiple quantum coherence (gHMQC), gradient-selected heteronuclear multiple bond coherence (gHMBC) and nuclear Overhauser effect spectroscopy (NOESY) experiments. All hydrogen coupling constants were measured, clarifying all the hydrogen signals multiplicities. Computational methods were also used to simulate the {sup 1}H and {sup 13}C chemical shifts and showed good agreement with the trans configuration of the substituents at C{sub 7} and C{sub 8}. (author)

  10. Complete NMR Assignment of Succinimide and Its Detection and Quantification in Peptides and Intact Proteins.

    Science.gov (United States)

    Grassi, Luigi; Regl, Christof; Wildner, Sabrina; Gadermaier, Gabriele; Huber, Christian G; Cabrele, Chiara; Schubert, Mario

    2017-11-21

    Detecting and quantifying post-translational modifications (PTMs) in full-length proteins is a challenge, especially in the case of spontaneously occurring, nonenzymatic PTMs. Such a PTM is the formation of succinimide (Snn) in a protein that occurs spontaneously in prone primary sequences and leads typically to an equilibrium between Snn and its hydrolysis products isoaspartate (isoAsp) and aspartate. In order to detect these modifications in proteins by NMR spectroscopy, chemical shift assignments of reference compounds are required. We used peptide synthesis and 2D NMR spectroscopy to assign all 1 H and 13 C chemical shifts of Snn and isoAsp and found characteristic chemical shift correlations. To provide chemical shift reference data suitable for comparison with data of denatured proteins, we repeated the assignment in 7 M urea (pH 2.3) and in DMSO. Most characteristic of Snn are the two downfield shifted carbonyl chemical shifts, the chemical shift correlations of Cβ-Hβ of Snn and Cα-Hα of the succeeding residue which are clearly distinct from random coil chemical shift correlations. The characteristic 2D NMR fingerprints of Snn were used to detect and quantify this PTM in the model protein lysozyme, the biotherapeutic filgrastim, and the Fc part of immunoglobulin G1. Mass spectrometry (MS) was applied as an additional independent method. The orthogonality of the NMR and MS techniques allows cross-validation, which is especially important to search for subtle PTMs in proteins. Studying PTMs by NMR spectroscopy is a promising method to analyze proteins and peptides from natural sources, recombinant expression, or chemical synthesis.

  11. 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

  12. 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.

  13. Solution-state NMR spectroscopy of famotidine revisited: spectral assignment, protonation sites, and their structural consequences.

    Science.gov (United States)

    Marosi, Attila; Szalay, Zsófia; Béni, Szabolcs; Szakács, Zoltán; Gáti, Tamás; Rácz, Ákos; Noszál, Béla; Demeter, Ádám

    2012-02-01

    Multinuclear one (1D-) and two-dimensional (2D) nuclear magnetic resonance (NMR) spectroscopic investigations of famotidine, the most potent and widely used histamine H(2)-receptor antagonist, were carried out in dimethyl sulfoxide-d(6) (DMSO-d(6)) and water. Previous NMR assignments were either incomplete or full assignment was based only on 1D spectra and quantum-chemical calculations. Our work revealed several literature misassignments of the (1)H, (13)C, and (15)N NMR signals and clarified the acid-base properties of the compound at the site-specific level. The erroneous assignment of Baranska et al. (J. Mol. Struct. 2001, 563) probably originates from an incorrect hypothesis about the major conformation of famotidine in DMSO-d(6). A folded conformation similar to that observed in the solid-state was also assumed in solution, stabilized by an intramolecular hydrogen bond involving one of the sulphonamide NH(2) protons and the thiazole nitrogen. Our detailed 1D and 2D NMR experiments enabled complete ab initio (1)H, (13)C, and (15)N assignments and disproved the existence of the sulphonamide NH hydrogen bond in the major conformer. Rather, the molecule is predominantly present in an extended conformation in DMSO-d(6). The aqueous acid-base properties of famotidine were studied by 1D (1)H- and 2D (1)H/(13)C heteronuclear multiple-bond correlation (HMBC) NMR-pH titrations. The experiments identified its basic centers including a new protonation step at highly acidic conditions, which was also confirmed by titrations and quantum-chemical calculations on a model compound, 2-[4-(sulfanylmethyl)-1,3-thiazol-2-yl]guanidine. Famotidine is now proved to have four protonation steps in the following basicity order: the sulfonamidate anion protonates at pH = 11.3, followed by the protonation of the guanidine group at pH = 6.8, whereas, in strong acidic solutions, two overlapping protonation processes occur involving the amidine and thiazole moieties.

  14. EZ-ASSIGN, a program for exhaustive NMR chemical shift assignments of large proteins from complete or incomplete triple-resonance data

    International Nuclear Information System (INIS)

    Zuiderweg, Erik R. P.; Bagai, Ireena; Rossi, Paolo; Bertelsen, Eric B.

    2013-01-01

    For several of the proteins in the BioMagResBank larger than 200 residues, 60 % or fewer of the backbone resonances were assigned. But how reliable are those assignments? In contrast to complete assignments, where it is possible to check whether every triple-resonance Generalized Spin System (GSS) is assigned once and only once, with incomplete data one should compare all possible assignments and pick the best one. But that is not feasible: For example, for 200 residues and an incomplete set of 100 GSS, there are 1.6 × 10 260 possible assignments. In “EZ-ASSIGN”, the protein sequence is divided in smaller unique fragments. Combined with intelligent search approaches, an exhaustive comparison of all possible assignments is now feasible using a laptop computer. The program was tested with experimental data of a 388-residue domain of the Hsp70 chaperone protein DnaK and for a 351-residue domain of a type III secretion ATPase. EZ-ASSIGN reproduced the hand assignments. It did slightly better than the computer program PINE (Bahrami et al. in PLoS Comput Biol 5(3):e1000307, 2009) and significantly outperformed SAGA (Crippen et al. in J Biomol NMR 46:281–298, 2010), AUTOASSIGN (Zimmerman et al. in J Mol Biol 269:592–610, 1997), and IBIS (Hyberts and Wagner in J Biomol NMR 26:335–344, 2003). Next, EZ-ASSIGN was used to investigate how well NMR data of decreasing completeness can be assigned. We found that the program could confidently assign fragments in very incomplete data. Here, EZ-ASSIGN dramatically outperformed all the other assignment programs tested

  15. Complete {sup 1}H and {sup 13}C NMR structural assignments for a group of four goyazensolide-type furanoheliangolides

    Energy Technology Data Exchange (ETDEWEB)

    Soares, Ana Carolina Ferreira; Silva, Aline Nazare; Matos, Priscilla Mendonca; Silva, Eder Henrique da; Heleno, Vladimir Constantino Gomes [Universidade de Franca, Franca, SP (Brazil). Nucleo de Pesquisas em Ciencias Exatas e Tecnologicas; Lopes, Norberto Peporine; Lopes, Joao Luis Callegari [Universidade de Sao Paulo (FCFRP/USP), Ribeirao Preto, SP (Brazil). Fac. de Ciencias Farmaceuticas de Ribeirao Preto. Dept. de Quimica e Fisica; Sass, Daiane Cristina, E-mail: vheleno_05@yahoo.com.br [Universidade de Sao Paulo (FFCLRP/USP), Ribeirao Preto, SP (Brazil). Fac. de Filosofia, Ciencias e Letras de Ribeirao Preto. Dept. de Quimica

    2012-07-01

    Four goyazensolide-type sesquiterpene lactones - lychnofolide, centratherin, goyazensolide and goyazensolide acetate - were thoroughly studied by NMR experimental techniques. {sup 1}H NMR, {sup 13}C NMR {l_brace}{sup 1}H{r_brace}, COSY, HMQC, HMBC, J-res. and NOE experiments were performed to provide the needed structural information. Complete and unequivocal assignment, including the determination of all multiplicities, was obtained for each structure and the data collections are presented in tables (author)

  16. A tabu search approach for the NMR protein structure-based assignment problem.

    Science.gov (United States)

    Cavuşlar, Gizem; Çatay, Bülent; Apaydın, Mehmet Serkan

    2012-01-01

    Spectroscopy is an experimental technique which exploits the magnetic properties of specific nuclei and enables the study of proteins in solution. The key bottleneck of NMR studies is to map the NMR peaks to corresponding nuclei, also known as the assignment problem. Structure-Based Assignment (SBA) is an approach to solve this computationally challenging problem by using prior information about the protein obtained from a homologous structure. NVR-BIP used the Nuclear Vector Replacement (NVR) framework to model SBA as a binary integer programming problem. In this paper, we prove that this problem is NP-hard and propose a tabu search (TS) algorithm (NVR-TS) equipped with a guided perturbation mechanism to efficiently solve it. NVR-TS uses a quadratic penalty relaxation of NVR-BIP where the violations in the Nuclear Overhauser Effect constraints are penalized in the objective function. Experimental results indicate that our algorithm finds the optimal solution on NVRBIP’s data set which consists of seven proteins with 25 templates (31 to 126 residues). Furthermore, it achieves relatively high assignment accuracies on two additional large proteins, MBP and EIN (348 and 243 residues, respectively), which NVR-BIP failed to solve. The executable and the input files are available for download at http://people.sabanciuniv.edu/catay/NVR-TS/NVR-TS.html.

  17. Complete NMR spectral assignment in gibbsite by first-principle calculations

    Energy Technology Data Exchange (ETDEWEB)

    Vyalikh, Anastasia; Scheler, Ulrich [IPF Dresden (Germany)

    2010-07-01

    The structure of the mineral gibbsite is often considered as a representative of many alumino-silicate clay minerals, and therefore we use it in the present study as a model compound to establish the suitability of the computational method. Here we apply a gradient-corrected DFT method with a plane-wave basis set to assign the crystallographically distinct Al sites in gibbsite and to relate them to the hydroxide network. The experimental observation is based on high-resolution solid-state {sup 27}Al NMR and {sup 1}H CRAMPS (combined rotation and multipulse spectroscopy) data. On the basis of DFT calculations, the {sup 1}H CRAMPS signals have been attributed to six symmetry independent hydrogen atoms and ascribed to two distinct types associated with intralayer and interlayer hydrogen bonds. The {sup 27}Al NMR spectrum shows signals for octahedral aluminium only, however with two distinguished signals. The correlation between experimental and theoretical NMR parameters demonstrates that the character of the hydrogen bonds formed by the hydroxide ions is responsible for the structural differentiation of Al sites. That is, the Al-I site (CQ=4.2 MHz) is surrounded by the OH-groups participating in 4 intralayer and 2 interlayer hydrogen bonds, while the Al-II site (CQ=2.4 MHz) is coordinated by the hydroxides, 2 of which point towards the intralayer cavities and 4 OH-bonds are aligned towards the interlayer gallery.

  18. NMR resonance assignments of a hypoallergenic isoform of the major birch pollen allergen Bet v 1.

    Science.gov (United States)

    Ahammer, Linda; Grutsch, Sarina; Wallner, Michael; Ferreira, Fatima; Tollinger, Martin

    2017-10-01

    In Northern America and Europe a great number of people are suffering from birch pollen allergy and pollen related food allergies. The trigger for these immunological reactions is the 17.5 kDa major birch pollen allergen Bet v 1, which belongs to the family of PR-10 (pathogenesis-related) proteins. In nature, Bet v 1 occurs as a mixture of various isoforms that possess different immunological properties despite their high sequence identities. Bet v 1.0102 (Bet v 1d), which is investigated here, is a hypoallergenic isoform of Bet v 1 and a potential candidate for allergen-specific immunotherapy. We assigned the backbone and side chain 1 H, 13 C and 15 N resonances of this protein and predicted its secondary structure. The NMR-chemical shift data indicate that Bet v 1.0102 is composed of three α-helices and a seven stranded β-sheet, in agreement with the known structure of the hyperallergenic isoform Bet v 1.0101 (Bet v 1a). Our resonance assignments create the foundation for detailed characterization of the dynamic properties of Bet v 1 isoforms by NMR relaxation measurements.

  19. Automating unambiguous NOE data usage in NVR for NMR protein structure-based assignments.

    Science.gov (United States)

    Akhmedov, Murodzhon; Çatay, Bülent; Apaydın, Mehmet Serkan

    2015-12-01

    Nuclear Magnetic Resonance (NMR) Spectroscopy is an important technique that allows determining protein structure in solution. An important problem in protein structure determination using NMR spectroscopy is the mapping of peaks to corresponding amino acids, also known as the assignment problem. Structure-Based Assignment (SBA) is an approach to solve this problem using a template structure that is homologous to the target. Our previously developed approach Nuclear Vector Replacement-Binary Integer Programming (NVR-BIP) computed the optimal solution for small proteins, but was unable to solve the assignments of large proteins. NVR-Ant Colony Optimization (ACO) extended the applicability of the NVR approach for such proteins. One of the input data utilized in these approaches is the Nuclear Overhauser Effect (NOE) data. NOE is an interaction observed between two protons if the protons are located close in space. These protons could be amide protons, protons attached to the alpha-carbon atom in the backbone of the protein, or side chain protons. NVR only uses backbone protons. In this paper, we reformulate the NVR-BIP model to distinguish the type of proton in NOE data and use the corresponding proton coordinates in the extended formulation. In addition, the threshold value over interproton distances is set in a standard manner for all proteins by extracting the NOE upper bound distance information from the data. We also convert NOE intensities into distance thresholds. Our new approach thus handles the NOE data correctly and without manually determined parameters. We accordingly adapt NVR-ACO solution methodology to these changes. Computational results show that our approaches obtain optimal solutions for small proteins. For the large proteins our ant colony optimization-based approach obtains promising results.

  20. 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

  1. Residue-specific pK(a) determination of lysine and arginine side chains by indirect N-15 and C-13 NMR spectroscopy : Application to apo calmodulin

    NARCIS (Netherlands)

    Andre, Ingemar; Linse, Sara; Mulder, Frans A. A.

    2007-01-01

    Electrostatic interactions in proteins can be probed experimentally through determination of residue-specific acidity constants, We describe here triple-resonance NMR techniques for direct determination of lysine and arginine side-chain protonation states in proteins. The experiments are based on

  2. Structure Determination of an Ag-I-Mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with H-1/N-15/Ag-109 NMR Spectroscopy

    Czech Academy of Sciences Publication Activity Database

    Dairaku, T.; Furuita, K.; Sato, H.; Šebera, Jakub; Nakashima, K.; Kondo, J.; Yamanaka, D.; Kondo, Y.; Okamoto, I.; Ono, A.; Sychrovský, Vladimír; Kojima, C.; Tanaka, Y.

    2016-01-01

    Roč. 22, č. 37 (2016), s. 13028-13031 ISSN 0947-6539 R&D Projects: GA ČR GA13-27676S Institutional support: RVO:61388963 Keywords : NMR * Ag * cytosine * DFT Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.317, year: 2016

  3. NMR backbone resonance assignments of the prodomain variants of BDNF in the urea denatured state.

    Science.gov (United States)

    Wang, Jing; Bains, Henrietta; Anastasia, Agustin; Bracken, Clay

    2018-04-01

    Brain derived neurotrophic factor (BDNF) is a member of the neurotrophin family of proteins which plays a central role in neuronal survival, growth, plasticity and memory. A single Val66Met variant has been identified in the prodomain of human BDNF that is associated with anxiety, depression and memory disorders. The structural differences within the full-length prodomain Val66 and Met66 isoforms could shed light on the mechanism of action of the Met66 and its impact on the development of neuropsychiatric-associated disorders. In the present study, we report the backbone 1 H, 13 C, and 15 N NMR assignments of both full-length Val66 and Met66 prodomains in the presence of 2 M urea. These conditions were utilized to suppress residual structure and aid subsequent native state structural investigations aimed at mapping and identifying variant-dependent conformational differences under native-state conditions.

  4. Complete assignments of NMR data and assessment of trypanocidal activity of new eremantholide C derivatives

    Directory of Open Access Journals (Sweden)

    DÊNIA A. SAÚDE-GUIMARÃES

    2014-12-01

    Full Text Available Chemical transformations of eremantholide C (1, a sesquiterpene lactone that was isolated from Lychnophora trichocarpha Spreng. led to five new derivatives: 1′,2′- epoxyeremantholide C (2, 5-n-propylamine-4,5-dihydro-1′,2′-epoxyeremantholide C (3, 5-n-propylammonium-4,5-dihydro-1′,2′-epoxyeremantholide C chloride (4, 5-n-propylammonium-4,5-dihydroeremantolide C chloride (5 and 16-O-ethyleremantholide C (6. The structures of all these derivatives were assigned on the basis of IR, MS, 1H and 13C NMR data by 1D and 2D techniques. Eremantholide C and the derivatives 2, 4 and 5 were evaluated against trypomastigotes Y and CL strains of Trypanosoma cruzi. Eremantholide C completely inhibited the growth of both the parasites strains while all derivatives were partially active against the CL strain and inactive against the Y strain.

  5. Complete assignments of NMR data and assessment of trypanocidal activity of new eremantholide C derivatives

    Energy Technology Data Exchange (ETDEWEB)

    Saude-Guimaraes, Denia Antunes, E-mail: saude@ef.ufop.br, E-mail: saudeguima@gmail.com [Universidade Federal de Ouro Preto (UFOP), MG (Brazil); Raslan, Delio S.; Chiari, Egler; Oliveira, Alaide B. de [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil)

    2014-12-15

    Chemical transformations of eremantholide C (1), a sesquiterpene lactone that was isolated from Lychnophora trichocarpha Spreng. led to five new derivatives: 1’,2’- epoxyeremantholide C (2), 5-n-propylamine-4,5-dihydro-1’,2’-epoxyeremantholide C (3), 5-n-propylammonium-4,5-dihydro-1’,2’-epoxyeremantholide C chloride (4), 5-n-propylammonium-4,5-dihydroeremantolide C chloride (5) and 16-O-ethyleremantholide C (6). The structures of all these derivatives were assigned on the basis of IR, MS, {sup 1}H and {sup 13}C NMR data by 1D and 2D techniques. Eremantholide C and the derivatives 2, 4 and 5 were evaluated against trypomastigotes Y and CL strains of Trypanosoma cruzi. Eremantholide C completely inhibited the growth of both the parasites strains while all derivatives were partially active against the CL strain and inactive against the Y strain. (author)

  6. 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.

  7. Probing the Carbonyl Functionality of a Petroleum Resin and Asphaltene through Oximation and Schiff Base Formation in Conjunction with N-15 NMR.

    Directory of Open Access Journals (Sweden)

    Kevin A Thorn

    Full Text Available Despite recent advances in spectroscopic techniques, there is uncertainty regarding the nature of the carbonyl groups in the asphaltene and resin fractions of crude oil, information necessary for an understanding of the physical properties and environmental fate of these materials. Carbonyl and hydroxyl group functionalities are not observed in natural abundance 13C nuclear magnetic resonance (NMR spectra of asphaltenes and resins and therefore require spin labeling techniques for detection. In this study, the carbonyl functionalities of the resin and asphaltene fractions from a light aliphatic crude oil that is the source of groundwater contamination at the long term USGS study site near Bemidji, Minnesota, have been examined through reaction with 15N-labeled hydroxylamine and aniline in conjunction with analysis by solid and liquid state 15N NMR. Ketone groups were revealed through 15N NMR detection of their oxime and Schiff base derivatives, and esters through their hydroxamic acid derivatives. Anilinohydroquinone adducts provided evidence for quinones. Some possible configurations of the ketone groups in the resin and asphaltene fractions can be inferred from a consideration of the likely reactions that lead to heterocyclic condensation products with aniline and to the Beckmann reaction products from the initially formed oximes. These include aromatic ketones and ketones adjacent to quaternary carbon centers, β-hydroxyketones, β-diketones, and β-ketoesters. In a solid state cross polarization/magic angle spinning (CP/MAS 15N NMR spectrum recorded on the underivatized asphaltene as a control, carbazole and pyrrole-like nitrogens were the major naturally abundant nitrogens detected.

  8. Probing the carbonyl functionality of a petroleum resin and asphaltene through oximation and schiff base formation in conjunction with N-15 NMR

    Science.gov (United States)

    Thorn, Kevin A.; Cox, Larry G.

    2015-01-01

    Despite recent advances in spectroscopic techniques, there is uncertainty regarding the nature of the carbonyl groups in the asphaltene and resin fractions of crude oil, information necessary for an understanding of the physical properties and environmental fate of these materials. Carbonyl and hydroxyl group functionalities are not observed in natural abundance 13C nuclear magnetic resonance (NMR) spectra of asphaltenes and resins and therefore require spin labeling techniques for detection. In this study, the carbonyl functionalities of the resin and asphaltene fractions from a light aliphatic crude oil that is the source of groundwater contamination at the long term USGS study site near Bemidji, Minnesota, have been examined through reaction with 15N-labeled hydroxylamine and aniline in conjunction with analysis by solid and liquid state 15N NMR. Ketone groups were revealed through 15N NMR detection of their oxime and Schiff base derivatives, and esters through their hydroxamic acid derivatives. Anilinohydroquinone adducts provided evidence for quinones. Some possible configurations of the ketone groups in the resin and asphaltene fractions can be inferred from a consideration of the likely reactions that lead to heterocyclic condensation products with aniline and to the Beckmann reaction products from the initially formed oximes. These include aromatic ketones and ketones adjacent to quaternary carbon centers, β-hydroxyketones, β-diketones, and β-ketoesters. In a solid state cross polarization/magic angle spinning (CP/MAS) 15N NMR spectrum recorded on the underivatized asphaltene as a control, carbazole and pyrrole-like nitrogens were the major naturally abundant nitrogens detected.

  9. Dynamic domains of amyloid fibrils can be site-specifically assigned with proton detected 3D NMR spectroscopy

    International Nuclear Information System (INIS)

    Falk, Alexander S.; Siemer, Ansgar B.

    2016-01-01

    Several amyloid fibrils have cores framed by highly dynamic, intrinsically disordered, domains that can play important roles for function and toxicity. To study these domains in detail using solid-state NMR spectroscopy, site-specific resonance assignments are required. Although the rapid dynamics of these domains lead to considerable averaging of orientation-dependent NMR interactions and thereby line-narrowing, the proton linewidths observed in these samples is far larger than what is regularly observed in solution. Here, we show that it is nevertheless possible to record 3D HNCO, HNCA, and HNcoCA spectra on these intrinsically disordered domains and to obtain site-specific assignments.

  10. Dynamic domains of amyloid fibrils can be site-specifically assigned with proton detected 3D NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Falk, Alexander S.; Siemer, Ansgar B., E-mail: asiemer@usc.edu [Keck School of Medicine of USC, Department of Biochemistry and Molecular Medicine, Zilkha Neurogenetic Institute (United States)

    2016-11-15

    Several amyloid fibrils have cores framed by highly dynamic, intrinsically disordered, domains that can play important roles for function and toxicity. To study these domains in detail using solid-state NMR spectroscopy, site-specific resonance assignments are required. Although the rapid dynamics of these domains lead to considerable averaging of orientation-dependent NMR interactions and thereby line-narrowing, the proton linewidths observed in these samples is far larger than what is regularly observed in solution. Here, we show that it is nevertheless possible to record 3D HNCO, HNCA, and HNcoCA spectra on these intrinsically disordered domains and to obtain site-specific assignments.

  11. 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.

  12. 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

  13. A conformational NMR analysis of methymycin aglycones: complete and unambiguous assignments of stereochemically diverse glycosylated methymycin analogs by 1D and 2D NMR techniques and molecular modeling.

    Science.gov (United States)

    Akhmedov, Novruz G; Gannett, Peter M; Wu, Bulan; Cummings, Matthew M; Train, Brian C

    2013-03-01

    The (1)H and (13)C NMR spectra of 10-deoxymethynolide (1), 8.9-dihydro-10-deoxymethynolide (2) and its glycosylated derivatives (3-9) were analyzed using gradient-selected NMR techniques, including 1D TOCSY, gCOSY, 1D NOESY (DPFGSENOE), NOESY, gHMBC, gHSQC and gHSQC-TOCSY. The NMR spectral parameters (chemical shifts and coupling constants) of 1-9 were determined by iterative analysis. For the first time, complete and unambiguous assignment of the (1)H NMR spectrum of 10-deoxymethynolide (1) has been achieved in CDCl(3), CD(3)OD and C(6)D(6) solvents. The (1)H NMR spectrum of 8,9-dihydro-10-deoxymethynolide (2) was recorded in CDCl(3), (CD(3))(2)CO and CD(3)OD solutions to determine the conformation. NMR-based conformational analysis of 1 and 2 in conjugation with molecular modeling concluded that the 12-membered ring of the macrolactones may predominantly exist in a single stable conformation in all solvents examined. In all cases, a change in solvent caused only small changes in chemical shifts and coupling constants, suggesting that all glycosylated methymycin analogs exist with similar conformations of the aglycone ring in solution. Copyright © 2013 John Wiley & Sons, Ltd.

  14. 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

  15. H-1, C-13, and N-15 NMR assignments of the hypothetical Nudix protein DR0079 from the extremely radiation-resistant bacterium Deinococcus radiodurans.

    Energy Technology Data Exchange (ETDEWEB)

    Buchko, Garry W.; Ni, Shuisong; Holbrook, Stephen R.; Kennedy, Michael A.

    2003-02-05

    Letter to the Editor. Biological context Deinococcus radiodurans is a bacterium that is extremely resistant to the lethal and mutagenic effects of ionizing radiation, ultraviolet radiation, and other physical and chemical DNA-damaging agents (Battista, 1997). It has been suggested that this resistance is due to unusually efficient DNA repair mechanisms (Minton, 1994). Analysis of the complete genome sequence of D. radiodurans reveals a full suite of genes with potential DNA repair activities (White et al, 1999), essentially all of which have functional homologues in other procaryotes. These hypothetical DNA repair genes display a high amount of redundancy and include 21 genes that have sequence homology with the Nudix family of polyphosphate pyrophosphohydrolases (Bessman et al., 1996). Nudix proteins are identified by the consensus sequence GX5EX7REUXEEXGU (where U= I, L, or V and X= any amino acid) that forms part of the catalytic site for diphosphate hydrolysis (Bessman et al., 1996). Consequently, a nucleoside diphosphate linkage is a feature common in Nudix substrates that include NADH, nucleotide sugars, dinucleotide polyphosphates, and (deoxy)ribonucleoside triphosphates (NTPs). The general biochemical function of the Nudix family of proteins is believed to be sanitizing the cell (Bessman et al., 1996). For example, MutT preferably hydrolyzes the promutagenic NTP 7,8-dihydro-8-oxoguanosine triphosphate to nucleotide monophosphate and inorganic phosphate. Despite the identification of over 450 putative Nudix proteins in genomes on the basis of the Nudix consensus sequence (Gabelli et al., 2001), few Nudix protein structures have been determined (Holbrook et al., 2002). To better understand the relevance, function, and mechanism of the Nudix family of proteins, and to better understand the roles played by the hypothetical D. radiodurans Nudix proteins in radiation-resistance, we have crystallized the hypothetical D.

  16. {sup 13}C-direct detected NMR experiments for the sequential J-based resonance assignment of RNA oligonucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Richter, Christian [Johann Wolfgang Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (Germany); Kovacs, Helena [Bruker BioSpin AG (Switzerland); Buck, Janina; Wacker, Anna [Johann Wolfgang Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (Germany); Fuertig, Boris [Max F. Perutz Laboratories (Austria); Bermel, Wolfgang [Bruker BioSpin GmbH (Germany); Schwalbe, Harald, E-mail: schwalbe@nmr.uni-frankfurt.d [Johann Wolfgang Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (Germany)

    2010-08-15

    We present here a set of {sup 13}C-direct detected NMR experiments to facilitate the resonance assignment of RNA oligonucleotides. Three experiments have been developed: (1) the (H)CC-TOCSY-experiment utilizing a virtual decoupling scheme to assign the intraresidual ribose {sup 13}C-spins, (2) the (H)CPC-experiment that correlates each phosphorus with the C4' nuclei of adjacent nucleotides via J(C,P) couplings and (3) the (H)CPC-CCH-TOCSY-experiment that correlates the phosphorus nuclei with the respective C1',H1' ribose signals. The experiments were applied to two RNA hairpin structures. The current set of {sup 13}C-direct detected experiments allows direct and unambiguous assignment of the majority of the hetero nuclei and the identification of the individual ribose moieties following their sequential assignment. Thus, {sup 13}C-direct detected NMR methods constitute useful complements to the conventional {sup 1}H-detected approach for the resonance assignment of oligonucleotides that is often hindered by the limited chemical shift dispersion. The developed methods can also be applied to large deuterated RNAs.

  17. Synthesis, three-dimensional structure, conformation and correct chemical shift assignment determination of pharmaceutical molecules by NMR and molecular modeling

    International Nuclear Information System (INIS)

    Azeredo, Sirlene O.F. de; Sales, Edijane M.; Figueroa-Villar, José D.

    2017-01-01

    This work includes the synthesis of phenanthrenequinone guanylhydrazone and phenanthro[9,10-e][1,2,4]triazin-3-amine to be tested as intercalate with DNA for treatment of cancer. The other synthesized product, 2-[(4-chlorophenylamino)methylene]malononitrile, was designed for future determination of its activity against leishmaniasis. A common problem about some articles on the literature is that some previously published compounds display error of their molecular structures. In this article it is shown the application of several procedures of nuclear magnetic resonance (NMR) to determine the complete molecular structure and the non questionable chemical shift assignment of the synthesized compounds, and also their analysis by molecular modeling to confirm the NMR results. To determine the capacity of pharmacological compounds to interact with biological targets is determined by docking. This work is to motivate the application of NMR and molecular modeling on organic synthesis, being a process that is very important for the study of the prepared compounds as interactions with biological targets by NMR. (author)

  18. Synthesis, three-dimensional structure, conformation and correct chemical shift assignment determination of pharmaceutical molecules by NMR and molecular modeling

    Energy Technology Data Exchange (ETDEWEB)

    Azeredo, Sirlene O.F. de; Sales, Edijane M.; Figueroa-Villar, José D., E-mail: jdfv2009@gmail.com [Instituto Militar de Engenharia (IME), Rio de Janeiro, RJ (Brazil). Grupo de Ressonância Magnética Nuclear e Química Medicinal

    2017-07-01

    This work includes the synthesis of phenanthrenequinone guanylhydrazone and phenanthro[9,10-e][1,2,4]triazin-3-amine to be tested as intercalate with DNA for treatment of cancer. The other synthesized product, 2-[(4-chlorophenylamino)methylene]malononitrile, was designed for future determination of its activity against leishmaniasis. A common problem about some articles on the literature is that some previously published compounds display error of their molecular structures. In this article it is shown the application of several procedures of nuclear magnetic resonance (NMR) to determine the complete molecular structure and the non questionable chemical shift assignment of the synthesized compounds, and also their analysis by molecular modeling to confirm the NMR results. To determine the capacity of pharmacological compounds to interact with biological targets is determined by docking. This work is to motivate the application of NMR and molecular modeling on organic synthesis, being a process that is very important for the study of the prepared compounds as interactions with biological targets by NMR. (author)

  19. Two-dimensional sup 1 H NMR studies on HPr protein from Staphylococcus aureus: Complete sequential assignments and secondary structure

    Energy Technology Data Exchange (ETDEWEB)

    Kalbitzer, H.R.; Neidig, K.P. (Max-Planck-Inst. for Medical Research, Heidelberg (West Germany)); Hengstenberg, W. (Univ. of Bochum (West Germany))

    1991-11-19

    Complete sequence-specific assignments of the {sup 1}H NMR spectrum of HPr protein from Staphylococcus aureus were obtained by two-dimensional NMR methods. Important secondary structure elements that can be derived from the observed nuclear Overhauser effects are a large antiparallel {beta}-pleated sheet consisting of four strands, A, B, C, D, a segment S{sub AB} consisting of an extended region around the active-center histidine (His-15) and an {alpha}-helix, a half-turn between strands B and C, a segment S{sub CD} which shows no typical secondary structure, and the {alpha}-helical, C-terminal segment S{sub term}. These general structural features are similar to those found earlier in HPr proteins from different microorganisms such as Escherichia coli, Bacillus subtilis, and Streptococcus faecalis.

  20. Structural elucidation and NMR assignments of a new pyrrolizidine alkaloid from Crotalaria vitellina Ker Gawl.

    Science.gov (United States)

    Casimiro Bezerra, Denise Aline; Fechine Tavares, Josean; dos Santos, Paula Ferreira; Castello Branco, Marianna Vieira Sobral; de Fátima Agra, Maria; Subrinho, Fernanda Lima; Braz-Filho, Raimundo; da Silva, Marcelo Sobral

    2013-08-01

    A new pyrrolizidine alkaloid, named crotavitelin, was isolated from fruits of Crotalaria vitellina, Fabaceae (Papilionoideae). The structure was established by spectroscopic techniques such as one-dimensional and two-dimensional NMR, IR, and MS. Copyright © 2013 John Wiley & Sons, Ltd.

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

    KAUST Repository

    Wang, Songlin

    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.

  2. NMR assignment of a KlbA intein precursor from Methanococcus jannaschii.

    Science.gov (United States)

    Johnson, Margaret A; Southworth, Maurice W; Perler, Francine B; Wüthrich, Kurt

    2007-07-01

    The backbone and side chain resonance assignments of a precursor of the KlbA intein from Methanococcus jannaschii have been determined, based on triple-resonance experiments with the uniformly [13C,15N]-labeled protein.

  3. Proton-detected MAS NMR experiments based on dipolar transfers for backbone assignment of highly deuterated proteins

    Science.gov (United States)

    Chevelkov, Veniamin; Habenstein, Birgit; Loquet, Antoine; Giller, Karin; Becker, Stefan; Lange, Adam

    2014-05-01

    Proton-detected solid-state NMR was applied to a highly deuterated insoluble, non-crystalline biological assembly, the Salmonella typhimurium type iii secretion system (T3SS) needle. Spectra of very high resolution and sensitivity were obtained at a low protonation level of 10-20% at exchangeable amide positions. We developed efficient experimental protocols for resonance assignment tailored for this system and the employed experimental conditions. Using exclusively dipolar-based interspin magnetization transfers, we recorded two sets of 3D spectra allowing for an almost complete backbone resonance assignment of the needle subunit PrgI. The additional information provided by the well-resolved proton dimension revealed the presence of two sets of resonances in the N-terminal helix of PrgI, while in previous studies employing 13C detection only a single set of resonances was observed.

  4. 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.

  5. 13C-detected NMR experiments for automatic resonance assignment of IDPs and multiple-fixing SMFT processing

    International Nuclear Information System (INIS)

    Dziekański, Paweł; Grudziąż, Katarzyna; Jarvoll, Patrik; Koźmiński, Wiktor; Zawadzka-Kazimierczuk, Anna

    2015-01-01

    Intrinsically disordered proteins (IDPs) have recently attracted much interest, due to their role in many biological processes, including signaling and regulation mechanisms. High-dimensional 13 C direct-detected NMR experiments have proven exceptionally useful in case of IDPs, providing spectra with superior peak dispersion. Here, two such novel experiments recorded with non-uniform sampling are introduced, these are 5D HabCabCO(CA)NCO and 5D HNCO(CA)NCO. Together with the 4D (HACA)CON(CA)NCO, an extension of the previously published 3D experiments (Pantoja-Uceda and Santoro in J Biomol NMR 59:43–50, 2014. doi: 10.1007/s10858-014-9827-1 10.1007/s10858-014-9827-1 ), they form a set allowing for complete and reliable resonance assignment of difficult IDPs. The processing is performed with sparse multidimensional Fourier transform based on the concept of restricting (fixing) some of spectral dimensions to a priori known resonance frequencies. In our study, a multiple-fixing method was developed, that allows easy access to spectral data. The experiments were tested on a resolution-demanding alpha-synuclein sample. Due to superior peak dispersion in high-dimensional spectrum and availability of the sequential connectivities between four consecutive residues, the overwhelming majority of resonances could be assigned automatically using the TSAR program

  6. Assignment of histidine resonances in the 1H NMR (500 MHz) spectrum of subtilisin BPN' using site-directed mutagenesis

    International Nuclear Information System (INIS)

    Bycroft, M.; Fersht, A.R.

    1988-01-01

    A spin-echo pulse sequence has been used to resolve the six histidine C-2H protons in the 500-MHz NMR spectrum of subtilisin BPN'. Five of these residues have been substituted by site-directed mutagenesis, and this has enabled a complete assignment of these protons to be obtained. Analysis of the pH titration curves of these signals has provided microscopic pK a 's for the six histidines in this enzyme. The pK a 's of the histidine residues in subtilisin BPN' have been compared with the values obtained for the histidines in the homologous enzyme from Bacillus licheniformis (subtilisin Carlsberg). Four of the five conserved histidines titrate with essentially identical pK a 's in the two enzymes. It therefore appears that the assignments made for these residues in subtilisin BPN' can be transferred to subtilisin Carlsberg. On the basis of these assignments, the one histidine that titrates with a substantially different pK a in the two enzymes can be assigned to histidine-238. This difference in pK a has been attributed to a Trp to Lys substitution at position 241 in subtilisin Carlsberg

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

    International Nuclear Information System (INIS)

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

    1989-01-01

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

  8. 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.

  9. NMR

    International Nuclear Information System (INIS)

    Kneeland, J.B.; Lee, B.C.P.; Whalen, J.P.; Knowles, R.J.R.; Cahill, P.T.

    1984-01-01

    Although still quite new, NMR imaging has already emerged as a safe, noninvasive, painless, and effective diagnostic modality requiring no ionizing radiation. Also, NMR appears already to have established itself as the method of choice for the examination of the brain spinal cord (excluding herniated disks). Another area in which NMR excels is in the examination of the pelvis. The use of surface coils offers the promise of visualizing structures with resolution unobtainable by any other means. In addition, NMR, with its superb visualization of vascular structures and potential ability to measure flow, may soon revolutionize the diagnosis of cardiovascular disease. Finally, NMR, through biochemically and physiologically based T/sub 1/ and T/sub 2/ indices or through spectroscopy, may provide a means of monitoring therapeutic response so as to permit tailoring of treatment to the individual patient. In short, NMR is today probably at the same stage as the x-ray was in Roentgen's day

  10. Protein residue linking in a single spectrum for magic-angle spinning NMR assignment

    Energy Technology Data Exchange (ETDEWEB)

    Andreas, Loren B.; Stanek, Jan; Marchand, Tanguy Le; Bertarello, Andrea; Paepe, Diane Cala-De; Lalli, Daniela; Krejčíková, Magdaléna; Doyen, Camille; Öster, Carl [Université de Lyon, Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (CNRS, ENS Lyon, UCB Lyon 1) (France); Knott, Benno; Wegner, Sebastian; Engelke, Frank [Bruker Biospin (Germany); Felli, Isabella C.; Pierattelli, Roberta [University of Florence, Department of Chemistry “Ugo Schiff“and Magnetic Resonance Center (CERM) (Italy); Dixon, Nicholas E. [University of Wollongong, School of Chemistry (Australia); Emsley, Lyndon; Herrmann, Torsten; Pintacuda, Guido, E-mail: guido.pintacuda@ens-lyon.fr [Université de Lyon, Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (CNRS, ENS Lyon, UCB Lyon 1) (France)

    2015-07-15

    Here we introduce a new pulse sequence for resonance assignment that halves the number of data sets required for sequential linking by directly correlating sequential amide resonances in a single diagonal-free spectrum. The method is demonstrated with both microcrystalline and sedimented deuterated proteins spinning at 60 and 111 kHz, and a fully protonated microcrystalline protein spinning at 111 kHz, with as little as 0.5 mg protein sample. We find that amide signals have a low chance of ambiguous linkage, which is further improved by linking in both forward and backward directions. The spectra obtained are amenable to automated resonance assignment using general-purpose software such as UNIO-MATCH.

  11. NMR backbone assignments of the tyrosine kinase domain of human fibroblast growth factor receptor 1.

    Science.gov (United States)

    Vajpai, Navratna; Schott, Anne-Kathrin; Vogtherr, Martin; Breeze, Alexander L

    2014-04-01

    Members of the fibroblast growth factor receptor tyrosine kinase family (FGFR1-4) play an important role in many signalling cascades. Although tightly regulated, aberrant activity of these enzymes may lead to, or become features of, disease pathologies including cancer. FGFR isoforms have been the subject of drug discovery programmes, with a number of kinase-domain inhibitors in pre-clinical and clinical development. Here, we present the first (83% complete) backbone resonance assignments of apo-FGFR1 kinase.

  12. Sequence-specific 1H NMR assignments and secondary structure of the Arc repressor of bacteriophage P22, as determined by two-dimensional 1H NMR spectroscopy

    International Nuclear Information System (INIS)

    Breg, J.N.; Boelens, R.; George, A.V.E.; Kaptein, R.

    1989-01-01

    The Arc repressor of bacteriophage P22 is a DNA binding protein that does not belong to any of the known classes of such proteins. The authors have undertaken a 1 H NMR study of the protein with the aim of elucidating its three-dimensional structure in solution and its mode of binding of operator DNA. Here the authors present the 1 H nuclear magnetic resonance (NMR) assignments of all backbone protons an most of the side-chain protons of Arc repressor. Elements of secondary structure have been identified on the basis of networks of characteristics sequential and medium-range nuclear Overhauser enhancements (NOEs). Two α-helical regions have been found in the peptide regions 16-29 and 35-45. The ends of the helices could not yet be firmly established and could extend to residue 31 for the first helix and to residue 49 for the second. Immediately before the first helix, between residues 8 and 14, a region is present with β-sheet characteristics dominated by a close proximity of the α-protons of residues 9 and 13. Because of the dimeric nature of the protein there are still two possible ways in which the NOEs in the β-sheet region can be interpreted. While the data presently do not allow an unambiguous choice between these two possibilities, some evidence is discussed that favors the latter (β-sheet between monomers). Since the N-terminal region of Arc is responsible for the sequence-specific recognition of its operator, the findings suggest the existence of a DNA binding motif in which a β-sheet region is present

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

    International Nuclear Information System (INIS)

    Mas, Guillaume; Crublet, Elodie; Hamelin, Olivier; Gans, Pierre; Boisbouvier, Jérôme

    2013-01-01

    The specific protonation of valine and leucine methyl groups in proteins is typically achieved by overexpressing proteins in M9/D 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 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

  14. 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.

  15. Isolation, purification, and full NMR assignments of cyclopamine from Veratrum californicum

    Directory of Open Access Journals (Sweden)

    Gallien Thomas N

    2008-06-01

    Full Text Available Abstract Background The Hedgehog signaling pathway is essential for embryogenesis and for tissue homeostasis in the adult. However, it may induce malignancies in a number of tissues when constitutively activated, and it may also have a role in other forms of normal and maladaptive growth. Cyclopamine, a naturally occurring steroidal alkaloid, specifically inhibits the Hedgehog pathway by binding directly to Smoothened, an important Hedgehog response element. To use cyclopamine as a tool to explore and/or inhibit the Hedgehog pathway in vivo, a substantial quantity is required, and as a practical matter cyclopamine has been effectively unavailable for usage in animals larger than mice. Results In this paper, we report a rapid and efficient isolation and purification of large quantities of cyclopamine from the roots and rhizomes of Veratrum californicum Dur. (the Corn Lily or Western false hellebore. We also provide unambiguous assignments of the carbon and proton resonances by using the multinuclear spectra and the spin coupling networks. Conclusion This method could meet a very real need within diverse scientific communities by allowing cyclopamine to become more readily available.

  16. Two new Ni(II) Schiff base complexes : X-ray absolute structure determination, synthesis of a N-15-labelled complex and full assignment of its H-1 NMR and C-13 NMR spectra

    NARCIS (Netherlands)

    Langer, Vratislav; Popkov, Alexander; Nadvornik, Milan; Lycka, Antonin

    2007-01-01

    The Ni(II) complex of the Schiff base of (S)-N-(2-benzoyl-4-chlorophenyl)-1-benzylpyrrolidine-2-carboxamide and glycine (1) [GKCI] and the hemihydrate of the Ni(II) complex of the Schiff base of (S)-N-(2-benzoylphenyl)-1-benzylpyrrolidine-2-carboxamide and 2-aminoisobutiric acid (2) Me(2)GK] were

  17. NMR backbone resonance assignments of the N, P domains of CopA, a copper-transporting ATPase, in the apo and ligand bound states.

    Science.gov (United States)

    Meng, Dan; Bruschweiler-Li, Lei; Zhang, Fengli; Brüschweiler, Rafael

    2015-04-01

    Copper-transporting ATPase, a member of P-type ATPase family, plays a key role in the homeostasis of cellular copper levels. Here, the backbone assignments of the directly connected N and P domains (292 residues, 31 kDa) of Cu-transporting ATPase in the ligand free and the AMPPCP-bound states are reported in solution. The NMR assignments pave the way for binding and dynamics studies of this enzyme to better understand its function.

  18. A complete 1H and 13C NMR data assignment for the diterpene methyl (-)-zanzibarate by 2D spectroscopy and NOE experiments.

    Science.gov (United States)

    Imamura, P M; Miranda, P C M L; Giacomini, R A

    2004-06-01

    The 1H and 13C NMR spectra of methyl (-)-zanzibarate (1), an ent-labdanic diterpene isolated from the epicarp of Hymenaea courbaril var. altissima (Leguminosaea, Cesalpinoideae, Detariae), was fully assigned by COSY experiments, 13C/1H shift correlation diagrams and NOE experiments. Copyright 2004 John Wiley & Sons, Ltd.

  19. (1)H, (13)C and (15)N NMR assignments for N- and O-acylethanolamines, important family of naturally occurring bioactive lipid mediators.

    Science.gov (United States)

    Ottria, Roberta; Casati, Silvana; Ciuffreda, Pierangela

    2012-12-01

    The complete (1)H, (13)C and (15)N NMR signal assignments of some N- and O-acylethanolamines, important family of naturally occurring bioactive lipid mediators, were achieved using one-dimensional and two-dimensional experiments (gs-HMQC and gs-HMBC). Copyright © 2012 John Wiley & Sons, Ltd.

  20. Complete {sup 1}H and {sup 13}C NMR assignments and anti fungal activity of two 8-hydroxy flavonoids in mixture

    Energy Technology Data Exchange (ETDEWEB)

    Johann, Susana; Smania Junior, Artur [Universidade Federal de Santa Catarina (UFSC), Florianopolis, SC (Brazil). Dept. de Microbiologia e Parasitologia. Lab. de Antibioticos; Pizzolatti, Moacir G. [Universidade Federal de Santa Catarina (UFSC), Florianopolis, SC (Brazil). Dept. de Quimica; Schripsema, Jan; Braz-Filho, Raimundo [Universidade Estadual do Norte Fluminense (UENF), Campos dos Goytacazes, RJ (Brazil). Setor de Quimica de Produtos Naturais. Lab. de Quimica e Funcao de Proteinas e Peptideos (LQFPP); Branco, Alexsandro [Universidade Estadual de Feira de Santana, BA (Brazil). Dept. de Saude. Lab. de Fitoquimica]. E-mail: branco@uefs.br

    2007-06-15

    A mixture of the two new flavonols 8-hydroxy-3, 4', 5, 6, 7-pentamethoxyflavone (1) and 8-hydroxy-3, 3', 4', 5, 6, 7-hexamethoxyflavone (2) was isolated from a commercial sample of Citrus aurantifolia. An array of one- ({sup 1}H NMR, {l_brace}{sup 1}H{r_brace} {sup -13}C NMR, and APT{sup -13}C NMR) and two-dimensional NMR techniques (COSY, NOESY, HMQC and HMBC) was used to achieve the structural elucidation and the complete {sup 1}H and {sup 13}C chemical shift assignments of these natural compounds. In addition, the antifungal activity of these compounds against phytopathogenic and human pathogenic fungi was investigated. (author)

  1. The infrared, Raman, NMR and UV spectra, ab initio calculations and spectral assignments of 2-amino-4-chloro-6-methoxypyrimidine.

    Science.gov (United States)

    Cinar, Z; Karabacak, M; Cinar, M; Kurt, M; Chinna Babu, P; Sundaraganesan, N

    2013-12-01

    The 2-amino-4-chloro-6-methoxypyrimidine abbreviated as ACMP have been investigated by both the experimental and theoretical methods; through this work we provide the essential fact about the structural and vibrational insights. The optimized molecular structure, atomic charges, vibrational frequencies and ultraviolet spectral interpretation of ACMP have been studied by performing DFT/B3LYP/6-311++G(df,pd) level of theory. The FT-IR, FT-Raman spectra were recorded in the region 4000-400 cm(-1) and 4000-50 cm(-1) respectively. The UV absorption spectrum of the compound that dissolved in ethanol and water solution were recorded in the range of 200-400 nm. The scaled wavenumbers are compared with the experimental values. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. Based on the UV spectrum and TD-DFT calculations, the electronic structure and the assignments of the absorption bands were carried out. The (1)H, (13)C and DEPT 135 nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated using with the Gauge Including Atomic Orbital (GIAO) method and compared with experimental results. Besides, molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis were investigated using theoretical calculations. Copyright © 2013 Elsevier B.V. All rights reserved.

  2. Editorial, n. 15, 2003

    Directory of Open Access Journals (Sweden)

    Editor Encontros Bibli

    2003-01-01

    Informação da UFSC, que já está em seu oitavo ano, por sua Comissão Editorial, compartilhada com a presença de colegas do Brasil e exterior, manifesta sua alegria por esta conquista e exulta pela coincidência neste ano das Comemorações dos trinta anos do Curso de Biblioteconomia da UFSC e o início do Mestrado em Ciência da Informação desta instituição. Nesta edição do primeiro semestre do ano de 2003, Encontros Bibli tem a satisfação de trazer quatro artigos, dois oriundos da produção de pesquisadores da Escola de Ciência da Informação da Universidade Federal de Minas Gerais e dois oriundos da produção de pesquisa realizada por pesquisadores do Departamento de Ciência da Informação da UFSC. Aos leitores desejamos que estas contribuições ensejem questões que contribuam com a produção de reflexões e interrogações geradoras de novas investigações as quais naturalmente virão a contribuir para o progresso do conhecimento nacional em Ciência da Informação. Um grande abraço a todos e a todas! Prof. Francisco das Chagas de Souza Editor Departamento de Ciência da Informação Universidade Federal de Santa Catarina Brasil Disponibilizado na WWW em 20/05/2003. Enc. Bibli: R. Eletr. Bibliotecon. Ci. Inf., Florianópolis, n.15, 1º sem. 2003. 1

  3. GFT projection NMR based resonance assignment of membrane proteins: application to subunit C of E. coli F(1)F (0) ATP synthase in LPPG micelles.

    Science.gov (United States)

    Zhang, Qi; Atreya, Hanudatta S; Kamen, Douglas E; Girvin, Mark E; Szyperski, Thomas

    2008-03-01

    G-matrix FT projection NMR spectroscopy was employed for resonance assignment of the 79-residue subunit c of the Escherichia coli F(1)F(0) ATP synthase embedded in micelles formed by lyso palmitoyl phosphatidyl glycerol (LPPG). Five GFT NMR experiments, that is, (3,2)D HNNCO, L-(4,3)D HNNC (alphabeta) C (alpha), L-(4,3)D HNN(CO)C (alphabeta) C (alpha), (4,2)D HACA(CO)NHN and (4,3)D HCCH, were acquired along with simultaneous 3D (15)N, (13)C(aliphatic), (13)C(aromatic)-resolved [(1)H,(1)H]-NOESY with a total measurement time of approximately 43 h. Data analysis resulted in sequence specific assignments for all routinely measured backbone and (13)C(beta) shifts, and for 97% of the side chain shifts. Moreover, the use of two G(2)FT NMR experiments, that is, (5,3)D HN{N,CO}{C (alphabeta) C (alpha)} and (5,3)D {C (alphabeta) C (alpha)}{CON}HN, was explored to break the very high chemical shift degeneracy typically encountered for membrane proteins. It is shown that the 4D and 5D spectral information obtained rapidly from GFT and G(2)FT NMR experiments enables one to efficiently obtain (nearly) complete resonance assignments of membrane proteins.

  4. Other compounds isolated from Simira glaziovii and the {sup 1}H and {sup 13}C NMR chemical shift assignments of new 1-epi-castanopsol

    Energy Technology Data Exchange (ETDEWEB)

    Araujo, Marcelo F. de; Vieira, Ivo J. Curcino [Universidade Federal Rural do Rio de Janeiro, Seropedica, RJ (Brazil). Dept. de Quimica; Braz-Filho, Raimundo [Universidade Estadual do Norte Fluminense (UENF), Campos dos Goytacases, RJ (Brazil). Centro de Ciencias Tecnologicas. Lab. de Ciencias Quimicas; Carvalho, Mario G. de, E-mail: mgeraldo@ufrrj.br [Universidade Federal do Rio de Janeiro (NPPN/UFRJ), RJ (Brazil). Centro de Ciencias da Saude. Nucleo de Pesquisa em Produtos Naturais

    2012-07-01

    A new triterpene, 1-epi-castanopsol, besides eleven known compounds: sitosterol, stigmasterol, campesterol, lupeol, lupenone, simirane B, syringaresinol, scopoletin, isofraxidin, 6,7,8-trimethoxycoumarin and harman, were isolated from the wood of Simira glaziovii. The structures of the known compounds were defined by 1D, 2D {sup 1}H, {sup 13}C NMR spectra data analyses and comparison with literature data. The detailed spectral data analyses allowed the definition of the structure of the new 1-epi isomer of castanopsol and performance of {sup 1}H and {sup 13}C NMR chemical shift assignments. (author)

  5. Principal component analysis for verifying 1H NMR spectral assignments. The case of 3-aryl (1,2,4)-oxadiazole-5-carbohydrazide benzylidene

    International Nuclear Information System (INIS)

    Silva, Joao Bosco P. da; Malvestiti, Ivani; Hallwass, Fernando; Ramos, Mozart N.; Leite, Lucia F.C. da Costa; Barreiro, Eliezer J.

    2005-01-01

    The 1 H NMR data set of a series of 3-aryl (1,2,4)-oxadiazole-5-carbohydrazide benzylidene derivatives synthesized in our group was analyzed using the chemometric technique of principal component analysis (PCA). Using the original 1H NMR data PCA allowed identifying some misassignments of the proton aromatic chemical shifts. As a consequence of this multivariate analysis, nuclear Overhauser difference experiments were performed to investigate the ambiguity of other assignments of the ortho and meta aromatic hydrogens for the compound with the bromine substituent. The effect of the 1,2,4-oxadiazole group as an electron acceptor, mainly for the hydrogens 12,13, has been highlighted. (author)

  6. Characterization of mu s-ms dynamics of proteins using a combined analysis of N-15 NMR relaxation and chemical shift: Conformational exchange in plastocyanin induced by histidine protonations

    DEFF Research Database (Denmark)

    Hass, M. A. S.; Thuesen, Marianne Hallberg; Christensen, Hans Erik Mølager

    2004-01-01

    variabilis (A.v. PCu) (Ma, L.; Hass, M. A. S.; Vierick, N.; Kristensen, S. M.; Ulstrup, J.; Led, J. J. Biochemistry 2003, 42, 320-330). The R-1 and R-2 relaxation rates of the backbone N-15 nuclei were measured at a series of pH and temperatures on an 15N labeled sample of A.v. PCu, and the 15 N chemical...

  7. NMR assignments and ligand-binding studies on a two-domain family GH19 chitinase allergen from Japanese cedar (Cryptomeria japonica) pollen.

    Science.gov (United States)

    Takashima, Tomoya; Ohnuma, Takayuki; Fukamizo, Tamo

    2017-04-01

    A two-domain family GH19 chitinase from Japanese cedar (Cryptomeria japonica) pollen, CJP-4, which consists of an N-terminal CBM18 domain and a GH19 catalytic domain, is known to be an important allergen, that causes pollinosis. We report here the resonance assignments of the NMR spectrum of CJP-4. The backbone resonances were almost completely assigned, and the secondary structure was estimated based on the chemical shift values. The addition of a chitin dimer to the enzyme solution perturbed the chemical shifts of the resonances of amino acid residues forming a long extended binding site spanning from the CBM18 domain to the GH19 catalytic domain.

  8. The Conformation and Assignment of the Proton NMR Spectrum in Water of DX600, a Bioactive Peptide with a Random Coil Conformation

    Directory of Open Access Journals (Sweden)

    Wayne E. Steinmetz

    2011-01-01

    Full Text Available DX600, a small peptide with 26 residues, is a potent, highly selective inhibitor of angiotensin converting enzyme 2 (ACE2. A range of NMR methods including TOCSY and ROESY yield an assignment of its proton spectrum in water and constraints on its conformation. Constrained molecular dynamics simulations of solvated DX600 show that the peptide's most abundant conformer adopts a predominantly random coil conformation. Constrained by the disulfide bond, its backbone defines an overhand knot with frayed ends.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1997-01-15

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

  10. 1H and 13C NMR assignments for the glycans in glycoproteins by using 2H/13C-labeled glucose as a metabolic precursor

    Energy Technology Data Exchange (ETDEWEB)

    Yamaguchi, Yoshiki; Takizawa, Takeshi; Kato, Koichi [University of Tokyo, Hongo, Bunkyo-ku, Graduate School of Pharmaceutical Sciences (Japan); Arata, Yoji [Institute of Physical and Chemical Research (RIKEN), Genomic Sciences Center (Japan); Shimada, Ichio [University of Tokyo, Hongo, Bunkyo-ku, Graduate School of Pharmaceutical Sciences (Japan)

    2000-12-15

    In order to understand the role of the glycans in glycoproteins in solution, structural information obtained by NMR spectroscopy is obviously required. However, the assignment of the NMR signals from the glycans in larger glycoproteins is still difficult, mainly due to the lack of appropriate methods for the assignment of the resonances originating from the glycans. By using [U-{sup 13}C{sub 6},{sup 2}H{sub 7}]glucose as a metabolic precursor, we have successfully prepared a glycoprotein whose glycan is uniformly labeled with {sup 13}C and partially with D at the sugar residues. The D to H exchange ratios at the C1-C6 positions of the sugar residues have been proven to provide useful information for the spectral assignments of the glycan in the glycoprotein. This is the first report on the residue-specific assignment of the anomeric resonances originating from a glycan attached to a glycoprotein by using the metabolic incorporation of hydrogen from the medium into a glycan labeled with [U-{sup 13}C{sub 6},{sup 2}H{sub 7}]glucose.

  11. Selective reversible deuteriation of oligodeoxynucleotides: simplification of two-dimensional nuclear Overhauser effect NMR spectra assignment of a non-self-complementary dodecamer duplex

    International Nuclear Information System (INIS)

    Brush, C.K.; Stone, M.P.; Harris, T.M.

    1988-01-01

    Oligodeoxynucleotides are reversibly deuteriated at the purine C8 and cytosine C5 positions with deuterioammonium bisulfite at pD 7.8. The exchange reaction is complete after 48 h at 65 0 C. When an oligomer deuteriated under these conditions is analyzed by 1 H nuclear magnetic resonance (NMR) spectroscopy, the purine H8 and cytosine H5 proton signals are selectively removed from the spectrum. A non-self-complementary oligodeoxynucleotide that has been deuteriated in this manner may be annealed with its complement and the resulting heteroduplex analyzed by two-dimensional nuclear Overhauser enhancement (NOESY) spectroscopy. The intense cytosine H5-H6 cross-peaks are also removed from the spectrum of the deuteriated strand, which further simplifies interpretation since these strong cross-peaks often interfere with less intense NOE cross-peaks arising from dipolar coupling between purine H8 or pyrimidine H6 and deoxyribose anomeric protons. The resulting spectral simplification allows unambiguous assignments to be made on NOEs that otherwise may be difficult to distinguish. The deuteriation procedure is demonstrated with the sequence d(CGTTATAATGCG)-d(CGCATTATAACG), which has previously been assigned by traditional NOESY methods. Although the assignment of this dodecadeoxynucleotide may be completed without deuteriation, several NOEs must be assigned indirectly because of degeneracies in the chemical shift of the purine H8 protons. This methodology should have wide applicability to NMR spectral interpretation of oligodeoxynucleotides, particularly to oligonucleotides of 12 bases or longer

  12. Natural abundance 15N NMR assignments delineate structural differences between intact and reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III.

    Science.gov (United States)

    Krishnamoorthi, R; Nemmers, S; Tobias, B

    1992-06-15

    15N NMR assignments were made to the backbone amide nitrogen atoms at natural isotopic abundance of intact and reactive-site (Arg5-Ile6) hydrolyzed Cucurbita maxima trypsin inhibitor III (CMTI-III and CMTI-III*, respectively) by means of 2D proton-detected heteronuclear single bond chemical shift correlation (HSBC) spectroscopy, utilizing the previously made sequence-specific 1H NMR assignments (Krishnamoorthi et al. (1992) Biochemistry 31, 898-904). Comparison of the 15N chemical shifts of the two forms of the inhibitor molecule revealed significant changes not only for residues located near the reactive-site region, but also for those distantly located. Residues Cys3, Arg5, Leu7, Met8, Cys10, Cys16, Glu19, His25, Tyr27, Cys28 and Gly29 showed significant chemical shift changes ranging from 0.3 to 6.1 ppm, thus indicating structural perturbations that were transmitted throughout the molecule. These findings confirm the earlier conclusions based on 1H NMR investigations.

  13. Assignments and structure determination of the catalytic domain of human fibroblast collagenase using 3D double and triple resonance NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    McCoy, Mark A.; Dellwo, Martin J.; Schneider, Diane M.; Banks, Tracey M.; Falvo, Joseph [Sterling Winthrop Pharmaceuticals Research Division (United States); Vavra, Karen J.; Mathiowetz, Alan M. [Eastman Kodak Company (United States); Qoronfleh, M. Walid; Ciccarelli, Richard; Cook, Ewell R. [Sterling Winthrop Pharmaceuticals Research Division (United States); Pulvino, Tricia A. [Eastman Kodak Company (United States); Wahl, Robert C.; Wang Hsin [Sterling Winthrop Pharmaceuticals Research Division (United States)

    1997-01-15

    We report here the backbone 1HN, 15N, 13C{alpha}, 13CO, and 1H{alpha} NMR assignments for the catalytic domain of human fibroblast collagenase (HFC). Three independent assignment pathways (matching 1H, 13C{alpha}, and 13CO resonances) were used to establish sequential connections. The connections using 13C{alpha} resonances were obtained from HNCOCA and HNCA experiments; 13CO connections were obtained from HNCO and HNCACO experiments. The sequential proton assignment pathway was established from a 3D(1H/15N) NOESY-HSQC experiment. Amino acid typing was accomplished using 13C and 15N chemical shifts, specific labeling of 15N-Leu, and spin pattern recognition from DQF-COSY. The secondary structure was determined by analyzing the 3D (1H/15N) NOESY-HSQC. A preliminary NMR structure calculation of HFC was found to be in agreement with recent X-ray structures of human fibroblast collagenase and human neutrophil collagenase as well as similar to recent NMR structures of a highly homologous protein, stromelysin. All three helices were located; a five-stranded {beta}-sheet (four parallel strands, one antiparallel strand) was also determined. {beta}-Sheet regions were identified by cross-strand d{alpha}N and dNN connections and by strong intraresidue d{alpha}N correlations, and were corroborated by observing slow amide proton exchange. Chemical shift changes in a selectively 15N-labeled sample suggest that substantial structural changes occur in the active site cleft on the binding of an inhibitor.

  14. Assignments and structure determination of the catalytic domain of human fibroblast collagenase using 3D double and triple resonance NMR spectroscopy

    International Nuclear Information System (INIS)

    McCoy, Mark A.; Dellwo, Martin J.; Schneider, Diane M.; Banks, Tracey M.; Falvo, Joseph; Vavra, Karen J.; Mathiowetz, Alan M.; Qoronfleh, M. Walid; Ciccarelli, Richard; Cook, Ewell R.; Pulvino, Tricia A.; Wahl, Robert C.; Wang Hsin

    1997-01-01

    We report here the backbone 1HN, 15N, 13Cα, 13CO, and 1Hα NMR assignments for the catalytic domain of human fibroblast collagenase (HFC). Three independent assignment pathways (matching 1H, 13Cα, and 13CO resonances) were used to establish sequential connections. The connections using 13Cα resonances were obtained from HNCOCA and HNCA experiments; 13CO connections were obtained from HNCO and HNCACO experiments. The sequential proton assignment pathway was established from a 3D(1H/15N) NOESY-HSQC experiment. Amino acid typing was accomplished using 13C and 15N chemical shifts, specific labeling of 15N-Leu, and spin pattern recognition from DQF-COSY. The secondary structure was determined by analyzing the 3D (1H/15N) NOESY-HSQC. A preliminary NMR structure calculation of HFC was found to be in agreement with recent X-ray structures of human fibroblast collagenase and human neutrophil collagenase as well as similar to recent NMR structures of a highly homologous protein, stromelysin. All three helices were located; a five-stranded β-sheet (four parallel strands, one antiparallel strand) was also determined. β-Sheet regions were identified by cross-strand dαN and dNN connections and by strong intraresidue dαN correlations, and were corroborated by observing slow amide proton exchange. Chemical shift changes in a selectively 15N-labeled sample suggest that substantial structural changes occur in the active site cleft on the binding of an inhibitor

  15. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1992-01-28

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

  17. Spectral analysis, vibrational assignments, NBO analysis, NMR, UV-Vis, hyperpolarizability analysis of 2-aminofluorene by density functional theory.

    Science.gov (United States)

    Jone Pradeepa, S; Sundaraganesan, N

    2014-05-05

    In this present investigation, the collective experimental and theoretical study on molecular structure, vibrational analysis and NBO analysis has been reported for 2-aminofluorene. FT-IR spectrum was recorded in the range 4000-400 cm(-1). FT-Raman spectrum was recorded in the range 4000-50 cm(-1). The molecular geometry, vibrational spectra, and natural bond orbital analysis (NBO) were calculated for 2-aminofluorene using Density Functional Theory (DFT) based on B3LYP/6-31G(d,p) model chemistry. (13)C and (1)H NMR chemical shifts of 2-aminofluorene were calculated using GIAO method. The computed vibrational and NMR spectra were compared with the experimental results. The total energy distribution (TED) was derived to deepen the understanding of different modes of vibrations contributed by respective wavenumber. The experimental UV-Vis spectra was recorded in the region of 400-200 nm and correlated with simulated spectra by suitably solvated B3LYP/6-31G(d,p) model. The HOMO-LUMO energies were measured with time dependent DFT approach. The nonlinearity of the title compound was confirmed by hyperpolarizabilty examination. Using theoretical calculation Molecular Electrostatic Potential (MEP) was investigated. Copyright © 2014 Elsevier B.V. All rights reserved.

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

    Energy Technology Data Exchange (ETDEWEB)

    Mote, Kaustubh R. [University of Minnesota, Department of Chemistry (United States); Gopinath, T. [University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics (United States); Traaseth, Nathaniel J. [New York University, Chemistry Department (United States); Kitchen, Jason; Gor' kov, Peter L.; Brey, William W. [National High Magnetic Field Laboratory (United States); Veglia, Gianluigi, E-mail: vegli001@umn.edu [University of Minnesota, Department of Chemistry (United States)

    2011-11-15

    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 {sup 1}H-{sup 15}N dipolar couplings (DC) and {sup 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 ([{sup 1}H,{sup 15}N]-SE-PISEMA-PDSD). The incorporation of 2D {sup 15}N/{sup 15}N spin diffusion experiments into this new 3D experiment leads to the complete and unambiguous assignment of the {sup 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.

  19. NMR assignments for the amino-terminal residues of trp repressor and their role in DNA binding

    International Nuclear Information System (INIS)

    Arrowsmith, C.H.; Carey, J.; Treat-Clemons, L.; Jardetzky, O.

    1989-01-01

    The trp repressor of Escherichia coli specifically binds to operator DNAs in three operons involved in tryptophan metabolism. The NMR spectra of repressor and a chymotryptic fragment lacking the six amino-terminal residues are compared. Two-dimensional J-correlated spectra of the two forms of the protein are superimposable except for cross-peaks that are associated with the N-terminal region. The chemical shifts and relaxation behavior of the N-terminal resonances suggest mobile arms. Spin-echo experiments on a ternary complex of repressor with L-tryptophan and operator DNA indicate that the termini are also disordered in the complex, although removal of the arms reduces the DNA binding energy. Relaxation measurements on the armless protein show increased mobility for several residues, probably due to helix fraying in the newly exposed N-terminal region. DNA binding by the armless protein does not reduce the mobility of these residues. Thus, it appears that the arms serve to stabilize the N-terminal helix but that this structural role does not explain their contribution to the DNA binding energy. These results suggest that the promiscuous DNA binding by the arms seen in the X-ray crystal structure is found in solution as well

  20. NMR resonance assignments for the N-terminal domain of the δ subunit of the E. coli γ clamp loader complex.

    Science.gov (United States)

    Alyami, Esmael M; Rizzo, Alessandro A; Beuning, Penny J; Korzhnev, Dmitry M

    2017-10-01

    The β-clamp protein and the γ clamp loader complex are essential components of bacterial DNA replication machinery. The β-clamp is a ring-shaped homodimer that encircles DNA and increases the efficiency of replication by providing a binding platform for DNA polymerases and other replication-related proteins. The β-clamp is loaded onto DNA by the five-subunit γ clamp loader complex in a multi-step ATP-dependent process. The initial steps of this process involve the cooperative binding of the β-clamp by the five subunits of ATP-bound clamp loader, which induces or traps an open conformation of the clamp. Remarkably, the δ subunit of the E. coli clamp loader, or even its 140 residue N-terminal domain (called mini-δ), alone can shift conformational equilibrium of the β-clamp towards the open state. Here we report nearly complete backbone and side-chain 1 H, 13 C and 15 N NMR resonance assignments of mini-δ that will facilitate NMR studies of the mechanisms of β-clamp opening and its loading on DNA by the clamp loader.

  1. 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

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

    Science.gov (United States)

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

    1992-01-28

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

  3. Assignment of the absolute configuration of hepatoprotective highly oxygenated triterpenoids using X-ray, ECD, NMR J-based configurational analysis and HSQC overlay experiments.

    Science.gov (United States)

    Wang, Xiaojuan; Liu, Jiabao; Pandey, Pankaj; Chen, Jiabao; Fronczek, Frank R; Parnham, Stuart; Qi, Xinzhu; Doerksen, Robert J; Ferreira, Daneel; Sun, Hua; Li, Shuai; Hamann, Mark T

    2017-12-01

    The plants of the genus Kadsura are widely distributed in China, South Korea, and Japan. Their roots and stems are traditionally used to treat blood diseases and pain. The main bioactive constituents of Kadsura longipedunculata comprise highly oxygenated triterpenoids. Schiartane-type nortriterpenoids showed anti-HIV, anti-HBV, and cytotoxic bioactivities. For such compounds, the absolute configuration influences the bioactivities, and hence its unambiguous determination is essential. In this work, the absolute configurations of three highly oxygenated schiartane-type nortriterpenoids were unequivocally assigned using X-ray, ECD, and J-based configuration analysis and HSQC overlay data. The ethanol extract of Kadsura longipedunculata Finet et Gagnep was purified by column chromatography using silica, Sephadex LH-20, and ODS as substrates. To help assign the absolute configuration of schiartane-type nortriterpenoids, X-ray diffraction analysis, ECD experiment compared to ab initio computed data, DP4+ analysis, HSQC overlay, NOESY, and J-based configuration analysis were carried out. Hetero- and homo-nuclear coupling constants were extracted from HETLOC experiments. Three new highly oxygenated triterpenoids, micrandilactone I (1), micrandilactone J (2), and 22,23-di-epi-micrandilactone J (3) were isolated. Their 2D structures were solved using NMR and HRESIMS data and their absolute configurations were elucidated using X-ray diffraction analysis, ECD experimental results compared to ab initio computed spectra, HSQC overlay, DP4+, NOESY, and J-based configuration analysis. Micrandilactone I (1) and 22,23-di-epi-micrandilactone J (3) showed moderate hepatoprotective activity against APAP-induced toxicity in HepG2 cells with cell survival rates of 53.0 and 50.2%, respectively, at 10μM (bicyclol, 49.0%), while micrandilactone J (2) was inactive. This is the first comprehensive stereochemical assignment of a non-crystalline schiartane-type nortriterpenoid like 3. This

  4. ¹H, ¹³C and ¹⁵N NMR assignments of the Escherichia coli Orf135 protein.

    Science.gov (United States)

    Kawasaki, Kumiko; Yoneyama, Momoko; Murata-Kamiya, Naoko; Harashima, Hideyoshi; Kojima, Chojiro; Ito, Yutaka; Kamiya, Hiroyuki; Mishima, Masaki

    2012-04-01

    Escherichia coli Orf135 protein is thought to be an enzyme that efficiently hydrolyzes oxidatively damaged nucleotides such as 2-hydroxy-dATP, 8-hydroxy-dGTP and 5-hydroxy-CTP, in addition to 5-methyl-dCTP, dCTP and CTP, thus preventing mutations in cells caused by unfavorable base pairing. Nucleotide pool sanitization by Orf135 is important since organisms are continually subjected to potential damage by reactive oxygen species produced during respiration. It is known that the frequency of spontaneous and H(2)O(2)-induced mutations is two to threefold higher in the orf135(-) strain compared with the wild-type. Orf135 is a member of the Nudix family of proteins which hydrolyze nucleoside diphosphate derivatives. Nudix hydrolases are characterized by the presence of a conserved motif, although they recognize various substrates and possess a variety of substrate binding pockets. We are interested in delineating the mechanism by which Orf135 recognizes oxidatively damaged nucleotides. To this end, we are investigating the tertiary structure of Orf135 and its interaction with substrate using NMR. Herein, we report on the (1)H, (13)C and (15)N resonance assignments of Orf135, which should contribute towards a structural understanding of Orf135 and its interaction with substrate.

  5. 1H, 13C and 15N NMR Assignments of the C1A and C1B Subdomains of PKC-delta

    Science.gov (United States)

    Ziemba, Brian P.; Booth, Jamie C.; Jones, David N. M.

    2015-01-01

    The Protein Kinase C family of enzymes is a group of serine/threonine kinases that play central roles in cell-cycle regulation, development and cancer. A key step in the activation of PKC is translocation to membranes and binding of membrane-associated activators including diacylglycerol (DAG). Interaction of novel and conventional isotypes of PKC with DAG and phorbol esters occurs through the two C1 regulatory domains (C1A and C1B), which exhibit distinct ligand binding selectivity that likely controls enzyme activation by different co-activators. PKC has also been implicated in physiological responses to alcohol consumption and it has been proposed that PKCα [1, 2], PKCε [3] and PKCδ [4, 5] contain specific alcohol-binding sites in their C1 domains. We are interested in understanding how ethanol affects signal transduction processes through its affects on the structure and function of the C1 domains of PKC. Here we present the 1H, 15N and 13C NMR chemical shift assignments for the Rattus norvegicus PKCδ C1A and C1B proteins. PMID:21132404

  6. Study of the BPP7a peptide and its {beta}-cyclodextrin complex: physicochemical characterization and complete sequence specific NMR assignments

    Energy Technology Data Exchange (ETDEWEB)

    Lula, Ivana; Sousa, Frederico B. de; Denadai, Angelo M.L.; Sinisterra, Ruben D.; Ianzer, Danielle; Santos, Robson A.S., E-mail: sinisterra@ufmg.br [Departamento de Quimica, Instituto de Ciencias Exatas and Departamento de Fisiologia e Biofisica, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, (Brazil); Camargo, Antonio C.M. de [Center for Applied Toxinology (CAT-CEPID), Instituto Butantan, Sao Paulo, SP (Brazil)

    2011-09-15

    The BPP7a heptapeptide, p-Glu1Asp2Gly3Pro4Ile5Pro6Pro7, forms an association complex with {beta}-cyclodextrin in a 1:1 molar ratio. The peptide and its complex were characterized by circular dichroism (CD) and isothermal titration calorimetry (ITC), which showed a very weak interaction between the {beta}-cyclodextrin and the peptide. Assignments of all hydrogen resonances of the peptide alone and as a complex were made using {sup 1}H nuclear magnetic resonance (NMR) experiments at 400 and 600 MHz. High resolution diffusion ordered spectroscopy (HR-DOSY) experiments were carried out to establish the self-aggregation state of BPP7a. It was also shown that the {beta}-cyclodextrin breaks the molecular clusters leading to complex formation. In addition, the anti-hypertensive activity of the BPP7a/{beta}-cyclodextrin complex was evaluated in spontaneous hypertensive rats (SHR), showing increased activity compared to that of pure BPP7a. (author)

  7. 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.

    Science.gov (United States)

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

    2012-08-01

    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.

  8. Multinuclear NMR resonance assignments and the secondary structure of Escherichia coli thioesterase/protease I: A member of a new subclass of lipolytic enzymes

    International Nuclear Information System (INIS)

    Lin Tahsien; Chen Chinpan; Huang Rongfong; Lee Yalin; Shaw Jeifu; Huang Taihuang

    1998-01-01

    Escherichia coli thioesterase/protease I is a 183 amino acid protein with a molecular mass of 20500. This protein belongs to a new subclass of lipolytic enzymes of the serine protease superfamily, but with a new GDSLS consensus motif, of which no structure has yet been determined. The protein forms a tetramer at pH values above 6.5 and exists as a monomer at lower pH values. Both monomer and tetramer are catalytically active. From analysis of a set of heteronuclear multidimensional NMR spectra with uniform and specific amino acid labeled protein samples, we have obtained near-complete resonance assignments of the backbone 1 H, 13 C and 15 N nuclei (BMRB databank accession number 4060). The secondary structure of E. coli thioesterase/protease I was further deduced from the consensus chemical shift indices, backbone short- and medium-range NOEs, and amide proton exchange rates. The protein was found to consist of four β-strands and seven α-helices, arranged in alternate order. The four β-strands were shown to form a parallel β-sheet. The topological arrangement of the β-strands of -1x, +2x, +1x appears to resemble that of the core region of the αβ hydrolase superfamily, typically found in common lipases and esterases. However, substantial differences, such as the number of β-strands and the location of the catalytic triad residues, make it difficult to give a definitive classification of the structure of E. coli thioesterase/protease I at present

  9. GFT projection NMR based resonance assignment of membrane proteins: application to subunit c of E. coli F{sub 1}F{sub 0} ATP synthase in LPPG micelles

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Qi [State University of New York at Buffalo, Department of Chemistry (United States); Atreya, Hanudatta S. [NMR Research Centre, Indian Institute of Science (India); Kamen, Douglas E.; Girvin, Mark E. [Albert Einstein College of Medicine, Biochemistry Department (United States); Szyperski, Thomas [State University of New York at Buffalo, Department of Chemistry (United States)], E-mail: szypersk@chem.buffalo.edu

    2008-03-15

    G-matrix FT projection NMR spectroscopy was employed for resonance assignment of the 79-residue subunit c of the Escherichia coli F{sub 1}F{sub 0} ATP synthase embedded in micelles formed by lyso palmitoyl phosphatidyl glycerol (LPPG). Five GFT NMR experiments, that is, (3,2)D HNNCO, L-(4,3)D HNNC{sup {alpha}}{sup {beta}}C{sup {alpha}}, L-(4,3)D HNN(CO)C{sup {alpha}}{sup {beta}}C{sup {alpha}}, (4,2)D HACA(CO)NHN and (4,3)D HCCH, were acquired along with simultaneous 3D {sup 15}N, {sup 13}C{sup aliphatic}, {sup 13}C{sup aromatic}-resolved [{sup 1}H,{sup 1}H]-NOESY with a total measurement time of {approx}43 h. Data analysis resulted in sequence specific assignments for all routinely measured backbone and {sup 13}C{sup {beta}} shifts, and for 97% of the side chain shifts. Moreover, the use of two G{sup 2}FT NMR experiments, that is, (5,3)D HN{l_brace}N,CO{r_brace}{l_brace}C{sup {alpha}}{sup {beta}}C{sup {alpha}}{r_brace} and (5,3)D {l_brace}C{sup {alpha}}{sup {beta}}C{sup {alpha}}{r_brace}{l_brace}CON{r_brace}HN, was explored to break the very high chemical shift degeneracy typically encountered for membrane proteins. It is shown that the 4D and 5D spectral information obtained rapidly from GFT and G{sup 2}FT NMR experiments enables one to efficiently obtain (nearly) complete resonance assignments of membrane proteins.

  10. The covariance of the differences between experimental and theoretical chemical shifts as an aid for assigning two-dimensional heteronuclear correlation solid-state NMR spectra

    Czech Academy of Sciences Publication Activity Database

    Czernek, Jiří; Brus, Jiří

    2014-01-01

    Roč. 608, 21 July (2014), s. 334-339 ISSN 0009-2614 R&D Projects: GA ČR(CZ) GA14-03636S Institutional support: RVO:61389013 Keywords : NMR * DFT * covariance Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.897, year: 2014

  11. Partial 1H NMR assignments of the Escherichia coli dihydrofolate reductase complex with folate: Evidence for a unique conformation of bound folate

    International Nuclear Information System (INIS)

    Falzone, C.J.; Benkovic, S.J.; Wright, P.E.

    1990-01-01

    Sequence-specific 1 H assignments have been made for over 25% of the amino acid side chains of Escherichia coli dihydrofolate reductase complexed with folate by using a variety of two-dimensional techniques. Proton resonances were assigned by using a combination of site-directed mutagenesis and a knowledge of the X-ray crystal structure. Unique sets of NOE connectivities present in hydrophobic pockets were matched with the X-ray structure and used to assign many of the residues. Other residues, particularly those near or in the active site, were assigned by site-directed mutagenesis. The ability to assign unambiguosly the proton resonances of these catalytically important residues allowed for extensive networks of NOE connectivities to follow from these assignments. As a consequence of these assignments, the orientation of the pterin ring of folate could be determined, and its conformation is similar to that of the productive dihydrofolate complex. Under these experimental conditions, only one bound form of the pterin ring could be detected

  12. Selective 'unlabeling' of amino acids in fractionally 13C labeled proteins: An approach for stereospecific NMR assignments of CH3 groups in Val and Leu residues

    Energy Technology Data Exchange (ETDEWEB)

    Atreya, H.S.; Chary, K.V.R. [Tata Institute of Fundamental Research, Department of Chemical Sciences (India)

    2001-03-15

    A novel methodology for stereospecific NMR assignments of methyl (CH{sub 3}) groups of Val and Leu residues in fractionally {sup 13}C-labeled proteins is presented. The approach is based on selective 'unlabeling' of specific amino acids in proteins while fractionally {sup 13}C-labeling the rest. A 2D [{sup 13}C-{sup 1}H] HSQC spectrum recorded on such a sample is devoid of peaks belonging to the 'unlabeled' amino acid residues. Such spectral simplification aids in unambiguous stereospecific assignment of diastereotopic CH{sub 3} groups in Val and Leu residues in large proteins. This methodology has been demonstrated on a 15 kDa calcium binding protein from Entamoeba histolytica (Eh-CaBP)

  13. N-15-labelled pyrazines of triterpenic acids

    Czech Academy of Sciences Publication Activity Database

    Vlk, M.; Mičolová, P.; Urban, M.; Kvasnica, Miroslav; Šaman, David; Šarek, J.

    2016-01-01

    Roč. 308, č. 2 (2016), s. 733-739 ISSN 0236-5731 R&D Projects: GA ČR GJ15-08202Y; GA MŠk(CZ) LO1304; GA MŠk(CZ) LO1204 Grant - others:GA MŠk(CZ) LK21310; GA TA ČR(CZ) TA03010027; CTU(CZ) SGS15/094/OHK4/1T/14 Institutional support: RVO:61389030 ; RVO:61388963 Keywords : N-15 * Triterpenic acid * Isotopic labelling Subject RIV: CC - Organic Chemistry Impact factor: 1.282, year: 2016

  14. The conformational stability, solvation and the assignments of the experimental infrared, Raman, 1H and 13C NMR spectra of the local anesthetic drug lidocaine

    Science.gov (United States)

    Badawi, Hassan M.; Förner, Wolfgang; Ali, Shaikh A.

    2015-05-01

    The structure, vibrational and 1H and 13C NMR spectra of the local anesthetic drug lidocaine were investigated by the B3LYP/6-311G∗∗ calculations. The molecule was predicted to have the non-planar cis (NCCN ∼ 0°) structures being about 2-6 kcal/mol lower in energy than the corresponding trans (NCCN ∼ 180°) forms. The calculated NCCN (9.6°) and CNCC (-132.2°) torsional angles were in a good qualitative agreement with the reported X-ray angles (3.1 and 13.0°, -102.67 and -77.9°, respectively, for H-bonded dimers). The Gibbs energy of solution of lidocaine in formamide, water, dimethylsulfoxide, acetonitrile, methanol, ethanol and chloroform solutions was estimated at the B3LYP level. The predicted affinity of lidocaine toward the alcohols, acetonitrile and chloroform solutions was in excellent agreement with the reported experimental solubility of the drug in organic solvents. The analysis of the observed vibrational spectra is consistent with the presence of lidocaine in only one conformation at room temperature. The 1H and 13C NMR spectra of lidocaine were interpreted by experimental and DFT calculated chemical shifts of the drug. The RMSD between experimental and theoretical 1H and 13C chemical shifts for lidocaine is 0.47 and 8.26 ppm, respectively.

  15. Backbone 1H, 13C, and 15N NMR assignments for the Cyanothece 51142 protein cce_0567: a protein associated with nitrogen fixation in the DUF683 family.

    Science.gov (United States)

    Buchko, Garry W; Sofia, Heidi J

    2008-06-01

    Cyanothece 51142 contains a 78-residue protein, cce_0567, that falls into the DUF683 family of proteins associated with nitrogen fixation. Here we report the assignment of most of the main chain and 13C(beta) side chain resonances of the approximately 40 kDa homo-tetramer.

  16. Characterization of Polyphenols from Plant Materials through Their Silylation and 29Si NMR Spectroscopy - Line Assignment through 29Si, 13C Spin-Spin Couplings

    Czech Academy of Sciences Publication Activity Database

    Schraml, Jan; Blechta, Vratislav; Sýkora, Jan; Soukupová, Ludmila; Cuřínová, Petra; Proněk, D.; Lachman, J.

    2005-01-01

    Roč. 43, č. 10 (2005), s. 829-834 ISSN 0749-1581 Institutional research plan: CEZ:AV0Z40720504 Keywords : line assignment * long-range couplings * polyphenols Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.553, year: 2005

  17. Further exploration of the conformational space of α-synuclein fibrils: solid-state NMR assignment of a high-pH polymorph.

    Science.gov (United States)

    Verasdonck, Joeri; Bousset, Luc; Gath, Julia; Melki, Ronald; Böckmann, Anja; Meier, Beat H

    2016-04-01

    Polymorphism is a common and important phenomenon for protein fibrils which has been linked to the appearance of strains in prion and other neurodegenerative diseases. Parkinson disease is a frequently occurring neurodegenerative pathology, tightly associated with the formation of Lewy bodies. These deposits mainly consist of α-synuclein in fibrillar, β-sheet-rich form. α-synuclein is known to form numerous different polymorphs, which show distinct structural features. Here, we describe the chemical shift assignments, and derive the secondary structure, of a polymorph that was fibrillized at higher-than-physiological pH conditions. The fibrillar core contains residues 40-95, with both the C- and N-terminus not showing any ordered, rigid parts. The chemical shifts are similar to those recorded previously for an assigned polymorph that was fibrillized at neutral pH.

  18. 1H, 13C, 15N backbone NMR assignments of the Staphylococcus aureus small multidrug-resistance pump (Smr) in a functionally active conformation.

    Science.gov (United States)

    Poget, Sébastien F; Harris, Richard; Cahill, Sean M; Girvin, Mark E

    2010-10-01

    The plasmid-encoded small multidrug resistance pump from S. aureus transports a variety of quaternary ammonium and other hydrophobic compounds, enhancing the bacterial host's resistance to common hospital disinfectants. The protein folds as a homo-dimer of four transmembrane helices each, and appears to be fully functional only in lipid bilayers. Here we report the backbone resonance assignments and implied secondary structure for (2)H(13)C(15)N Smr reconstituted into lipid bicelles. Significant changes were observed between the chemical shifts of the protein in lipid bicelles compared to those in detergent micelles.

  19. NMR study of non-structural proteins-part III:1H,13C,15N backbone and side-chain resonance assignment of macro domain from Chikungunya virus (CHIKV).

    Science.gov (United States)

    Lykouras, Michail V; Tsika, Aikaterini C; Lichière, Julie; Papageorgiou, Nicolas; Coutard, Bruno; Bentrop, Detlef; Spyroulias, Georgios A

    2018-04-01

    Macro domains are conserved protein domains found in eukaryotic organisms, bacteria, and archaea as well as in certain viruses. They consist of 130-190 amino acids and can bind ADP-ribose. Although the exact role of these domains is not fully understood, the conserved binding affinity for ADP-ribose indicates that this ligand is important for the function of the domain. Such a macro domain is also present in the non-structural protein 3 (nsP3) of Chikungunya Alphavirus (CHIKV) and consists of 160 amino acids. In this study we describe the high yield expression of the macro domain from CHIKV and its preliminary structural analysis via solution NMR spectroscopy. The macro domain seems to be folded in solution and an almost complete backbone assignment was achieved. In addition, the α/β/α sandwich topology with 4 α-helices and 6 β-strands was predicted by TALOS+.

  20. 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.

  1. Backbone 1H, 13C, 15N NMR assignments of the unliganded and substrate ternary complex forms of mevalonate diphosphate decarboxylase from Streptococcus pneumoniae.

    Science.gov (United States)

    Reuther, Guido; Harris, Richard; Girvin, Mark; Leyh, Thomas S

    2011-04-01

    Mevalonate diphosphate decarboxylase (MDD) catalyzes the ATP-dependent decarboxylation of diphosphomevalonate (DPM) to produce isopentenyl diphosphate (IPP), the molecular "building block" for more than 25,000 distinct isoprenoids, including cholesterol, steroid hormones and terpenoids. Here, we present the first backbone assignment of Streptococcus pneumoniae MDD in the unliganded state and in a ternary complex with DPM and AMPPCP--a nucleotide analogue unable to transfer the γ-phosphoryl group. The secondary chemical shifts for the unliganded form are in good agreement with the crystal structure of Streptococcus pyogenes (~70% sequence identity). The addition of substrate and nucleotide to the enzyme results in chemical shift changes of cross peaks that correspond to residues in the binding pocket.

  2. Backbone NMR resonance assignments of the nucleotide binding domain of the ABC multidrug transporter LmrA from Lactococcus lactis in its ADP-bound state.

    Science.gov (United States)

    Hellmich, Ute A; Duchardt-Ferner, Elke; Glaubitz, Clemens; Wöhnert, Jens

    2012-04-01

    LmrA from Lactococcus lactis is a multidrug transporter and a member of the ATP binding cassette (ABC) transporter family. ABC transporters consist of a transmembrane domain (TMD) and a nucleotide binding domain (NBD). The NBD contains the highly conserved signature motifs of this transporter superfamily. In the case of LmrA, the TMD and the NBD are expressed as a single polypeptide. LmrA catalyzes the extrusion of hydrophobic compounds including antibiotics from the cell membrane at the expense of ATP hydrolysis. ATP binds to the NBD, where binding and hydrolysis induce conformational changes that lead to the extrusion of the substrate via the TMD. Here, we report the (1)H, (13)C and (15)N backbone chemical shift assignments of the isolated 263 amino acid containing NBD of LmrA in its ADP bound state.

  3. Backbone ¹H, ¹³C, ¹⁵N NMR assignments of yeast OMP synthase in unliganded form and in complex with orotidine 5'-monophosphate.

    Science.gov (United States)

    Hansen, Michael Riis; Harris, Richard; Barr, Eric W; Cheng, Hong; Girvin, Mark E; Grubmeyer, Charles

    2014-04-01

    The type I phosphoribosyltransferase OMP synthase (EC 2.4.2.10) is involved in de novo synthesis of pyrimidine nucleotides forming the UMP precursor orotidine 5'-monophosphate (OMP). The homodimeric enzyme has a Rossman α/β core topped by a base-enclosing "hood" domain and a flexible domain-swapped catalytic loop. High-resolution X-ray structures of the homologous Salmonella typhimurium and yeast enzymes show that a general compacting of the core as well as movement of the hood and a major disorder-to-order transition of the loop occur upon binding of ligands MgPRPP and orotate. Here we present backbone NMR assignments for the unliganded yeast enzyme (49 kDa) and its complex with product OMP. We were able to assign 212-213 of the 225 non-proline backbone (15)N and amide proton resonances. Significant difference in chemical shifts of the amide cross peaks occur in regions of the structure that undergo movement upon ligand occupancy in the S. typhimurium enzyme.

  4. 1H and 15N NMR assignment and solution structure of the SH3 domain of spectrin: Comparison of unrefined and refined structure sets with the crystal structure

    International Nuclear Information System (INIS)

    Blanco, Francisco J.; Ortiz, Angel R.; Serrano, Luis

    1997-01-01

    The assignment of the 1 H and 15 Nnuclear magnetic resonance spectra of the Src-homology region 3 domain of chicken brain α-spectrin has been obtained. A set of solution structures has been determined from distance and dihedral angle restraints,which provide a reasonable representation of the protein structure in solution, as evaluated by a principal component analysis of the global pairwise root-mean-square deviation (rmsd) in a large set of structures consisting of the refined and unrefined solution structures and the crystal structure. The solution structure is well defined, with a lower degree of convergence between the structures in the loop regions than in the secondary structure elements. The average pairwise rmsd between the 15 refined solution structures is 0.71 ± 0.13 A for the backbone atoms and 1.43 ± 0.14 A for all heavy atoms. The solution structure is basically the same as the crystal structure. The average rmsd between the 15 refined solution structures and the crystal structure is 0.76 A for the backbone atoms and 1.45 ± 0.09 A for all heavy atoms. There are, however, small differences probably caused by intermolecular contacts in the crystal structure

  5. 1H, 13C, 15N backbone and side chain NMR resonance assignments of the N-terminal NEAr Iron transporter domain 1 (NEAT 1) of the hemoglobin receptor IsdB of Staphylococcus aureus

    Science.gov (United States)

    Fonner, Brittany A.; Tripet, Brian P.; Lui, Mengyao; Zhu, Hui; Lei, Benfang; Copié, Valérie

    2013-01-01

    Staphylococcus aureus is an opportunistic pathogen that causes skin and severe infections in mammals. Critical to S. aureus growth is its ability to scavenge iron from host cells. To this effect, S. aureus has evolved a sophisticated pathway to acquire heme from hemoglobin (Hb) as a preferred iron source. The pathway is comprised of nine iron-regulated surface determinant (Isd) proteins involved in heme capture, transport, and degradation. A key protein of the heme acquisition pathway is the surface-anchored hemoglobin receptor protein IsdB, which is comprised of two NEAr transporter (NEAT) domains that act in concert to bind Hb and extract heme for subsequent transfer to downstream acquisition pathway proteins. Despite significant advances in the structural knowledge of other Isd proteins, the structural mechanisms and molecular basis of the IsdB-mediated heme acquisition process are not well understood. In order to provide more insights into the mode of function of IsdB, we have initiated NMR structural studies of the first NEAT domain of IsdB (IsdBN1). Herein, we report the near complete 1H, 13C and 15N resonance assignments of backbone and side chain atoms, and the secondary structural topology of the 148-residue IsdB NEAT 1 domain. The NMR results are consistent with the presence of eight β-strands and one α-helix characteristic of an immunoglobulin-like fold observed in other NEAT domain family proteins. This work provides a solid framework to obtain atomic-level insights toward understanding how IsdB mediates IsdB-Hb protein-protein interactions critical for heme capture and transfer. PMID:23686822

  6. N-[4-(3-Methyl-3-phenyl-cyclobutyl)-thiazol-2-yl]- N'-pyridin-2-ylmethylene-chloro-acetic acid hydrazide: Synthesis and configurational assignment based on X-ray, 1H, and 13C NMR and theoretical calculations

    Science.gov (United States)

    Demir, Sibel; Dinçer, Muharrem; Çukurovali, Alaaddin; Yılmaz, Ibrahim

    2017-11-01

    In this study, quantum chemical calculations based on the density functional theory have been carried out to examine the effects of N-[4-(3-methyl-3-phenyl-cyclobutyl)-thiazol-2-yl]- N'-pyridin-2-ylmethylene- chloro-acetic acid hydrazide. The calculated values are compared with the experimental data available for these molecules as a mean of validation of our proposed chemistry model. Aided by normal coordinate analysis and potential energy distributions, a confident vibrational assignment of all fundamentals is proposed herein. Additional support is given by 1H and 13C NMR spectra recorded with the sample dissolved in CDCl3 and by predicted chemical shifts at the B3LYP/6-31G( d)/6-311G+( d) levels obtained using the gauge-invariant atomic orbital method. The calculated HOMO and LUMO energies also confirm that the charge transfer occurs within the molecule. Thiazole-based compounds are potential storehouse for exploiting CH···O and CH···N hydrogen bonding interactions for molecular self-assembly.

  7. Novel DNA packaging recognition in the unusual bacteriophage N15

    International Nuclear Information System (INIS)

    Feiss, Michael; Geyer, Henriette; Klingberg, Franco; Moreno, Norma; Forystek, Amanda; Maluf, Nasib Karl; Sippy, Jean

    2015-01-01

    Phage lambda's cosB packaging recognition site is tripartite, consisting of 3 TerS binding sites, called R sequences. TerS binding to the critical R3 site positions the TerL endonuclease for nicking cosN to generate cohesive ends. The N15 cos (cos N15 ) is closely related to cos λ , but whereas the cosB N15 subsite has R3, it lacks the R2 and R1 sites and the IHF binding site of cosB λ . A bioinformatic study of N15-like phages indicates that cosB N15 also has an accessory, remote rR2 site, which is proposed to increase packaging efficiency, like R2 and R1 of lambda. N15 plus five prophages all have the rR2 sequence, which is located in the TerS-encoding 1 gene, approximately 200 bp distal to R3. An additional set of four highly related prophages, exemplified by Monarch, has R3 sequence, but also has R2 and R1 sequences characteristic of cosB–λ. The DNA binding domain of TerS-N15 is a dimer. - Highlights: • There are two classes of DNA packaging signals in N15-related phages. • Phage N15's TerS binding site: a critical site and a possible remote accessory site. • Viral DNA recognition signals by the λ-like bacteriophages: the odd case of N15

  8. Novel DNA packaging recognition in the unusual bacteriophage N15

    Energy Technology Data Exchange (ETDEWEB)

    Feiss, Michael [Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242 (United States); Geyer, Henriette, E-mail: henriettegeyer@gmail.com [Division of Viral Infections, Robert Koch Institute, Berlin (Germany); Division of Viral Infections, Robert Koch Institute, Berlin (Germany); Klingberg, Franco, E-mail: franco.klingberg@thermofisher.com [Flow Cytometry, Imaging & Microscopy, Thermo Fisher Scientific, Frankfurter Strasse 129B 64293 Darmstadt (Germany); Flow Cytometry, Imaging & Microscopy, Thermo Fisher Scientific, Frankfurter Strasse 129B 64293 Darmstadt (Germany); Moreno, Norma, E-mail: nmoreno@islander.tamucc.edu [Texas A& M University – Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, United States. (United States); Texas A& M University – Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, United States. (United States); Forystek, Amanda, E-mail: eamanda-forystek@uiowa.edu [Flow Cytometry, Imaging & Microscopy, Thermo Fisher Scientific, Frankfurter Strasse 129B 64293 Darmstadt (Germany); Room # 2911 JPP, Dept. of Psychiatry, The University of Iowa, 200 Hawkins Drive, Iowa City, Iowa, 52242 (United States); Maluf, Nasib Karl, E-mail: fKarl.Maluf@ap-lab.com [Flow Cytometry, Imaging & Microscopy, Thermo Fisher Scientific, Frankfurter Strasse 129B 64293 Darmstadt (Germany); Alliance Protein Laboratories, Inc. 6042 Cornerstone Court West, Suite ASan Diego, CA 92121, USA. (United States); Sippy, Jean [Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242 (United States)

    2015-08-15

    Phage lambda's cosB packaging recognition site is tripartite, consisting of 3 TerS binding sites, called R sequences. TerS binding to the critical R3 site positions the TerL endonuclease for nicking cosN to generate cohesive ends. The N15 cos (cos{sup N15}) is closely related to cos{sup λ}, but whereas the cosB{sup N15} subsite has R3, it lacks the R2 and R1 sites and the IHF binding site of cosB{sup λ}. A bioinformatic study of N15-like phages indicates that cosB{sup N15} also has an accessory, remote rR2 site, which is proposed to increase packaging efficiency, like R2 and R1 of lambda. N15 plus five prophages all have the rR2 sequence, which is located in the TerS-encoding 1 gene, approximately 200 bp distal to R3. An additional set of four highly related prophages, exemplified by Monarch, has R3 sequence, but also has R2 and R1 sequences characteristic of cosB–λ. The DNA binding domain of TerS-N15 is a dimer. - Highlights: • There are two classes of DNA packaging signals in N15-related phages. • Phage N15's TerS binding site: a critical site and a possible remote accessory site. • Viral DNA recognition signals by the λ-like bacteriophages: the odd case of N15.

  9. Development of Two-Dimensional NMR

    Indian Academy of Sciences (India)

    IAS Admin

    The development of Fourier transform NMR in the mid. 1960's, did parallel processing of the collection of NMR data, increased the signal/noise ratio by two orders of magnitude and made it possible to record the proton NMR spectra of small proteins which contain hundreds of resonances. The assignment of these ...

  10. NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment

    OpenAIRE

    Jang, Richard; Wang, Yan; Xue, Zhidong; Zhang, Yang

    2015-01-01

    NMR-I-TASSER, an adaption of the I-TASSER algorithm combining NMR data for protein structure determination, recently joined the second round of the CASD-NMR experiment. Unlike many molecular dynamics-based methods, NMR-I-TASSER takes a molecular replacement-like approach to the problem by first threading the target through the PDB to identify structural templates which are then used for iterative NOE assignments and fragment structure assembly refinements. The employment of multiple templates...

  11. Accredited Standards Committee N15 Developments And Future Directions

    International Nuclear Information System (INIS)

    Mathews, Caroline E.; May, Melanie; Preston, Lynne

    2009-01-01

    Accredited Standards Committee (ASC) N15, Methods of Nuclear Material Control, is sponsored by the Institute of Nuclear Materials Management (INMM) to develop standards for protection, control and accounting of special nuclear materials in all phases of the nuclear fuel cycle, including analytical procedures where necessary and special to this purpose, except that physical protection of special nuclear material within a nuclear power plant is not included. Voluntary consensus standards complement federal regulations and technical standards and fulfill an important role for the nuclear regulatory agencies. This paper describes the N15 standards development process, with INMM as the Standards Developing Organization (SDO) and the N15 Committee responsible for implementation. Key components of the N15 standards development process include ANSI accreditation; compliance with the ANSI Essential Requirements (ER), coordination with other SDOs, communication with stakeholders, maintenance of balance between interest categories, and ANSI periodic audits. Recent and future ASC N15 activities are discussed, with a particular focus on new directions in anticipation of renewed growth in nuclear power.

  12. Principal component analysis for verifying {sup 1}H NMR spectral assignments. The case of 3-aryl (1,2,4)-oxadiazole-5-carbohydrazide benzylidene; Aplicacao de analise de componentes principais para verificacao de atribuicoes de sinais nos espetros de RMN 1H. O caso dos 3-aril (1,2,4)-oxadiazol-5-carboidrazida benzilidenos

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Joao Bosco P. da; Malvestiti, Ivani; Hallwass, Fernando; Ramos, Mozart N. [Pernambuco Univ., Recife, PE (Brazil). Dept. de Quimica Fundamental]. E-mail: paraiso@ufpe.br; Leite, Lucia F.C. da Costa [Universidade Catolica de Pernambuco, Recife, PE (Brazil). Dept. de Quimica; Barreiro, Eliezer J. [Universidade Federal, Rio de Janeiro, RJ (Brazil). Faculdade de Farmacia

    2005-06-01

    The {sup 1}H NMR data set of a series of 3-aryl (1,2,4)-oxadiazole-5-carbohydrazide benzylidene derivatives synthesized in our group was analyzed using the chemometric technique of principal component analysis (PCA). Using the original 1H NMR data PCA allowed identifying some misassignments of the proton aromatic chemical shifts. As a consequence of this multivariate analysis, nuclear Overhauser difference experiments were performed to investigate the ambiguity of other assignments of the ortho and meta aromatic hydrogens for the compound with the bromine substituent. The effect of the 1,2,4-oxadiazole group as an electron acceptor, mainly for the hydrogens 12,13, has been highlighted. (author)

  13. Fundamentals of Protein NMR Spectroscopy

    CERN Document Server

    Rule, Gordon S

    2006-01-01

    NMR spectroscopy has proven to be a powerful technique to study the structure and dynamics of biological macromolecules. Fundamentals of Protein NMR Spectroscopy is a comprehensive textbook that guides the reader from a basic understanding of the phenomenological properties of magnetic resonance to the application and interpretation of modern multi-dimensional NMR experiments on 15N/13C-labeled proteins. Beginning with elementary quantum mechanics, a set of practical rules is presented and used to describe many commonly employed multi-dimensional, multi-nuclear NMR pulse sequences. A modular analysis of NMR pulse sequence building blocks also provides a basis for understanding and developing novel pulse programs. This text not only covers topics from chemical shift assignment to protein structure refinement, as well as the analysis of protein dynamics and chemical kinetics, but also provides a practical guide to many aspects of modern spectrometer hardware, sample preparation, experimental set-up, and data pr...

  14. 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.

  15. Final report on improved N15 analyser NOI-6e

    International Nuclear Information System (INIS)

    Meier, G.; Hollenthoner, S.

    1985-05-01

    This report gives a general view of the computerized NOI-6e nitrogen analyzer. The construction of the new prototype is described. The new version of the N15 analyzer together with the microcomputer program which has been developed improves the convenience of operation and also has high reliability. Many practical test measurements have been made. The most important result is the remarkable reduction of the standard deviation σsub(x): a standard deviation of less than 0.5% is achieved. We have not found such a low standard deviation in descriptions of similar analyzers which use emission spectroscopy

  16. Synthesis and NMR Elucidation of Novel Pentacycloundecane ...

    African Journals Online (AJOL)

    Herein we report the synthesis and NMR elucidation of five novel pentacycloundecane (PCU)-derived short peptides as potential HIV protease inhibitors. 1H and 13C spectral analysis show major overlapping of methine resonance of the PCU 'cage' thereby making it extremely difficult to assign the NMR signals. Attachment ...

  17. Flavonoids from Lonchocarpus araripensis (Leguminoseae): isolation, unequivocal assignment of NMR signals {sup 1}H and {sup 13}C and conformational analysis; Flavonoides de Lonchocarpus araripensis (Leguminoseae): isolamento, atribuicao inequivoca dos sinais de RMN {sup 1}H e {sup 13}C e analise conformacional

    Energy Technology Data Exchange (ETDEWEB)

    Lima, Almi F.; Ferreira, Daniele A.; Monte, Francisco Jose Q., E-mail: fmonte@dqoi.ufc.br [Universidade Federal do Ceara (UFC), Fortaleza, CE (Brazil). Centro de Ciencias. Departamento de Quimica Organica e Inorganica; Braz-Filho, Raimundo [Universidade Estadual do Norte Fluminense (UENF), Campo dos Goytacazes, RJ (Brazil). Centro de Ciencias Tecnologicas. Laboratorio de Ciencias Quimicas

    2014-07-01

    In a continuing investigation for potentially bioactive natural products, flavonoids were isolated from Lonchocarpus araripensis (Leguminoseae) and identified as 3-methoxy-6-O-prenyl-6'',6''-dimethylchromene-[7,8,2'',3'']-flavone (1), 3,6-dimethoxy-6'',6''-dimethylchromene-[7,8,2'',3'']-flavone (2) and 3,5,8-trimethoxy-[6,7,2{sup ,}3{sup ]}-furanoflavone (3). This is the first time compound 3 has been described. Compound 2 has been previously isolated from roots while this is the first time 1 is reported in this species. Complete NMR assignments are given for 1 ,2 and 3 together with the determination of conformation for 1. (author)

  18. Out-and-back {sup 13}C-{sup 13}C scalar transfers in protein resonance assignment by proton-detected solid-state NMR under ultra-fast MAS

    Energy Technology Data Exchange (ETDEWEB)

    Barbet-Massin, Emeline; Pell, Andrew J. [University of Lyon, CNRS/ENS Lyon/UCB Lyon 1, Centre de RMN a Tres Hauts Champs (France); Jaudzems, Kristaps [Latvian Institute of Organic Synthesis (Latvia); Franks, W. Trent; Retel, Joren S. [Leibniz-Institut fuer Molekulare Pharmakologie (Germany); Kotelovica, Svetlana; Akopjana, Inara; Tars, Kaspars [Biomedical Research and Study Center (Latvia); Emsley, Lyndon [University of Lyon, CNRS/ENS Lyon/UCB Lyon 1, Centre de RMN a Tres Hauts Champs (France); Oschkinat, Hartmut [Leibniz-Institut fuer Molekulare Pharmakologie (Germany); Lesage, Anne; Pintacuda, Guido, E-mail: guido.pintacuda@ens-lyon.fr [University of Lyon, CNRS/ENS Lyon/UCB Lyon 1, Centre de RMN a Tres Hauts Champs (France)

    2013-08-15

    We present here {sup 1}H-detected triple-resonance H/N/C experiments that incorporate CO-CA and CA-CB out-and-back scalar-transfer blocks optimized for robust resonance assignment in biosolids under ultra-fast magic-angle spinning (MAS). The first experiment, (H)(CO)CA(CO)NH, yields {sup 1}H-detected inter-residue correlations, in which we record the chemical shifts of the CA spins in the first indirect dimension while during the scalar-transfer delays the coherences are present only on the longer-lived CO spins. The second experiment, (H)(CA)CB(CA)NH, correlates the side-chain CB chemical shifts with the NH of the same residue. These high sensitivity experiments are demonstrated on both fully-protonated and 100 %-H{sup N} back-protonated perdeuterated microcrystalline samples of Acinetobacter phage 205 (AP205) capsids at 60 kHz MAS.

  19. Synthesis and NMR Elucidation of Novel Pentacycloundecane ...

    African Journals Online (AJOL)

    NICO

    2012-01-24

    Jan 24, 2012 ... research in this field, the NMR assignments of five PCU deriva- tives (1–5) ... macology.4,11 We have recently reported a family of PCU lactam .... These assignments are presented in Table 2. RESEARCH ARTICLE. R. Karpoormath, O.K. Onajole, T. Naicker, T. Govender, G.E.M. Maguire and H.G. Kruger.

  20. Stereospecific assignments in proteins using exact NOEs

    Energy Technology Data Exchange (ETDEWEB)

    Orts, Julien; Vögeli, Beat; Riek, Roland, E-mail: roland.riek@phys.chem.ethz.ch [Swiss Federal Institute of Technology, Laboratory of Physical Chemistry (Switzerland); Güntert, Peter, E-mail: guentert@em.uni-frankfurt.de [Goethe University Frankfurt am Main, Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry (Germany)

    2013-10-18

    Recently developed methods to measure distances in proteins with high accuracy by “exact” nuclear Overhauser effects (eNOEs) make it possible to determine stereospecific assignments, which are particularly important to fully exploit the accuracy of the eNOE distance measurements. Stereospecific assignments are determined by comparing the eNOE-derived distances to protein structure bundles calculated without stereospecific assignments, or an independently determined crystal structure. The absolute and relative CYANA target function difference upon swapping the stereospecific assignment of a diastereotopic group yields the respective stereospecific assignment. We applied the method to the eNOE data set that has recently been obtained for the third immunoglobulin-binding domain of protein G (GB3). The 884 eNOEs provide relevant data for 47 of the total of 75 diastereotopic groups. Stereospecific assignments could be established for 45 diastereotopic groups (96 %) using the X-ray structure, or for 27 diastereotopic groups (57 %) using structures calculated with the eNOE data set without stereospecific assignments, all of which are in agreement with those determined previously. The latter case is relevant for structure determinations based on eNOEs. The accuracy of the eNOE distance measurements is crucial for making stereospecific assignments because applying the same method to the traditional NOE data set for GB3 with imprecise upper distance bounds yields only 13 correct stereospecific assignments using the X-ray structure or 2 correct stereospecific assignments using NMR structures calculated without stereospecific assignments.

  1. ¹H, ¹³C, ¹⁵N backbone and side chain NMR resonance assignments of the N-terminal NEAr iron transporter domain 1 (NEAT 1) of the hemoglobin receptor IsdB of Staphylococcus aureus.

    Science.gov (United States)

    Fonner, Brittany A; Tripet, Brian P; Lui, Mengyao; Zhu, Hui; Lei, Benfang; Copié, Valérie

    2014-04-01

    Staphylococcus aureus is an opportunistic pathogen that causes skin and severe infections in mammals. Critical to S. aureus growth is its ability to scavenge iron from host cells. To this effect, S. aureus has evolved a sophisticated pathway to acquire heme from hemoglobin (Hb) as a preferred iron source. The pathway is comprised of nine iron-regulated surface determinant (Isd) proteins involved in heme capture, transport, and degradation. A key protein of the heme acquisition pathway is the surface-anchored hemoglobin receptor protein IsdB, which is comprised of two NEAr transporter (NEAT) domains that act in concert to bind Hb and extract heme for subsequent transfer to downstream acquisition pathway proteins. Despite significant advances in the structural knowledge of other Isd proteins, the structural mechanisms and molecular basis of the IsdB-mediated heme acquisition process are not well understood. In order to provide more insights into the mode of function of IsdB, we have initiated NMR structural studies of the first NEAT domain of IsdB (IsdB(N1)). Herein, we report the near complete (1)H, (13)C and (15)N resonance assignments of backbone and side chain atoms, and the secondary structural topology of the 148-residue IsdB NEAT 1 domain. The NMR results are consistent with the presence of eight β-strands and one α-helix characteristic of an immunoglobulin-like fold observed in other NEAT domain family proteins. This work provides a solid framework to obtain atomic-level insights toward understanding how IsdB mediates IsdB-Hb protein-protein interactions critical for heme capture and transfer.

  2. Aplicação de análise de componentes principais para verificação de atribuições de sinais nos espetros de RMN ¹H: o caso dos 3-aril (1,2,4-oxadiazol-5-carboidrazida benzilidenos Principal component analysis for verifying ¹H NMR spectral assignments: the case of 3-aryl (1,2,4-oxadiazol-5-carbohydrazide benzylidenes

    Directory of Open Access Journals (Sweden)

    João Bosco P. da Silva

    2005-06-01

    Full Text Available The ¹H NMR data set of a series of 3-aryl (1,2,4-oxadiazol-5-carbohydrazide benzylidene derivatives synthesized in our group was analyzed using the chemometric technique of principal component analysis (PCA. Using the original ¹H NMR data PCA allowed identifying some misassignments of the proton aromatic chemical shifts. As a consequence of this multivariate analysis, nuclear Overhauser difference experiments were performed to investigate the ambiguity of other assignments of the ortho and meta aromatic hydrogens for the compound with the bromine substituent. The effect of the 1,2,4-oxadiazol group as an electron acceptor, mainly for the hydrogens 12,13, has been highlighted.

  3. nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.

    Science.gov (United States)

    Schober, Daniel; Jacob, Daniel; Wilson, Michael; Cruz, Joseph A; Marcu, Ana; Grant, Jason R; Moing, Annick; Deborde, Catherine; de Figueiredo, Luis F; Haug, Kenneth; Rocca-Serra, Philippe; Easton, John; Ebbels, Timothy M D; Hao, Jie; Ludwig, Christian; Günther, Ulrich L; Rosato, Antonio; Klein, Matthias S; Lewis, Ian A; Luchinat, Claudio; Jones, Andrew R; Grauslys, Arturas; Larralde, Martin; Yokochi, Masashi; Kobayashi, Naohiro; Porzel, Andrea; Griffin, Julian L; Viant, Mark R; Wishart, David S; Steinbeck, Christoph; Salek, Reza M; Neumann, Steffen

    2018-01-02

    NMR is a widely used analytical technique with a growing number of repositories available. As a result, demands for a vendor-agnostic, open data format for long-term archiving of NMR data have emerged with the aim to ease and encourage sharing, comparison, and reuse of NMR data. Here we present nmrML, an open XML-based exchange and storage format for NMR spectral data. The nmrML format is intended to be fully compatible with existing NMR data for chemical, biochemical, and metabolomics experiments. nmrML can capture raw NMR data, spectral data acquisition parameters, and where available spectral metadata, such as chemical structures associated with spectral assignments. The nmrML format is compatible with pure-compound NMR data for reference spectral libraries as well as NMR data from complex biomixtures, i.e., metabolomics experiments. To facilitate format conversions, we provide nmrML converters for Bruker, JEOL and Agilent/Varian vendor formats. In addition, easy-to-use Web-based spectral viewing, processing, and spectral assignment tools that read and write nmrML have been developed. Software libraries and Web services for data validation are available for tool developers and end-users. The nmrML format has already been adopted for capturing and disseminating NMR data for small molecules by several open source data processing tools and metabolomics reference spectral libraries, e.g., serving as storage format for the MetaboLights data repository. The nmrML open access data standard has been endorsed by the Metabolomics Standards Initiative (MSI), and we here encourage user participation and feedback to increase usability and make it a successful standard.

  4. Guiding automated NMR structure determination using a global optimization metric, the NMR DP score

    International Nuclear Information System (INIS)

    Huang, Yuanpeng Janet; Mao, Binchen; Xu, Fei; Montelione, Gaetano T.

    2015-01-01

    ASDP is an automated NMR NOE assignment program. It uses a distinct bottom-up topology-constrained network anchoring approach for NOE interpretation, with 2D, 3D and/or 4D NOESY peak lists and resonance assignments as input, and generates unambiguous NOE constraints for iterative structure calculations. ASDP is designed to function interactively with various structure determination programs that use distance restraints to generate molecular models. In the CASD–NMR project, ASDP was tested and further developed using blinded NMR data, including resonance assignments, either raw or manually-curated (refined) NOESY peak list data, and in some cases 15 N– 1 H residual dipolar coupling data. In these blinded tests, in which the reference structure was not available until after structures were generated, the fully-automated ASDP program performed very well on all targets using both the raw and refined NOESY peak list data. Improvements of ASDP relative to its predecessor program for automated NOESY peak assignments, AutoStructure, were driven by challenges provided by these CASD–NMR data. These algorithmic improvements include (1) using a global metric of structural accuracy, the discriminating power score, for guiding model selection during the iterative NOE interpretation process, and (2) identifying incorrect NOESY cross peak assignments caused by errors in the NMR resonance assignment list. These improvements provide a more robust automated NOESY analysis program, ASDP, with the unique capability of being utilized with alternative structure generation and refinement programs including CYANA, CNS, and/or Rosetta

  5. Interpretations of NMR images

    International Nuclear Information System (INIS)

    Shi, J.Z.; McFarland, W.D.; Chen, S.S.; Sadhu, V.K.

    1986-01-01

    Two color display schemes are generally considered in medical images: pseudo-color and color composite. Psuedo-color technique maps the intensity means of a single monochrome image into a three dimensional color space, the gray level is thus replaced by the assigned color. Such a psuedo-color assignment is somewhat arbitrary but may be advantageous if the monochrome image is composed of simple intensity patterns. A good example of psuedo-color application is in nuclear medicine: The change of gray levels can be simply determined and the isocounts from two regions with different surroundings can be readily recognized. However, the use of psuedo-color in CT or MR imaging is controversial because it does not give additional information and may exaggerate insignificant gray scale differences. The color composite technique maps three parametric image data into a three dimensional color space, and thus three monochrome images are merged to form a single color image. The color composite technique increases the number of ways information can be displayed and provides both quantitative and qualitative data about the object or event represented. This paper describes the application of color composite in NMR images

  6. EXPERIMENTAL AND THEORETICAL NMR STUDY OF 4-(1 ...

    African Journals Online (AJOL)

    Preferred Customer

    increased to cover various kinds of compounds, including biological, inorganic and organometallic compounds [8]. 1D and 2D hetero- and homonuclear NMR methods enable to get full assignments and structural information of organic compounds [9-11]. For the theoretical NMR investigations, the gauge including atomic ...

  7. Method development in quantitative NMR towards metrologically traceable organic certified reference materials used as 31P qNMR standards

    OpenAIRE

    Weber, Michael; Hellriegel, Christine; Rueck, Alexander; Wuethrich, Juerg; Jenks, Peter; Obkircher, Markus

    2014-01-01

    Quantitative nuclear magnetic resonance (qNMR) spectroscopy is employed by an increasing number of analytical and industrial laboratories for the assignment of content and quantitative determination of impurities. Within the last few years, it was demonstrated that 1H qNMR can be performed with high accuracy leading to measurement uncertainties below 1?% relative. It was even demonstrated that the combination of 1H qNMR with metrological weighing can lead to measurement uncertainties below 0....

  8. Protein Side-Chain Resonance Assignment and NOE Assignment Using RDC-Defined Backbones without TOCSY Data3

    Science.gov (United States)

    Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

    2011-01-01

    One bottleneck in NMR structure determination lies in the laborious and time-consuming process of side-chain resonance and NOE assignments. Compared to the well-studied backbone resonance assignment problem, automated side-chain resonance and NOE assignments are relatively less explored. Most NOE assignment algorithms require nearly complete side-chain resonance assignments from a series of through-bond experiments such as HCCH-TOCSY or HCCCONH. Unfortunately, these TOCSY experiments perform poorly on large proteins. To overcome this deficiency, we present a novel algorithm, called NASCA (NOE Assignment and Side-Chain Assignment), to automate both side-chain resonance and NOE assignments and to perform high-resolution protein structure determination in the absence of any explicit through-bond experiment to facilitate side-chain resonance assignment, such as HCCH-TOCSY. After casting the assignment problem into a Markov Random Field (MRF), NASCA extends and applies combinatorial protein design algorithms to compute optimal assignments that best interpret the NMR data. The MRF captures the contact map information of the protein derived from NOESY spectra, exploits the backbone structural information determined by RDCs, and considers all possible side-chain rotamers. The complexity of the combinatorial search is reduced by using a dead-end elimination (DEE) algorithm, which prunes side-chain resonance assignments that are provably not part of the optimal solution. Then an A* search algorithm is employed to find a set of optimal side-chain resonance assignments that best fit the NMR data. These side-chain resonance assignments are then used to resolve the NOE assignment ambiguity and compute high-resolution protein structures. Tests on five proteins show that NASCA assigns resonances for more than 90% of side-chain protons, and achieves about 80% correct assignments. The final structures computed using the NOE distance restraints assigned by NASCA have backbone RMSD 0

  9. PVT Degradation Studies: NMR Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Herman M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Kouzes, Richard T. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2017-06-06

    Under certain environmental conditions, polyvinyl toluene (PVT) plastic scintillator has been observed to undergo internal fogging. Nuclear magnetic resonance spectroscopy has been used to elucidate the state of water inside the PVT. The deuterium NMR results show that water absorbed by PVT under warm, humid conditions enters several distinct environments, and when the PVT is transferred from incubation to ambient temperature and humidity the water is lost on a time scale of a few hours from these samples. Most of the deuterium NMR peaks can be assigned to bulk liquid water, but almost 35% of the detected signal intensity is contained in a resonance that resembles spectra of water contained in nanometer-scale pores in mesoporous carbon.

  10. NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment

    International Nuclear Information System (INIS)

    Jang, Richard; Wang, Yan; Xue, Zhidong; Zhang, Yang

    2015-01-01

    NMR-I-TASSER, an adaption of the I-TASSER algorithm combining NMR data for protein structure determination, recently joined the second round of the CASD-NMR experiment. Unlike many molecular dynamics-based methods, NMR-I-TASSER takes a molecular replacement-like approach to the problem by first threading the target through the PDB to identify structural templates which are then used for iterative NOE assignments and fragment structure assembly refinements. The employment of multiple templates allows NMR-I-TASSER to sample different topologies while convergence to a single structure is not required. Retroactive and blind tests of the CASD-NMR targets from Rounds 1 and 2 demonstrate that even without using NOE peak lists I-TASSER can generate correct structure topology with 15 of 20 targets having a TM-score above 0.5. With the addition of NOE-based distance restraints, NMR-I-TASSER significantly improved the I-TASSER models with all models having the TM-score above 0.5. The average RMSD was reduced from 5.29 to 2.14 Å in Round 1 and 3.18 to 1.71 Å in Round 2. There is no obvious difference in the modeling results with using raw and refined peak lists, indicating robustness of the pipeline to the NOE assignment errors. Overall, despite the low-resolution modeling the current NMR-I-TASSER pipeline provides a coarse-grained structure folding approach complementary to traditional molecular dynamics simulations, which can produce fast near-native frameworks for atomic-level structural refinement

  11. NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment.

    Science.gov (United States)

    Jang, Richard; Wang, Yan; Xue, Zhidong; Zhang, Yang

    2015-08-01

    NMR-I-TASSER, an adaption of the I-TASSER algorithm combining NMR data for protein structure determination, recently joined the second round of the CASD-NMR experiment. Unlike many molecular dynamics-based methods, NMR-I-TASSER takes a molecular replacement-like approach to the problem by first threading the target through the PDB to identify structural templates which are then used for iterative NOE assignments and fragment structure assembly refinements. The employment of multiple templates allows NMR-I-TASSER to sample different topologies while convergence to a single structure is not required. Retroactive and blind tests of the CASD-NMR targets from Rounds 1 and 2 demonstrate that even without using NOE peak lists I-TASSER can generate correct structure topology with 15 of 20 targets having a TM-score above 0.5. With the addition of NOE-based distance restraints, NMR-I-TASSER significantly improved the I-TASSER models with all models having the TM-score above 0.5. The average RMSD was reduced from 5.29 to 2.14 Å in Round 1 and 3.18 to 1.71 Å in Round 2. There is no obvious difference in the modeling results with using raw and refined peak lists, indicating robustness of the pipeline to the NOE assignment errors. Overall, despite the low-resolution modeling the current NMR-I-TASSER pipeline provides a coarse-grained structure folding approach complementary to traditional molecular dynamics simulations, which can produce fast near-native frameworks for atomic-level structural refinement.

  12. Metabolism of nonessential N-15-labeled amino acids and the measurement of human whole-body protein synthesis rates

    Science.gov (United States)

    Stein, T. P.; Settle, R. G.; Albina, J. A.; Melnick, G.; Dempsey, D. T.

    1991-01-01

    Eight N-15-labeled nonessential amino acids plus (N-15)H4Cl were administered over a 10-h period to four healthy adult males using a primed-constant dosage regimen. The amount of N-15 excreted in the urine and the urinary ammonia, hippuric acid, and plasma alanine N-15 enrichments were measured. There was a high degree of consistency across subjects in the ordering of the nine compounds based on the fraction of N-15 excreted.

  13. Faculty Assignment Classification System.

    Science.gov (United States)

    Whatcom Community Coll., Ferndale, WA.

    This document outlines the point-based faculty assignment classification system in effect at Whatcom Community College (Washington). The purpose of the point system is to provide an equitable and flexible means of compensating faculty members based on a system of assigning quantitative values to tasks. Teaching, which includes classroom…

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

    Directory of Open Access Journals (Sweden)

    de Brevern Alexandre G

    2005-09-01

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

  15. Application of C30B15N15 heterofullerene in the isoniazid drug delivery: DFT studies

    Science.gov (United States)

    Hazrati, Mehrnoosh Khodam; Bagheri, Zargham; Bodaghi, Ali

    2017-05-01

    Using density functional theory, we have investigated the potential application of a C30B15N15 heterofullerene in anti-cancer isoniazid drug delivery. It was found that isoniazid prefers to attach via its -NH2 group to a boron atom of the C30B15N15 with releasing a large energy of about 21.91 kcal/mol. Our partial density of states analysis demonstrates that the boron atoms significantly contribute in generation of virtual orbitals of C30B15N15 fullerene, indicating that these atoms will be suitable for nucleophilic attack rather than carbon atoms. In addition to the large released energy, the electronic properties C30B15N15 are significantly sensitive to the isoniazid attachment which can recognize the drug trajectory by affecting the fluorescence emission properties. Unlike, different nanostructures whose structures need to be manipulated to be suitable for drug delivery, the C30B15N15 fullerene can be used in the pristine form. We proposed a drug release mechanism in cancer tissues, representing that in the low pH of the cancer cells the drug and C30B15N15 fullerene are considerably protonated, thereby separating the drug from the surface of the fullerene. The reaction mechanism of the drug with the fullerene is changed from covalence in natural environment to hydrogen bonding in acidic cancer cells.

  16. Crystallographically-based analysis of the NMR spectra of maghemite

    International Nuclear Information System (INIS)

    Spiers, K.M.; Cashion, J.D.

    2012-01-01

    All possible iron environments with respect to nearest neighbour vacancies in vacancy-ordered and vacancy-disordered maghemite have been evaluated and used as the foundation for a crystallographically-based analysis of the published NMR spectra of maghemite. The spectral components have been assigned to particular configurations and excellent agreement obtained in comparing predicted spectra with published spectra taken in applied magnetic fields. The broadness of the published NMR lines has been explained by calculations of the magnetic dipole fields at the various iron sites and consideration of the supertransferred hyperfine fields. - Highlights: ► Analysis of 57 Fe NMR of maghemite based on vacancy ordering and nearest neighbour vacancies. ► Assignment of NMR spectral components based on crystallographic analysis of unique iron sites. ► Strong agreement between predicted spectra and published spectra taken in applied magnetic fields. ► Maghemite NMR spectral broadening due to various iron sites and supertransferred hyperfine field.

  17. NMR of lignins

    Science.gov (United States)

    John Ralph; Larry L. Landucci

    2010-01-01

    This chapter will consider the basic aspects and findings of several forms of NMR spectroscopy, including separate discussions of proton, carbon, heteronuclear, and multidimensional NMR. Enhanced focus will be on 13C NMR, because of its qualitative and quantitative importance, followed by NMR’s contributions to our understanding of lignin...

  18. An introduction to biological NMR spectroscopy

    International Nuclear Information System (INIS)

    Marion, Dominique

    2013-01-01

    NMR spectroscopy is a powerful tool for biologists interested in the structure, dynamics, and interactions of biological macromolecules. This review aims at presenting in an accessible manner the requirements and limitations of this technique. As an introduction, the history of NMR will highlight how the method evolved from physics to chemistry and finally to biology over several decades. We then introduce the NMR spectral parameters used in structural biology, namely the chemical shift, the J-coupling, nuclear Overhauser effects, and residual dipolar couplings. Resonance assignment, the required step for any further NMR study, bears a resemblance to jigsaw puzzle strategy. The NMR spectral parameters are then converted into angle and distances and used as input using restrained molecular dynamics to compute a bundle of structures. When interpreting a NMR-derived structure, the biologist has to judge its quality on the basis of the statistics provided. When the 3D structure is a priori known by other means, the molecular interaction with a partner can be mapped by NMR: information on the binding interface as well as on kinetic and thermodynamic constants can be gathered. NMR is suitable to monitor, over a wide range of frequencies, protein fluctuations that play a crucial role in their biological function. In the last section of this review, intrinsically disordered proteins, which have escaped the attention of classical structural biology, are discussed in the perspective of NMR, one of the rare available techniques able to describe structural ensembles. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 16 MCP). (authors)

  19. 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....

  20. 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)

  1. NMR stratagems for the study of multiple kinetic hydrogen/deuterium isotope effects of proton exchange. Example: Di-p-fluorophenylformamidine/THF

    International Nuclear Information System (INIS)

    Limbach, H.H.; Meschede, L.; Scherer, G.

    1989-01-01

    Stratagems are presented for the determination of kinetic isotope effects of proton exchange reactions by dynamic NMR spectroscopy. In such experiments, lineshape analyses and/or polarization transfer experiments are performed on the exchanging protons or deuterons as well as on remote spins, as a function of the deuterium fraction in the mobile proton sites. These methods are NMR analogs of previous proton inventory techniques involving classical kinetic methods. A theory is developed in order to derive the kinetic isotope effects as well as the number of transferred protons from the experimental NMR spectra. The technique is then applied to the problem of proton exchange in the system 15 N, 15 N'-di-p-fluorophenylformamidine, a nitrogen analog of formic acid, dissolved in tetrahydrofuran-d 8 (THF). DFFA forms two conformers in THF to which s-trans and s-cis structures have been assigned. Only the s-trans conformer is able to dimerize and exchange protons. Lineshape simulations and magnetization transfer experiments were carried out at 189,2 K, at a concentration of 0.02 mol l -1 , as a function of the deuterium fraction D in the 1 H- 15 N sites. Using 1 H NMR spectroscopy, a linear dependence of the inverse proton lifetimes on D was observed. From this it was concluded that two protons are transported in the rate limiting step of the proton exchange. This result is expected for a double proton transfer in an s-trans dimer with a cyclic structure. The full kinetic HH/HD/DD isotope effects of 233:11:1 at 189 K were determined through 19 F NMR experiments on the same samples. The deviation from the rule of geometric mean, although substantial, is much smaller than found in previous studies of intramolecular HH transfer reactions. Possible causes of this effect are discussed. (orig.)

  2. The use of N15 for studying the mechanism of transformation in the soil and plant

    International Nuclear Information System (INIS)

    Alchater, M.S.

    1995-01-01

    This research pertains to the study of the mechanism of transformation of added N 15 in the soil and plant in an attempt to determine the competition between microbial biomass and the plant for the use of N fertilizer in the form of (N 15 H 4)2 So 4. Additional amounts of barley straw were added as a source of energy. The study led to determining the real utilization coefficient of the canopy and the root system which amounted to 79% of N 15 added alone. Whereas it amounted to the treatments in which barley straw was added to N 15. Furthermore, there was a decrease in the amount of organic N 15 in the form of Gamma-amine as compared with other forms of organic N which also decreased to lesser degree. The results also indicated that the important N in the immobilization of nitrogen, as observed in previous field trials. Nitrogen balance and the contribution of soil N to plant nutrition were also calculated. 2 figs., 5 tabs

  3. 42 CFR 433.146 - Rights assigned; assignment method.

    Science.gov (United States)

    2010-10-01

    ... 42 Public Health 4 2010-10-01 2010-10-01 false Rights assigned; assignment method. 433.146 Section... Assignment of Rights to Benefits § 433.146 Rights assigned; assignment method. (a) Except as specified in... rights to any medical care support available under an order of a court or an administrative agency, and...

  4. Random Cell Identifiers Assignment

    Directory of Open Access Journals (Sweden)

    Robert Bestak

    2012-01-01

    Full Text Available Despite integration of advanced functions that enable Femto Access Points (FAPs to be deployed in a plug-and-play manner, the femtocell concept still cause several opened issues to be resolved. One of them represents an assignment of Physical Cell Identifiers (PCIs to FAPs. This paper analyses a random based assignment algorithm in LTE systems operating in diverse femtocell scenarios. The performance of the algorithm is evaluated by comparing the number of confusions for various femtocell densities, PCI ranges and knowledge of vicinity. Simulation results show that better knowledge of vicinity can significantly reduce the number of confusions events.

  5. Rapid prediction of multi-dimensional NMR data sets

    International Nuclear Information System (INIS)

    Gradmann, Sabine; Ader, Christian; Heinrich, Ines; Nand, Deepak; Dittmann, Marc; Cukkemane, Abhishek; Dijk, Marc van; Bonvin, Alexandre M. J. J.; Engelhard, Martin; Baldus, Marc

    2012-01-01

    We present a computational environment for Fast Analysis of multidimensional NMR DAta Sets (FANDAS) that allows assembling multidimensional data sets from a variety of input parameters and facilitates comparing and modifying such “in silico” data sets during the various stages of the NMR data analysis. The input parameters can vary from (partial) NMR assignments directly obtained from experiments to values retrieved from in silico prediction programs. The resulting predicted data sets enable a rapid evaluation of sample labeling in light of spectral resolution and structural content, using standard NMR software such as Sparky. In addition, direct comparison to experimental data sets can be used to validate NMR assignments, distinguish different molecular components, refine structural models or other parameters derived from NMR data. The method is demonstrated in the context of solid-state NMR data obtained for the cyclic nucleotide binding domain of a bacterial cyclic nucleotide-gated channel and on membrane-embedded sensory rhodopsin II. FANDAS is freely available as web portal under WeNMR (http://www.wenmr.eu/services/FANDAShttp://www.wenmr.eu/services/FANDAS).

  6. 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

  7. Case Assignment in Agrammatism.

    Science.gov (United States)

    Ruigendijk, Esther; van Zonneveld, Ron; Bastiaanse, Roelien

    1999-01-01

    This study evaluated the omission patterns of case markers in the spontaneous speech of 12 Dutch and German adult speakers with agrammatic aphasia within the framework of Chomsky's case theory. Data supported the hypothesis that, if no case assigner is produced, the noun will receive nominative case by default or the case-marking morpheme will be…

  8. NMR-spectroscopy

    International Nuclear Information System (INIS)

    Lundin, A.G.; Fedin, Eh.I.

    1986-01-01

    Physical foundations are given and the most important areas of nuclear magnetic resonance (NMR) application in physics, chemistry, biology are described. A detailed review of the investigations conducted and the NMR applications in different science and technology fields is presented. The method basic experimental variants, including such new ones as high resolution in a solid body; rare isotope resonance; two-dimensional and multi-quantum fourier-spectroscopy; large molecule NMR; NMR tomography and NMR intrascopy etc. are considered. The instruments are briefly described. NMR is characterized as one of the most important investigation methods of the material composition, its molecular and crystal structure, visualization of the living organism and nonmetallic object inner structure

  9. DIFFERENTIATION IN N15 UPTAKE AND THE ORGANIZATION OF AN ARCTIC TUNDRA PLANT COMMUNITY

    Science.gov (United States)

    We used N15 soil-labeling techniques to examine how the dominant species in a N-limited, tussock tundra plant community partitioned soil N, and how such partitioning may contribute to community organization. The five most abundant species were well differentiated with respect to...

  10. Scaffolding students’ assignments

    DEFF Research Database (Denmark)

    Slot, Marie Falkesgaard

    2013-01-01

    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......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...

  11. Assignment Tracking Android Application

    OpenAIRE

    Akanni, Feranmi Timothy

    2016-01-01

    One of the common ways of checking that knowledge is impacted into students at every level of education is by giving various tasks to students and part of the responsibilities of the teacher is to give assignments to students and check the solution provided by the students. Increase in technology development involves a number of mobile applications that are being developed and released on a daily basis, out of which Android operating application is one of the dominant mobile application. T...

  12. Nitrogen fixation in different chickpea cultivars as affected by iron application N-15 Technique

    International Nuclear Information System (INIS)

    Gadalla, A.M.; Soliman, S.M.; Abdelmonem, M.

    1995-01-01

    With development of new cultivars of winter chickpea, it became important to evaluate the potential of these cultivars to fix nitrogen from air, and the effect of different agronomic factors on this important process. Greenhouse experiment was conducted to screen five cultivars of chickpea for N 2- fixation ability as affected by iron application. These cultivars were Giza 1,2,531 and 88 as compared with L 3 which was developed from the genotype NEC 1055 by irradiation. N 2- fixation was estimated using N-15 technique. Plant materials were collected after 55 days from planing. Plants samples were analysed for total N-15 atom excess. Results show that Giza 88 gave the highest dry matter as well as nitrogen fixation. Nitrogen derived from air (NDFA) ranged from 27 to 50% due to variety difference and iron treatment. 1 fig., 3 tabs

  13. The use of N-15 labelling to study the turnover and utilization of ruminant manure N

    DEFF Research Database (Denmark)

    Sørensen, P.; Jensen, E.S.

    1998-01-01

    An improved understanding of the cycling of animal manure N is a prerequisite for malting better use of this N source. A sheep was fed N-15-Iabelled grass in order to study the fate of N-15-Iabelled ruminant manure N in the plant-soil system. The uniformity of labelling was found to be satisfactory...... when an appropriate feeding strategy was used. The mineralization of labelled faecal N was compared to the mineralization of labelled feed N and indigestible feed N by measuring residual labelled organic N in unplanted topsoil in the field. After18 months, 61% of both faecal N and feed N was recovered...... was low irrespective of the slurry distribution in soil. The results demonstrate that the contact between animal manure and the soil matrix significantly influences the short-term turnover and availability of faecal and ammonium N in slurry, especially in fine-textured soils....

  14. A community resource of experimental data for NMR / X-ray crystal structure pairs.

    Science.gov (United States)

    Everett, John K; Tejero, Roberto; Murthy, Sarath B K; Acton, Thomas B; Aramini, James M; Baran, Michael C; Benach, Jordi; Cort, John R; Eletsky, Alexander; Forouhar, Farhad; Guan, Rongjin; Kuzin, Alexandre P; Lee, Hsiau-Wei; Liu, Gaohua; Mani, Rajeswari; Mao, Binchen; Mills, Jeffrey L; Montelione, Alexander F; Pederson, Kari; Powers, Robert; Ramelot, Theresa; Rossi, Paolo; Seetharaman, Jayaraman; Snyder, David; Swapna, G V T; Vorobiev, Sergey M; Wu, Yibing; Xiao, Rong; Yang, Yunhuang; Arrowsmith, Cheryl H; Hunt, John F; Kennedy, Michael A; Prestegard, James H; Szyperski, Thomas; Tong, Liang; Montelione, Gaetano T

    2016-01-01

    We have developed an online NMR / X-ray Structure Pair Data Repository. The NIGMS Protein Structure Initiative (PSI) has provided many valuable reagents, 3D structures, and technologies for structural biology. The Northeast Structural Genomics Consortium was one of several PSI centers. NESG used both X-ray crystallography and NMR spectroscopy for protein structure determination. A key goal of the PSI was to provide experimental structures for at least one representative of each of hundreds of targeted protein domain families. In some cases, structures for identical (or nearly identical) constructs were determined by both NMR and X-ray crystallography. NMR spectroscopy and X-ray diffraction data for 41 of these "NMR / X-ray" structure pairs determined using conventional triple-resonance NMR methods with extensive sidechain resonance assignments have been organized in an online NMR / X-ray Structure Pair Data Repository. In addition, several NMR data sets for perdeuterated, methyl-protonated protein samples are included in this repository. As an example of the utility of this repository, these data were used to revisit questions about the precision and accuracy of protein NMR structures first outlined by Levy and coworkers several years ago (Andrec et al., Proteins 2007;69:449-465). These results demonstrate that the agreement between NMR and X-ray crystal structures is improved using modern methods of protein NMR spectroscopy. The NMR / X-ray Structure Pair Data Repository will provide a valuable resource for new computational NMR methods development. © 2015 The Protein Society.

  15. Functional studies using NMR

    International Nuclear Information System (INIS)

    McCready, V.R.; Leach, M.O.; Sutton; Ell, P.

    1986-01-01

    The object of this book is to discuss and evaluate an area of Nuclear Magnetic Resonance which to date has been less emphasized than it might be, namely the use of NMR for functional studies. The book commences with a discussion of the areas in which the NMR techniques might be needed due to deficiencies in other techniques. The physics of NMR especially relating to functional measurement are then explained. Technical factors in producing functional images are discussed and the use of paramagnetic substances for carrying out flow studies are detailed. Particular attention is paid to specific studies in the various organs. The book ends with a survey of imaging in each organ and the relation of NMR images to other techniques such as ultrasound, nuclear medicine and X-rays

  16. Functional studies using NMR

    International Nuclear Information System (INIS)

    McCready, V.R.; Leach, M.; Ell, P.J.

    1987-01-01

    This volume is based on a series of lectures delivered at a one-day teaching symposium on functional and metabolic aspects of NMR measurements held at the Middlesex Hospital Medical School on 1st September 1985 as a part of the European Nuclear Medicine Society Congress. Currently the major emphasis in medical NMR in vivo is on its potential to image and display abnormalities in conventional radiological images, providing increased contrast between normal and abnormal tissue, improved definition of vasculature, and possibly an increased potential for differential diagnosis. Although these areas are undeniably of major importance, it is probable that NMR will continue to complement conventional measurement methods. The major potential benefits to be derived from in vivo NMR measurements are likely to arise from its use as an instrument for functional and metabolic studies in both clinical research and in the everyday management of patients. It is to this area that this volume is directed

  17. UC Merced NMR Instrumentation Acquisition

    Science.gov (United States)

    2015-06-18

    UC Merced NMR Instrumentation Acquisition For the UC Merced NMR Instrumentation Acquisition proposal, a new 400 MHz and an upgraded 500 MHz NMR...valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS. University of California - Merced 5200 North Lake Road Merced , CA 95343...UC Merced NMR Instrumentation Acquisition Report Title For the UC Merced NMR Instrumentation Acquisition proposal, a new 400 MHz and an upgraded 500

  18. 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...

  19. Metabolism of Nonessential N15-Labeled Amino Acids and the Measurement of Human Whole-Body Protein Synthesis Rates

    Science.gov (United States)

    Stein, T. P.; Settle, R. G.; Albina, J. A.; Dempsey, D. T.; Melnick, G.

    1991-01-01

    Eight N-15 labeled nonessential amino acids plus (15)NH4Cl were administered over a 10 h period to four healthy adult males using a primed-constant dosage regimen. The amount of N-15 excreted in the urine and the urinary ammonia, hippuric acid, and plasma alanine N-15 enrichments were measured. There was a high degree of consistency across subjects in the ordering of the nine compounds based on the fraction of N-15 excreted (Kendall coefficient of concordance W = 0.83, P is less than 0.01). Protein synthesis rates were calculated from the urinary ammonia plateau enrichment and the cumulative excretion of N-15. Glycine was one of the few amino acids that gave similar values by both methods.

  20. The utility of N-15 nuclear magnetic resonance spectroscopy for the study of natural products

    International Nuclear Information System (INIS)

    Randall, E.W.

    1978-01-01

    The utility of 15 N NMR spectroscopy for the study of natural products and the difficulties which must be overcome arte discussed. The widespread use of pulse Fourier techniques, decouplings, larger magnetic fields and large tube sizes allows a large number of 15 N studies of natural products, the more recent and important of these being peptides, nucleosides and nucleotides. Sites of protonation, tautomerism, sites of nitrosation and proton exchange behaviour for some of these natrual products have been studied. (A.G.)

  1. Interactive Assignments for Online Students

    Directory of Open Access Journals (Sweden)

    Pam Lowry

    2009-04-01

    Full Text Available Students can experience first hand through interactive assignments what is involved in teaching an online course. Most students develop a whole new appreciation for the student learning process. Faculty are beginning to realize that online instruction is more than a series of readings posted to a course management system. This paper summarizes the faculty member's instructional strategies involved when creating student interaction assignments. The paper also summarizes the assignments, discussion board, and trends in education from the student's perspective. In summary, it concludes with the faculty's overall perspective concerning these assignments and how the assignments could be more effective for the student.

  2. DNA oligonucleotide conformations: high resolution NMR studies

    International Nuclear Information System (INIS)

    Mellema, J.-R.

    1984-01-01

    The present work describes a DNA double-helix model, which is well comparable with the models derived from fibre-diffraction studies. The model has a mononucleotide repeat with torsion angles in accordance with average geometries as derived from 1 H NMR studies. Special attention was paid to reduce the number of short H-H nonbonding contacts, which are abundantly present in the 'classical' fibre-diffraction models. Chapter 3 describes the first complete assignment of a 1 H NMR spectrum of a DNA tetramer, d(TAAT). Preliminary conformational data derived from the spectral parameters recorded at 27 0 C are given. A more detailed analysis employing temperature-dependence studies is given in Chapter 4. (Auth.)

  3. HIGH FIELD 13C NMR SPECTROSCOPIC ANALYSIS OF THE ...

    African Journals Online (AJOL)

    a

    2 carbon atoms of Sat in the β and α glyceridic positions. The. 34.114 ppm ... Table 1. 13C NMR chemical shifts of Jatropha curcas oil. Chemical shift (ppm). Assignment. 173.388. C-1, Sat. 173.302. C-1, O, L (α). 172.887. C-1, O, L (β). 34.223.

  4. Teaching NMR Using Online Textbooks

    Directory of Open Access Journals (Sweden)

    Joseph P. Hornak

    1999-12-01

    Full Text Available Nuclear magnetic resonance (NMR spectroscopy has almost become an essential analytical tool for the chemist. High-resolution one- and multi-dimensional NMR, timedomain NMR, and NMR microscopy are but a few of the NMR techniques at a chemist's disposal to determine chemical structure and dynamics. Consequently, even small chemistry departments are finding it necessary to provide students with NMR training and experience in at least some of these techniques. The hands-on experience is readily provided with access to state-of-the-art commercial spectrometers. Instruction in the principles of NMR is more difficult to achieve as most instructors try to teach NMR using single organic or analytical chemistry book chapters with static figures. This paper describes an online textbook on NMR spectroscopy called The Basics of NMR (http://www.cis.rit.edu/htbooks/nmr/ suitable for use in teaching the principles of NMR spectroscopy. The book utilizes hypertext and animations to present the principles of NMR spectroscopy. The book can be used as a textbook associated with a lecture or as a stand-alone teaching tool. Conference participants are encouraged to review the textbook and evaluate its suitability for us in teaching NMR spectroscopy to undergraduate chemistry majors.

  5. Method development in quantitative NMR towards metrologically traceable organic certified reference materials used as (31)P qNMR standards.

    Science.gov (United States)

    Weber, Michael; Hellriegel, Christine; Rueck, Alexander; Wuethrich, Juerg; Jenks, Peter; Obkircher, Markus

    2015-04-01

    Quantitative nuclear magnetic resonance (qNMR) spectroscopy is employed by an increasing number of analytical and industrial laboratories for the assignment of content and quantitative determination of impurities. Within the last few years, it was demonstrated that (1)H qNMR can be performed with high accuracy leading to measurement uncertainties below 1 % relative. It was even demonstrated that the combination of (1)H qNMR with metrological weighing can lead to measurement uncertainties below 0.1 % when highly pure substances are used. Although qNMR reference standards are already available as certified reference materials (CRM) providing traceability on the basis of (1)H qNMR experiments, there is an increasing demand for purity assays on phosphorylated organic compounds and metabolites requiring CRM for quantification by (31)P qNMR. Unfortunately, the number of available primary phosphorus standards is limited to a few inorganic CRM which only can be used for the analysis of water-soluble analytes but fail when organic solvents must be employed. This paper presents the concept of value assignment by (31)P qNMR measurements for the development of CRM and describes different approaches to establish traceability to primary Standard Reference Material from the National Institute of Standards and Technology (NIST SRM). Phosphonoacetic acid is analyzed as a water-soluble CRM candidate, whereas triphenyl phosphate is a good candidate for the use as qNMR reference material in organic solvents. These substances contain both nuclei, (1)H and (31)P, and the concept is to show that it is possible to indirectly quantify a potential phosphorus standard via its protons using (1)H qNMR. The same standard with its assigned purity can then be used for the quantification of an analyte via its phosphorus using (31)P qNMR. For the validation of the concept, triphenyl phosphate and phosphonoacetic acid have been used as (31)P qNMR standards to determine the purity of the analyte

  6. Microprocessorized NMR measurement

    International Nuclear Information System (INIS)

    Rijllart, A.

    1984-01-01

    An MC68000 CAMAC microprocessor system for fast and accurate NMR signal measurement will be presented. A stand-alone CAMAC microprocessor system (MC68000 STAC) with a special purpose interface sweeps a digital frequency synthesizer and digitizes the NMR signal with a 16-bit ADC of 17 μs conversion time. It averages the NMR signal data over many sweeps and then transfers it through CAMAC to a computer for calculation of the signal parameters. The computer has full software control over the timing and sweep settings of this signal averager, and thus allows optimization of noise suppression. Several of these processor systems can be installed in the same crate for parallel processing, and the flexibility of the STAC also allows easy adaptation to other applications such as transient recording or phase-sensitive detection. (orig.)

  7. 1D AND 2D NMR STUDIES OF BENZYL O–VANILLIN

    Directory of Open Access Journals (Sweden)

    Mohammed Hadi Al–Douh

    2010-06-01

    Full Text Available The reaction of o-vanillin A with benzyl bromide B2 in acetone as the solvent and K2CO3 as a base in the presence of tetra-n-butylammonium iodide (TBAI as catalyst formed benzyl o-vanillin, C. The complete assignments of C using PROTON, APT, DEPT-135, COSY, NOESY, HMQC and HMBC NMR in both CDCl3 and acetone-d6 are discussed, and the coupling constants J are reported in Hertz (Hz.     Keywords: 1H NMR; 13C NMR; 2D NMR; Benzyl o-Vanillin

  8. Application of 2D-NMR with room temperature NMR probes for the assessment of the higher order structure of filgrastim.

    Science.gov (United States)

    Brinson, Robert G; Ghasriani, Houman; Hodgson, Derek J; Adams, Kristie M; McEwen, Ian; Freedberg, Darón I; Chen, Kang; Keire, David A; Aubin, Yves; Marino, John P

    2017-07-15

    The higher order structure (HOS) of biotherapeutics is a critical quality attribute that can be evaluated by nuclear magnetic resonance (NMR) spectroscopy at atomic resolution. NMR spectral mapping of HOS can be used to establish HOS consistency of a biologic across manufacturing changes or to compare a biosimilar to an innovator reference product. A previous inter-laboratory study performed using filgrastim drug products demonstrated that two-dimensional (2D)-NMR 1 H N - 15 N H heteronuclear correlation spectroscopy is a highly robust and precise method for mapping the HOS of biologic drugs at natural abundance using high sensitivity NMR 'cold probes.' Here, the applicability of the 2D-NMR method to fingerprint the HOS of filgrastim products is demonstrated using lower sensitivity, room temperature NMR probes. Combined chemical shift deviation and principal component analysis are used to illustrate the performance and inter-laboratory precision of the 2D-NMR method when implemented on room temperature probes. Published by Elsevier B.V.

  9. International symposium on NMR spectroscopy

    International Nuclear Information System (INIS)

    The publication consists of 32 papers and presentations from the field of NMR spectroscopy applications submitted to the International Symposium on NMR Spectroscopy held at Smolenice between 29 Sep and 3 Oct, 1980. (B.S.)

  10. Structural and spectral assignment of three forskolin-like diterpenoids isolated from Plectranthus ornatus.

    Science.gov (United States)

    Rijo, Patrícia; Simões, M Fátima; Rodríguez, Benjamín

    2005-07-01

    Three labdane diterpenoids were isolated from an acetone extract of Plectranthus ornatus. Their structures, closely related to that of forskolin, were determined by NMR studies. Unambiguous and complete assignments of the 1H and 13C NMR chemical shifts for these substances are presented. The assignments are based on 2D shift-correlated [1H, 1H-COSY, 1H, 13C-gHSQC-1J (C,H), 1H, 13C-gHMBC-(n)J (C,H) (n = 2 and 3)] and NOE experiments. Copyright 2005 John Wiley & Sons, Ltd

  11. Autonomous driving in NMR.

    Science.gov (United States)

    Perez, Manuel

    2017-01-01

    The automatic analysis of NMR data has been a much-desired endeavour for the last six decades, as it is the case with any other analytical technique. This need for automation has only grown as advances in hardware; pulse sequences and automation have opened new research areas to NMR and increased the throughput of data. Full automatic analysis is a worthy, albeit hard, challenge, but in a world of artificial intelligence, instant communication and big data, it seems that this particular fight is happening with only one technique at a time (let this be NMR, MS, IR, UV or any other), when the reality of most laboratories is that there are several types of analytical instrumentation present. Data aggregation, verification and elucidation by using complementary techniques (e.g. MS and NMR) is a desirable outcome to pursue, although a time-consuming one if performed manually; hence, the use of automation to perform the heavy lifting for users is required to make the approach attractive for scientists. Many of the decisions and workflows that could be implemented under automation will depend on the two-way communication with databases that understand analytical data, because it is desirable not only to query these databases but also to grow them in as much of an automatic manner as possible. How these databases are designed, set up and the data inside classified will determine what workflows can be implemented. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  12. NMR, water and plants

    NARCIS (Netherlands)

    As, van H.

    1982-01-01

    This Thesis describes the application of a non-destructive pulsed proton NMR method mainly to measure water transport in the xylem vessels of plant stems and in some model systems. The results are equally well applicable to liquid flow in other biological objects than plants, e.g. flow of blood and

  13. NMR of unfolded proteins

    Indian Academy of Sciences (India)

    Unknown

    2005-01-03

    Jan 3, 2005 ... out' response to environmental changes with structural complexity ... of 3D structure at atomic resolution of folded proteins ...... 5.14 HIV-1 protease. NMR identification of local structural preferences in. HIV-1 protease in the 'unfolded state' at 6 M gua- nidine hydrochloride has been reported.49 Analyses.

  14. Single-sided NMR

    CERN Document Server

    Casanova, Federico; Blümich, Bernhard

    2011-01-01

    Single-Sided NMR describes the design of the first functioning single-sided tomograph, the related measurement methods, and a number of applications. One of the key advantages to this method is the speed at which the images are obtained.

  15. Espectro infrarrojo de [zn(mh34](re042 com substituicion isotópica 14n/15n

    Directory of Open Access Journals (Sweden)

    Claudio Téllez

    1983-11-01

    Full Text Available The infrared spectra of [Zn(15NH34] (Re042 and the isotopoc shift 14N/15N (Zn-n for the metal-ligand band, is reportedInforma-se o espectro infravermelho do complexo de Zn(II, [Zn(15NH341(Re04 e o deslocamento isotópico 14N/15N, para a banda metal - ligante v(Zn-N.

  16. NMR for chemists and biologists

    CERN Document Server

    Carbajo, Rodrigo J

    2013-01-01

    This book offers a concise introduction to the field of nuclear magnetic resonance or NMR. It presents the basic foundations of NMR in a non-mathematical way and provides an overview of both recent and important biological applications of NMR.

  17. CASD-NMR 2: robust and accurate unsupervised analysis of raw NOESY spectra and protein structure determination with UNIO

    International Nuclear Information System (INIS)

    Guerry, Paul; Duong, Viet Dung; Herrmann, Torsten

    2015-01-01

    UNIO is a comprehensive software suite for protein NMR structure determination that enables full automation of all NMR data analysis steps involved—including signal identification in NMR spectra, sequence-specific backbone and side-chain resonance assignment, NOE assignment and structure calculation. Within the framework of the second round of the community-wide stringent blind NMR structure determination challenge (CASD-NMR 2), we participated in two categories of CASD-NMR 2, namely using either raw NMR spectra or unrefined NOE peak lists as input. A total of 15 resulting NMR structure bundles were submitted for 9 out of 10 blind protein targets. All submitted UNIO structures accurately coincided with the corresponding blind targets as documented by an average backbone root mean-square deviation to the reference proteins of only 1.2 Å. Also, the precision of the UNIO structure bundles was virtually identical to the ensemble of reference structures. By assessing the quality of all UNIO structures submitted to the two categories, we find throughout that only the UNIO–ATNOS/CANDID approach using raw NMR spectra consistently yielded structure bundles of high quality for direct deposition in the Protein Data Bank. In conclusion, the results obtained in CASD-NMR 2 are another vital proof for robust, accurate and unsupervised NMR data analysis by UNIO for real-world applications

  18. The assessment of nitrogen balance under flooding and saturation circumstances using N-15

    International Nuclear Information System (INIS)

    Abouseeda, M.; Khater, A.; Soliman, S.

    1995-01-01

    The use 15 N- balance techniques has already identified N-loss as a major problem in lowland rice management. Ammonium sulphate labelled with 5% N-15 atom ex. as a basal fertilized through special column in order to study the effect of flooding and saturation condition on the potential loss of nitrogen fertilizer. Rice straw at a rate of 1% was incorporated with the soil in order to study the role of rice straw (as a source of organic matter) on N-loss. Results show that the application of rice straw under flooding condition resulted in an increase of the biomass. It was observed that flooding circumstances may reduce the loss of nitrogen. Since N-recovery under flood and saturation rhizosphere (with plant) conditions were about 75% and 56%, respectively. The effect of rice root (rhizosphere) on nitrification has been observed. Results of flood and non flood rhizossphere show that the nitrogen recovery were about 75% and 86%, respectively. Results show an indirect evidence that the process of rhizosphere nitrification denitrification resulted in a significant amount of N-loss.It is evident that deep placement and flooded condition proved to be an effective means of reducing the potential of N-loss. 1 fig., 3 tabs

  19. NMR Studies of Peroxidases.

    Science.gov (United States)

    Veitch, Nigel Charles

    Available from UMI in association with The British Library. Requires signed TDF. Peroxidases are a haem-containing group of enzymes with a wide diversity of function within biological systems. While a common characteristic is the ability to catalyse the conversion of hydrogen peroxide to water, it is the accompanying processes of hormone synthesis and degradation which have generated such a high level of interest. However, information at the molecular level is limited to a single well-resolved crystal structure, that of yeast cytochrome c peroxidase. This thesis presents a strategy for the investigation of peroxidase structure and function based on proton nuclear magnetic resonance spectroscopy, a technique which has the ability to address aspects of both protein structure and protein dynamics in solution. The application of one- and two-dimensional NMR techniques has been developed in the context of plant peroxidases, notably the isoenzyme HRP-C derived from the horseradish root. Characterisation of the proton NMR spectra of HRP -C in resting and ligated states provided new information enabling the structure of the binding site for aromatic donor molecules, such as indole-3-propionic, ferulic and benzhydroxamic acids, to be resolved. In order to overcome difficulties encountered with a protein of the complexity of peroxidase, additional information was obtained from chemical shift parameters and the use of peroxidase variants produced by site-directed mutagenesis. A comparative study using NMR spectroscopy was undertaken for wild-type recombinant HRP-C expressed in Escherichia coli, and two protein variants with substitutions made to residues located on the distal side of the haem pocket, Phe41 to Val and Arg38 to Lys. NMR analyses of a plant peroxidase from barley grains and the fungal peroxidase from Coprinus cinereus were also successful using methods conceived with HRP-C. Examination of three specifically constructed recombinant protein variants of C. cinereus

  20. NMR, water and plants

    International Nuclear Information System (INIS)

    As, H. van.

    1982-01-01

    This thesis describes the application of a non-destructive pulsed proton NMR method mainly to measure water transport in the xylem vessels of plant stems and in some model systems. The results are equally well applicable to liquid flow in other biological objects than plants, e.g. flow of blood and other body fluids in human and animals. The method is based on a pulse sequence of equidistant π pulses in combination with a linear magnetic field gradient. (Auth.)

  1. Business Etiquette (My Favorite Assignment).

    Science.gov (United States)

    Forbes, Cassie

    1990-01-01

    Describes an assignment for a business communication course in which students give an oral presentation on some aspect of business manners and etiquette, thus increasing their awareness of the impact of social graces on communication in the business setting. (SR)

  2. 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...

  3. Ultra-violet absorption cross sections of isotopically substituted nitrous oxide species: 14N14NO, 15N14NO, 14N15NO and 15N15NO

    Directory of Open Access Journals (Sweden)

    P. von Hessberg

    2004-01-01

    Full Text Available The isotopically substituted nitrous oxide species 14N14NO, 15N14NO, 14N15NO and 15N15NO were investigated by ultra-violet (UV absorption spectroscopy. High precision cross sections were obtained for the wavelength range 181 to 218nm at temperatures of 233 and 283K. These data are used to calculate photolytic isotopic fractionation constants as a function of wavelength. The fractionation constants were used in a three-dimensional chemical transport model in order to simulate the actual fractionation of N2O in the stratosphere, and the results were found to be in good agreement with field studies.

  4. Characterization of D-glucaric acid using NMR, x-ray crystal structure, and MM3 molecular modeling analyses

    Science.gov (United States)

    D-glucaric acid was characterized in solution by comparing NMR spectra from the isotopically unlabeled molecule with those from D-glucaric acid labeled with deuterium or carbon-13 atoms. The NMR studies provided unequivocal assignments for all carbon atoms and non-hydroxyl protons of the molecule. ...

  5. NMR spectroscopic study and DFT calculations of GIAO NMR ...

    African Journals Online (AJOL)

    1H, proton coupled and decoupled 13C, DEPT, HETCOR NMR spectra, the magnitude of one bond 1JCH coupling constants and 13C NMR spin-lattice relaxation time (T1) of 1,9-diaminononane (danon, C9H22N2) have been reported for the first time. 1H, 13C NMR chemical shifts and 1JCH coupling constants of danon ...

  6. NMR imaging of the spine

    Energy Technology Data Exchange (ETDEWEB)

    Han, J.S. (Case Western Reserve Univ. School of Medicine, Cleveland, OH); Kaufman, B.; El Yousef, S.J.; Benson, J.E.; Bonstelle, C.T.; Alfidi, R.J.; Haaga, J.R.; Yeung, H.; Huss, R.G.

    1983-12-01

    The usefulness of nuclear magnetic resonance (NMR) images in the evaluation of spinal disorders below the craniocervical junction was studied. Six normal subjects and 41 patients with various spinal abnormalities were examined. NMR proved capable of demonstrating important normal and pathologic anatomic structures; it was useful in the evaluation of syringohydromyelia and cystic spinal cord tumors, and the bright signal intensity of lipoma was quite impressive. In the evaluation of herniated disk, NMR images offered a new perspective by visualizing abnormal degradation of the signal intensity of the nucleus pulposus itself. NMR images were least valuable in the evaluation of spondylosis and spinal stenosis. Although NMR imaging of the spine is still in a very early developmental stage, the absence of both ionizing radiation and risks associated with contrast material makes it especially attractive as a new diagnostic method. This limited experience with currently available equipment suggests that, with technical refinement, the efficacy of NMR of the spine will increase.

  7. Variable-temperature NMR and conformational analysis of Oenothein B

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Suzana C.; Carvalho, Ariadne G.; Fortes, Gilmara A.C.; Ferri, Pedro H.; Oliveira, Anselmo E. de, E-mail: suzana.quimica.ufg@hotmail.com [Universidade Federal de Goias (UFGO), Goiania, GO (Brazil). Instituto de Quimica

    2014-02-15

    Oenothein B is a dimeric hydrolyzable tannin with a wide range of biological activities, such as antitumour, anti-inflammatory and antiviral. Its nuclear magnetic resonance (NMR) at room temperature show duplications and broadening of signals. Experiments of 1D and 2D NMR at lower temperatures were useful for the complete NMR assignments of all hydrogens and carbons. The 3D structure of the most stable conformer was determined for the first time by nuclear Overhauser effect spectroscopy (NOESY) experiment (-20 deg C) and density functional theory (DFT)(B3LYP/6-31G)/ polarizable continuum model (PCM) quantum chemical calculations. The favoured conformation showed a highly compacted geometry and a lack of symmetry, in which the two valoneoyl groups showed distinct conformational parameters and stabilities. (author)

  8. Intraresidue HNCA and COHNCA Experiments for Protein Backbone Resonance Assignment

    Science.gov (United States)

    Brutscher, Bernhard

    2002-05-01

    Two novel experiments, intra-HNCA and intra-COHNCA, are presented for sequential backbone resonance assignment of 13C, 15N labeled proteins. The advantage with respect to conventional pulse schemes is the suppression of the sequential 15N→13Cα coherence transfer pathway, which can be separately obtained from a HNCOCA correlation experiment. This results in a two-fold reduction of the number of detected correlation peaks. Spectral simplification is especially important for efficient automated assignment protocols as required in the context of high-throughput protein studies by NMR. The performance of the new experiments is demonstrated on an 18-kDa protein fragment of the E. coli sulfite reductase and compared to conventional techniques in terms of sensitivity and resolution.

  9. Processing DOSY NMR Data by Chemometric Methods

    NARCIS (Netherlands)

    Huo, R.

    2006-01-01

    DOSY NMR can be used as a non-invasive separation method for complex mixtures. It is more and more attractive for industrial laboratories, for the main advantage DOSY NMR over routine separation methods such as LC-NMR is easy and economical implementation. With NMR instruments, DOSY NMR data can be

  10. 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)

  11. nmr spectroscopic study and dft calculations of giao nmr shieldings

    African Journals Online (AJOL)

    Preferred Customer

    NMR is a sensitive and versatile probe of molecular-scale structure and dynamics in solids and liquids. It has been widely used in chemistry, materials and geochemistry [21-23] and it enables one to get faster and easier structural information. The standard 1D and 2D hetero and homonuclear NMR experiments are enough ...

  12. Nitrate and ammonium influxes in soybean (Glycine max) roots : Direct comparison of N-13 and N-15 tracing

    NARCIS (Netherlands)

    Clarkson, DT; Gojon, A; Saker, LR; Wiersema, PK; Purves, JV; Tillard, P; Arnold, GM; Paans, AJM; Vaalburg, W; Stulen, [No Value

    We compared influxes and internal transport in soybean plants (Glycine max cv. Kingsoy) of labelled N from external solutions where either ammonium or nitrate was labelled with the stable isotope N-15 and the radioactive isotope N-13. The objective was to see whether mass spectrometric

  13. First Measurement of the 14N/15N Ratio in the Analog of the Sun Progenitor OMC-2 FIR4

    Science.gov (United States)

    Kahane, Claudine; Jaber Al-Edhari, Ali; Ceccarelli, Cecilia; López-Sepulcre, Ana; Fontani, Francesco; Kama, Mihkel

    2018-01-01

    We present a complete census of the 14N/15N isotopic ratio in the most abundant N-bearing molecules toward the cold envelope of the protocluster OMC-2 FIR4, the best known Sun progenitor. To this scope, we analyzed the unbiased spectral survey obtained with the IRAM 30 m telescope at 3, 2, and 1 mm. We detected several lines of CN, HCN, HNC, HC3N, N2H+, and their respective 13C and 15N isotopologues. The lines’ relative fluxes are compatible with LTE conditions, and moderate line opacities have been corrected via a population diagram method or theoretical relative intensity ratios of the hyperfine structures. The five species lead to very similar 14N/15N isotopic ratios, without any systematic difference between amine- and nitrile-bearing species as previously found in other protostellar sources. The weighted average of the 14N/15N isotopic ratio is 270 ± 30. This 14N/15N value is remarkably consistent with the [250–350] range measured for the local galactic ratio but significantly differs from the ratio measured in comets (around 140). High-angular resolution observations are needed to examine whether this discrepancy is maintained at smaller scales. In addition, using the CN, HCN, and HC3N lines, we derived a 12C/13C isotopic ratio of 50 ± 5.

  14. DNA Packaging Specificity of Bacteriophage N15 with an Excursion into the Genetics of a Cohesive End Mismatch.

    Directory of Open Access Journals (Sweden)

    Michael Feiss

    Full Text Available During DNA replication by the λ-like bacteriophages, immature concatemeric DNA is produced by rolling circle replication. The concatemers are processed into mature chromosomes with cohesive ends, and packaged into prohead shells, during virion assembly. Cohesive ends are generated by the viral enzyme terminase, which introduces staggered nicks at cos, an approx. 200 bp-long sequence containing subsites cosQ, cosN and cosB. Interactions of cos subsites of immature concatemeric DNA with terminase orchestrate DNA processing and packaging. To initiate DNA packaging, terminase interacts with cosB and nicks cosN. The cohesive ends of N15 DNA differ from those of λ at 2/12 positions. Genetic experiments show that phages with chromosomes containing mismatched cohesive ends are functional. In at least some infections, the cohesive end mismatch persists through cyclization and replication, so that progeny phages of both allelic types are produced in the infected cell. N15 possesses an asymmetric packaging specificity: N15 DNA is not packaged by phages λ or 21, but surprisingly, N15-specific terminase packages λ DNA. Implications for genetic interactions among λ-like bacteriophages are discussed.

  15. Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach.

    Science.gov (United States)

    Lemak, Alexander; Steren, Carlos A; Arrowsmith, Cheryl H; Llinás, Miguel

    2008-05-01

    ABACUS [Grishaev et al. (2005) Proteins 61:36-43] is a novel protocol for automated protein structure determination via NMR. ABACUS starts from molecular fragments defined by unassigned J-coupled spin-systems and involves a Monte Carlo stochastic search in assignment space, probabilistic sequence selection, and assembly of fragments into structures that are used to guide the stochastic search. Here, we report further development of the two main algorithms that increase the flexibility and robustness of the method. Performance of the BACUS [Grishaev and Llinás (2004) J Biomol NMR 28:1-101] algorithm was significantly improved through use of sequential connectivities available from through-bond correlated 3D-NMR experiments, and a new set of likelihood probabilities derived from a database of 56 ultra high resolution X-ray structures. A Multicanonical Monte Carlo procedure, Fragment Monte Carlo (FMC), was developed for sequence-specific assignment of spin-systems. It relies on an enhanced assignment sampling and provides the uncertainty of assignments in a quantitative manner. The efficiency of the protocol was validated on data from four proteins of between 68-116 residues, yielding 100% accuracy in sequence specific assignment of backbone and side chain resonances.

  16. Effective Homework Assignments. Research Brief

    Science.gov (United States)

    Cooper, Harris

    2008-01-01

    Perhaps more than any question other than "How much time should students spend doing homework?" parents and educators want to know, "What kinds of homework assignments are most effective?" Clearly, the answers to this question vary according to many factors, especially the developmental level of students and the topic area. Generally, answers are…

  17. 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....

  18. High resolution deuterium NMR studies of bacterial metabolism

    International Nuclear Information System (INIS)

    Aguayo, J.B.; Gamcsik, M.P.; Dick, J.D.

    1988-01-01

    High resolution deuterium NMR spectra were obtained from suspensions of five bacterial strains: Escherichia coli, Clostridium perfringens, Klebsiella pneumoniae, Proteus mirabilis, and Staphylococcus aureus. Deuterium-labeled D-glucose at C-1, C-2, and C-6 was used to monitor dynamically anaerobic metabolism. The flux of glucose through the various bacterial metabolic pathways could be determined by following the disappearance of glucose and the appearance of the major end products in the 2H NMR spectrum. The presence of both labeled and unlabeled metabolites could be detected using 1H NMR spectroscopy since the proton resonances in the labeled species are shifted upfield due to an isotopic chemical shift effect. The 1H-1H scalar coupling observed in both the 2H and 1H NMR spectra was used to assign definitively the resonances of labeled species. An increase in the intensity of natural abundance deuterium signal of water can be used to monitor pathways in which a deuteron is lost from the labeled metabolite. The steps in which label loss can occur are outlined, and the influence these processes have on the ability of 2H NMR spectroscopy to monitor metabolism are assessed

  19. THz Dynamic Nuclear Polarization NMR.

    Science.gov (United States)

    Nanni, Emilio A; Barnes, Alexander B; Griffin, Robert G; Temkin, Richard J

    2011-08-29

    Dynamic nuclear polarization (DNP) increases the sensitivity of nuclear magnetic resonance (NMR) spectroscopy by using high frequency microwaves to transfer the polarization of the electrons to the nuclear spins. The enhancement in NMR sensitivity can amount to a factor of well above 100, enabling faster data acquisition and greatly improved NMR measurements. With the increasing magnetic fields (up to 23 T) used in NMR research, the required frequency for DNP falls into the THz band (140-600 GHz). Gyrotrons have been developed to meet the demanding specifications for DNP NMR, including power levels of tens of watts; frequency stability of a few megahertz; and power stability of 1% over runs that last for several days to weeks. Continuous gyrotron frequency tuning of over 1 GHz has also been demonstrated. The complete DNP NMR system must include a low loss transmission line; an optimized antenna; and a holder for efficient coupling of the THz radiation to the sample. This paper describes the DNP NMR process and illustrates the THz systems needed for this demanding spectroscopic application. THz DNP NMR is a rapidly developing, exciting area of THz science and technology.

  20. NMR imaging studies of coal

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Z.R.; Zhang, P.Z.; Ding, G.L.; Li, L.Y.; Ye, C.H. [University of Science and Technology, Beijing (China). Dept. of Chemistry

    1996-06-01

    The permeation transportation and swelling behavior of solvents into coal are investigated by NMR imaging using pyridine-d{sub 5} and acetone-d{sub 6}. Images of coal swollen with deuterated solvents illuminate proton distributions of mobile phases within the coal macromolecular networks. More information about the chemical and physical structure of coal can be obtained using NMR imaging techniques.

  1. NMR imaging of osteoarticular pathology

    Energy Technology Data Exchange (ETDEWEB)

    Frocrain, L.; Duvauferrier, R.; Gagey, N. and others

    1987-01-01

    NMR imaging is assuming an increasingly important role in the diagnosis of osteo-articular disorders. Semiological descriptions of the mean pathological disorders of the locomotor system are presented. Some investigation strategies are proposed to compare NMR imaging with other imaging techniques in various pathological states.

  2. NMR in pulsed magnetic field

    KAUST Repository

    Abou-Hamad, Edy

    2011-09-01

    Nuclear magnetic resonance (NMR) experiments in pulsed magnetic fields up to 30.4 T focused on 1H and 93Nb nuclei are reported. Here we discuss the advantage and limitation of pulsed field NMR and why this technique is able to become a promising research tool. © 2011 Elsevier Inc. All Rights Reserved.

  3. Quantum Information Processing by NMR

    Indian Academy of Sciences (India)

    Keywords. NMR; quantum information processing; quantum computing; qubits; pseudopure states; quantum; pseudopure states; quantum gates; quantum simulations; decoherence. ... T S Mahesh1. Department of Physics and NMR Research Center, Indian Institute of Science Education and Research, Pune 411 008, India ...

  4. Resistive NMR of intracranial hematomas

    Energy Technology Data Exchange (ETDEWEB)

    Zimmerman, R.A.; Bilaniuk, L.T.; Grossman, R.I.; Levine, R.S.; Lynch, R.; Goldberg, H.I.; Samuel, L.; Edelstein, W.; Bottomley, P.; Redington, R.W.

    1985-01-01

    Comparison between computed tomography and nuclear magnetic resonance imaging in 17 patients with intracranial hematomas indicate a distinct role for NMR in evaluating the stable patient with hematoma. NMR is useful for delineating the extent of the hematoma, the relationship of the hematoma to brain anatomy, and the presence of hematoma at a time when the hematoma is isodense on CT.

  5. Structural Biology: Practical NMR Applications

    CERN Document Server

    Teng, Quincy

    2005-01-01

    This textbook begins with an overview of NMR development and applications in biological systems. It describes recent developments in instrument hardware and methodology. Chapters highlight the scope and limitation of NMR methods. While detailed math and quantum mechanics dealing with NMR theory have been addressed in several well-known NMR volumes, chapter two of this volume illustrates the fundamental principles and concepts of NMR spectroscopy in a more descriptive manner. Topics such as instrument setup, data acquisition, and data processing using a variety of offline software are discussed. Chapters further discuss several routine stategies for preparing samples, especially for macromolecules and complexes. The target market for such a volume includes researchers in the field of biochemistry, chemistry, structural biology and biophysics.

  6. Complete 1H NMR spectral analysis of ten chemical markers of Ginkgo biloba

    OpenAIRE

    Napolitano, José G.; Lankin, David C.; Chen, Shao-Nong; Pauli, Guido F.

    2012-01-01

    The complete and unambiguous 1H NMR assignments of ten marker constituents of Ginkgo biloba are described. The comprehensive 1H NMR profiles (fingerprints) of ginkgolide A, ginkgolide B, ginkgolide C, ginkgolide J, bilobalide, quercetin, kaempferol, isorhamnetin, isoquercetin, and rutin in DMSO-d6 were obtained through the examination of 1D 1H NMR and 2D 1H,1H-COSY data, in combination with 1H iterative Full Spin Analysis (HiFSA). The computational analysis of discrete spin systems allowed a ...

  7. Complete 1H NMR spectral analysis of ten chemical markers of Ginkgo biloba.

    Science.gov (United States)

    Napolitano, José G; Lankin, David C; Chen, Shao-Nong; Pauli, Guido F

    2012-08-01

    The complete and unambiguous (1)H NMR assignments of ten marker constituents of Ginkgo biloba are described. The comprehensive (1)H NMR profiles (fingerprints) of ginkgolide A, ginkgolide B, ginkgolide C, ginkgolide J, bilobalide, quercetin, kaempferol, isorhamnetin, isoquercetin, and rutin in DMSO-d(6) were obtained through the examination of 1D (1)H NMR and 2D (1)H,(1)H-COSY data, in combination with (1)H iterative full spin analysis (HiFSA). The computational analysis of discrete spin systems allowed a detailed characterization of all the (1)H NMR signals in terms of chemical shifts (δ(H)) and spin-spin coupling constants (J(HH)), regardless of signal overlap and higher order coupling effects. The capability of the HiFSA-generated (1)H fingerprints to reproduce experimental (1)H NMR spectra at different field strengths was also evaluated. As a result of this analysis, a revised set of (1)H NMR parameters for all ten phytoconstituents was assembled. Furthermore, precise (1)H NMR assignments of the sugar moieties of isoquercetin and rutin are reported for the first time. Copyright © 2012 John Wiley & Sons, Ltd.

  8. Fleet Assignment Using Collective Intelligence

    Science.gov (United States)

    Antoine, Nicolas E.; Bieniawski, Stefan R.; Kroo, Ilan M.; Wolpert, David H.

    2004-01-01

    Product distribution theory is a new collective intelligence-based framework for analyzing and controlling distributed systems. Its usefulness in distributed stochastic optimization is illustrated here through an airline fleet assignment problem. This problem involves the allocation of aircraft to a set of flights legs in order to meet passenger demand, while satisfying a variety of linear and non-linear constraints. Over the course of the day, the routing of each aircraft is determined in order to minimize the number of required flights for a given fleet. The associated flow continuity and aircraft count constraints have led researchers to focus on obtaining quasi-optimal solutions, especially at larger scales. In this paper, the authors propose the application of this new stochastic optimization algorithm to a non-linear objective cold start fleet assignment problem. Results show that the optimizer can successfully solve such highly-constrained problems (130 variables, 184 constraints).

  9. {sup 11}B-NMR spectroscopic study on the interaction of epinephrine and p-BPA

    Energy Technology Data Exchange (ETDEWEB)

    Ichihara, K.; Yoshino, K. [Shinshu Univ., Department of Chemistry, Matsumoto, Nagano (Japan)

    2000-10-01

    It is studied that p-BPA (p-bronophenylalanine) which formed complex with catechol functional group has interaction with epinephrine by {sup 11}B-NMR. Two {sup 11}B-NMR resonance signals were observed at pH 7.0. The signal at 29.6 ppm is assigned to p-BPA and at 10.8 ppm is assigned to that of complex. We can determine complex formation constants (logK') in various pH. (author)

  10. Merremoside D: de novo synthesis of the purported structure, NMR analysis, and comparison of spectral data.

    Science.gov (United States)

    Sharif, Ehesan U; Wang, Hua-Yu Leo; Akhmedov, Novruz G; O'Doherty, George A

    2014-01-17

    The first synthesis of the purported structure of Merremoside D has been achieved in 22 longest linear steps. The de novo asymmetric synthesis relied on the use of asymmetric catalysis to selectively install all 21 stereocenters in the final compounds from commercially available achiral starting materials. Adiabatic gradient 2D NMR techniques (gHSQCAD, gHMBCAD, gH2BCAD, gHSQCTOXYAD, ROESYAD) were used to completely assign the structure of synthetic Merremoside D. Comparison of our assignments with the limited NMR data reported for natural Merremoside D allows for the tentative confirmation of its structure.

  11. Correlation between low-temperature creep and intergranular diffusion of Kh16N15M3B type steel

    International Nuclear Information System (INIS)

    Solonin, M.I.; Kondrat'ev, V.P.; Krasina, T.A.; Voejkov, V.P.; Tarasyuk, V.B.; Fedorov, G.B.; Ryabenko, A.V.

    1990-01-01

    The results are presented for Kh16N15M3B type steel containing different amounts of carbon, molybdenum and niobium that was tested the diffusion mobility of iron-59 species. It is shown that at 400-500 deg C the diffusion of iron-59 is only intergranular. The correlation established between creep and diffusion. It is shwn that the activation energies for creep and intergranular diffusion correlate. 5 refs.; 4 figs.; 3 tabs

  12. A global analysis of NMR distance constraints from the PDB

    International Nuclear Information System (INIS)

    Vranken, Wim

    2007-01-01

    Information obtained from Nuclear Magnetic Resonance (NMR) experiments is encoded as a set of constraint lists when calculating three-dimensional structures for a protein. With the amount of constraint data from the world wide Protein Data Bank (wwPDB) that is now available, it is possible to do a global, large-scale analysis using only information from the constraints, without taking the coordinate information into account. This article describes such an analysis of distance constraints from NOE data based on a set of 1834 NMR PDB entries containing 1909 protein chains. In order to best represent the quality and extent of the data that is currently deposited at the wwPDB, only the original data as deposited by the authors was used, and no attempt was made to 'clean up' and further interpret this information. Because the constraint lists provide a single set of data, and not an ensemble of structural solutions, they are easier to analyse and provide a reduced form of structural information that is relevant for NMR analysis only. The online resource resulting from this analysis makes it possible to check, for example, how often a particular contact occurs when assigning NOESY spectra, or to find out whether a particular sequence fragment is likely to be difficult to assign. In this respect it formalises information that scientists with experience in spectrum analysis are aware of but cannot necessarily quantify. The analysis described here illustrates the importance of depositing constraints (and all other possible NMR derived information) along with the structure coordinates, as this type of information can greatly assist the NMR community

  13. Annual reports on NMR spectroscopy

    CERN Document Server

    Webb, Graham A; McCarthy, M J

    1995-01-01

    Over recent years, no other technique has grown to such importance as that of NMR spectroscopy. It is used in all branches of science where precise structural determination is required and where the nature of interactions and reactions in solution is being studied. Annual Reports on NMR Spectroscopy has established itself as a means for the specialist and non-specialist alike to become familiar with new applications of the technique in all branches of chemistry, including biochemistry, and pharmaceutics. This volume focuses on theoretical aspects of NMR nuclear shielding and on applications of

  14. Influence of N-15 labelled urea and azotobacter on corn yield and nitrogen budget as affected by organic matter

    International Nuclear Information System (INIS)

    Soliman, S.M.; Abdelmonem, M.A.

    1995-01-01

    As sandy soils of Egypt are poor in their chemical and physical properties, their fertilization with chemical or biological fertilizer is essential. The reported greenhouse experiment was conducted, using sandy soil of Egypt to evaluate the impact of urea fertilizer, applied alone combined with nitrification inhibitors (DCD) or (N-serve) on (corn yield and N-losses) as compared with inoculation with azotobacter under organic matter treatment as soil amendment. Total dry matter was recorded, while N-uptake by corn, and N-recovery due to inoculation with azotobacter was determined using N-15 dilution technique. Data obtained indicated that, application of DCD or N-serve with urea increased corn dry matter weight as well N-15 recovery. Significant increase in N-recovery was obtained due to nitrification inhibitor application and azotobacter inoculation. N-15 losses were reduced due to application of DCD and N-serve from 45% and respectively. Use of bio fertilizers and nitrification inhibitors could play an important role in corn production in sandy soil, as well as decrease the losses of applied N-fertilizers. fig., 3 tabs

  15. (3,2)D GFT-NMR experiments for fast data collection from proteins

    International Nuclear Information System (INIS)

    Xia Youlin; Zhu Guang; Veeraraghavan, Sudha; Gao Xiaolian

    2004-01-01

    High throughput structure determination of proteins will contribute to the success of proteomics investigations. The G-Matrix Fourier Transformation NMR (GFT-NMR) method significantly shortens experimental time by reducing the number of the dimensions of data acquisition for isotopically labeled proteins (Kim, S. and Szyperski, T. (2003) J. Am. Chem. Soc.125, 1385). We demonstrate herein a suite of ten 3D → 2D or (3,2)D GFT-NMR experiments using 13 C/ 15 N-labeled ubiquitin. These experiments were completed within 18 hours, representing a 4- to 18-fold reduction in data acquisition time compared to the corresponding conventional 3D experiments. A subset of the GFT-NMR experiments, (3,2)D HNCO, HNCACB, HN(CO)CACB, and 2D 1 H- 15 N HSQC, which are necessary for backbone assignments, were carried out within 6 hours. To facilitate the analysis of the GFT-NMR spectra, we developed automated procedures for viewing and analyzing the GFT-NMR spectra. Our overall strategy allows (3,2)D GFT-NMR experiments to be readily performed and analyzed. Nevertheless, the increase in spectral overlap and the reduction in signal sensitivity in these fast NMR experiments presently limit their application to relatively small proteins

  16. NMR Studies of Polymer Nanocomposites

    National Research Council Canada - National Science Library

    Greenbaum, Steve

    2001-01-01

    .... The primary tool is pulsed field gradient NMR. A static field gradient method was developed which makes possible variable pressure diffusion measurement, and the application to the important fuel cell membrane NAFION constitute the first results...

  17. β-NMR sample optimization

    CERN Document Server

    Zakoucka, Eva

    2013-01-01

    During my summer student programme I was working on sample optimization for a new β-NMR project at the ISOLDE facility. The β-NMR technique is well-established in solid-state physics and just recently it is being introduced for applications in biochemistry and life sciences. The β-NMR collaboration will be applying for beam time to the INTC committee in September for three nuclei: Cu, Zn and Mg. Sample optimization for Mg was already performed last year during the summer student programme. Therefore sample optimization for Cu and Zn had to be completed as well for the project proposal. My part in the project was to perform thorough literature research on techniques studying Cu and Zn complexes in native conditions, search for relevant binding candidates for Cu and Zn applicable for ß-NMR and eventually evaluate selected binding candidates using UV-VIS spectrometry.

  18. Optical pumping and xenon NMR

    International Nuclear Information System (INIS)

    Raftery, M.D.

    1991-11-01

    Nuclear Magnetic Resonance (NMR) spectroscopy of xenon has become an important tool for investigating a wide variety of materials, especially those with high surface area. The sensitivity of its chemical shift to environment, and its chemical inertness and adsorption properties make xenon a particularly useful NMR probe. This work discusses the application of optical pumping to enhance the sensitivity of xenon NMR experiments, thereby allowing them to be used in the study of systems with lower surface area. A novel method of optically-pumping 129 Xe in low magnetic field below an NMR spectrometer and subsequent transfer of the gas to high magnetic field is described. NMR studies of the highly polarized gas adsorbed onto powdered samples with low to moderate surface areas are now possible. For instance, NMR studies of optically-pumped xenon adsorbed onto polyacrylic acid show that xenon has a large interaction with the surface. By modeling the low temperature data in terms of a sticking probability and the gas phase xenon-xenon interaction, the diffusion coefficient for xenon at the surface of the polymer is determined. The sensitivity enhancement afforded by optical pumping also allows the NMR observation of xenon thin films frozen onto the inner surfaces of different sample cells. The geometry of the thin films results in interesting line shapes that are due to the bulk magnetic susceptibility of xenon. Experiments are also described that combine optical pumping with optical detection for high sensitivity in low magnetic field to observe the quadrupoler evolution of 131 Xe spins at the surface of the pumping cells. In cells with macroscopic asymmetry, a residual quadrupolar interaction causes a splitting in the 131 Xe NMR frequencies in bare Pyrex glass cells and cells with added hydrogen

  19. 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.

  20. Data Analysis and Tissue Type Assignment for Glioblastoma Multiforme

    Directory of Open Access Journals (Sweden)

    Yuqian Li

    2014-01-01

    Full Text Available Glioblastoma multiforme (GBM is characterized by high infiltration. The interpretation of MRSI data, especially for GBMs, is still challenging. Unsupervised methods based on NMF by Li et al. (2013, NMR in Biomedicine and Li et al. (2013, IEEE Transactions on Biomedical Engineering have been proposed for glioma recognition, but the tissue types is still not well interpreted. As an extension of the previous work, a tissue type assignment method is proposed for GBMs based on the analysis of MRSI data and tissue distribution information. The tissue type assignment method uses the values from the distribution maps of all three tissue types to interpret all the information in one new map and color encodes each voxel to indicate the tissue type. Experiments carried out on in vivo MRSI data show the feasibility of the proposed method. This method provides an efficient way for GBM tissue type assignment and helps to display information of MRSI data in a way that is easy to interpret.

  1. NMR imaging in theory and in practice

    International Nuclear Information System (INIS)

    Taylor, D.G.; Inamdar, R.; Bushell, M.-C.

    1988-01-01

    This review, completed in 1988, covers basic theory, NMR imaging (selective excitation, image acquisition and reconstruction, spatial localisation of NMR parameters, factors affecting accuracy of NMR parameters, image quality considerations), and NMR imaging in clinical practice. The authors conclude that current NMR technology enables one to image the human body with a clarity matching x-ray CT, in terms of contrast differentiation in soft tissues being superior. (U.K.)

  2. NMR resonance assignments of NarE, a putative ADP-ribosylating toxin from Neisseria meningitidis

    OpenAIRE

    Carlier, Ludovic; Koehler, Christian; Veggi, Daniele; Pizza, Mariagrazia; Soriani, Marco; Boelens, Rolf; Bonvin, Alexandre M. J. J.

    2010-01-01

    NarE is a 16 kDa protein identified from Neisseria meningitidis, one of the bacterial pathogens responsible for meningitis. NarE belongs to the ADP-ribosyltransferase family and catalyses the transfer of ADP-ribose moieties to arginine residues in target protein acceptors. Many pathogenic bacteria utilize ADP-ribosylating toxins to modify and alter essential functions of eukaryotic cells. NarE was proposed to bind iron through a Fe–S center which is supposed to be implied in catalysis. We hav...

  3. NMR resonance assignments of NarE, a putative ADP-ribosylating toxin from Neisseria meningitidis

    NARCIS (Netherlands)

    Carlier, L.P.A.; Köhler, Christian; Veggi, D.; Pizza, M.; Soriani, M.; Boelens, R.; Bonvin, A.M.J.J.

    2011-01-01

    NarE is a 16 kDa protein identified from Neisseria meningitidis, one of the bacterial pathogens responsible for meningitis. NarE belongs to the ADP-ribosyltransferase family and catalyses the transfer of ADP-ribose moieties to arginine residues in target protein acceptors. Many pathogenic bacteria

  4. 1H and 15N NMR resonance assignments and secondary structure of titin type I domains

    Energy Technology Data Exchange (ETDEWEB)

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

    1997-01-15

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

  5. More General Optimal Offset Assignment

    Directory of Open Access Journals (Sweden)

    Sven Mallach

    2015-06-01

    Full Text Available This manuscript presents exact approaches to the general offset assignment problem arising in the address code generation phase of compilers for application-specific processors. First, integer programming models for architecture-dependent and theoretically motivated special cases of the problem are established. Then, these models are extended to provide the first widely applicable formulations for the most general problem setting, supporting processors with several address registers and complex addressing capabilities. Existing heuristics are similarly extended and practical applicability of the proposed methods is demonstrated by experimental evaluation using an established and large benchmark set. The experiments allow us to study the impact of exploiting more complex memory addressing capabilities on the address computation costs of real-world programs. We also show how to integrate operand reordering techniques for commutative instructions into existing solution approaches.

  6. The Random Quadratic Assignment Problem

    Science.gov (United States)

    Paul, Gerald; Shao, Jia; Stanley, H. Eugene

    2011-11-01

    The quadratic assignment problem, QAP, is one of the most difficult of all combinatorial optimization problems. Here, we use an abbreviated application of the statistical mechanics replica method to study the asymptotic behavior of instances in which the entries of at least one of the two matrices that specify the problem are chosen from a random distribution P. Surprisingly, the QAP has not been studied before using the replica method despite the fact that the QAP was first proposed over 50 years ago and the replica method was developed over 30 years ago. We find simple forms for C min and C max , the costs of the minimal and maximum solutions respectively. Notable features of our results are the symmetry of the results for C min and C max and their dependence on P only through its mean and standard deviation, independent of the details of P.

  7. Medical applications of NMR imaging and NMR spectroscopy with stable isotopes. Summary

    International Nuclear Information System (INIS)

    Matwiyoff, N.A.

    1983-01-01

    The current status of NMR imaging and NMR spectroscopy are summarized. For the most part examples from the March 1983 Puerto Rico symposium are used to illustrate the utility of NMR in medicine. 18 refs., 5 figs

  8. Medical applications of NMR imaging and NMR spectroscopy with stable isotopes. Summary

    Energy Technology Data Exchange (ETDEWEB)

    Matwiyoff, N.A.

    1983-01-01

    The current status of NMR imaging and NMR spectroscopy are summarized. For the most part examples from the March 1983 Puerto Rico symposium are used to illustrate the utility of NMR in medicine. 18 refs., 5 figs.

  9. Assignment Choice, Effort, and Assignment Completion: Does Work Ethic Predict Those Who Choose Higher-Effort Assignments?

    Science.gov (United States)

    Parkhurst, John T.; Fleisher, Matthew S.; Skinner, Christopher H.; Woehr, David J.; Hawthorn-Embree, Meredith L.

    2011-01-01

    After completing the Multidimensional Work-Ethic Profile (MWEP), 98 college students were given a 20-problem math computation assignment and instructed to stop working on the assignment after completing 10 problems. Next, they were allowed to choose to finish either the partially completed assignment that had 10 problems remaining or a new…

  10. Development and Investigation of NMR tools for chiral compound identification

    Energy Technology Data Exchange (ETDEWEB)

    Alam, Todd Michael [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electronic, Optical and Nano Materials; Lansdon, Rick [Oak Ridge Inst. for Science and Education (ORISE), Oak Ridge, TN (United States)

    2014-09-01

    The goal behind the assigned summer project was to investigate the ability of nuclear magnetic resonance spectroscopy (NMR) to identify enantiomers of select chiral organo-fluorophosphates (OFPs) compounds which are analogs of chemical warfare agents (CWAs, e.g. Sarin). This involved investigations utilizing chiral solvating agents (CSAs) and characterizing the binding phenomena with cyclodextrins. The resolution of OFPs enantiomers using NMR would be useful for research into toxicodynamics and toxicokinetics in biological systems due to the widely differing properties of the CWA enantiomers [1]. The optimization of decontamination abilities in the case of a CWA events, with this method’s potential rapidity and robustness, as well as the development of models correlating chiral compounds with CSAs for optimal resolution are all rational benefits of this research.

  11. Backbone resonance assignments of human cytosolic dNT-1 nucleotidase

    Czech Academy of Sciences Publication Activity Database

    Hnízda, Aleš; Skleničková, Radka; Pachl, Petr; Fábry, Milan; Tošner, Z.; Brynda, Jiří; Veverka, Václav

    2014-01-01

    Roč. 8, č. 2 (2014), s. 425-428 ISSN 1874-2718 R&D Projects: GA MŠk(CZ) LK11205; GA ČR GA203/09/0820 Institutional support: RVO:61388963 ; RVO:68378050 Keywords : 5 '-nucleotidase * haloacid dehalogenase superfamily * backbone assignments * NMR * perdeuterated protein * dimer * pyrimidine nucleotides Subject RIV: CE - Biochemistry; EB - Genetics ; Molecular Biology (UMG-J) Impact factor: 0.760, year: 2014

  12. (1)H, (13)C and (15)N resonance assignments of human FK506 binding protein 25.

    Science.gov (United States)

    Prakash, Ajit; Shin, Joon; Yoon, Ho Sup

    2015-04-01

    Human FKBP25, a nuclear protein, is a member of FK506 binding protein family (FKBP) and binds to immunosuppressive drugs such as FK506 and rapamycin. Human FKBP25 interacts with several nuclear proteins and regulates nuclear events. To understand the molecular basis of such interactions, we have performed NMR studies. Here, we report (1)H, (15)N and (13)C resonance assignments of the full-length human FKBP25 protein.

  13. 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

  14. 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

  15. Molecular dynamics of ethisterone studied by 1H NMR, IINS and quantum mechanical calculations

    International Nuclear Information System (INIS)

    Holderna-Natkaniec, Krystyna; Jurga, Kazimierz; Natkaniec, Ireneusz; Nowak, Dorota; Szyczewski, Andrzej

    2005-01-01

    The low frequency region in the generalized phonon density of states has been measured for ethisterone by means of neutron scattering. Assignment of the spectral features is facilitated by comparison with results from molecular simulations. The torsional out-of-plane modes of two methyl groups are separated. This finding is consistent with the results of 1 H NMR studies

  16. NMR study of 1,4-dihydropyridine derivatives endowed with long alkyl and functionalized chains

    International Nuclear Information System (INIS)

    Suarez, Margarita; Salfran, Esperanza; Rodriguez, Hortensia; Coro, Julieta; Molero, Dolores; Saez, Elena; Martinez-Alvarez, Roberto; Martin, Nazario

    2011-01-01

    The 1 H , 13 C and 15 N NMR spectroscopic data for 1,4-dihydropyridine endowed with long alkyl and functionalized chain on C-3 and C-5, have been fully assigned by combination of one- and two dimensional experiments (DEPT, HMBC, HMQC, COSY, nOe). (author)

  17. NMR, MP2 and DFT Study of Thiophenoxyketenimines (o-ThioSchiff bases)

    DEFF Research Database (Denmark)

    Saeed, Bahjat Ali; Elias, Rita Sabah; Kamounah, Fadhil S.

    2018-01-01

    Five new thiophenoxyketinimines have been synthesized. 1 H and 13 C NMR spectra as well as deuterium isotope effects on 13 C chemical shifts are determined, and spectra are assigned. DFT and MP2 calculations of both structures, chemical shifts, and isotope effects on chemical shifts are done. The...

  18. Characterization of bixin by LC-MS and LC-NMR.

    Science.gov (United States)

    Rehbein, Jens; Dietrich, Benjamin; Grynbaum, Marc David; Hentschel, Petra; Holtin, Karsten; Kuehnle, Maximilian; Schuler, Paul; Bayer, Marc; Albert, Klaus

    2007-10-01

    An overview upon modern analytical techniques for the isolation, separation, and structural identification of the essential bioactive carotenoid bixin is given. Isolation from biological matrices is performed by matrix solid phase dispersion (MSPD). The extract is separated with shape-selective C(30 )columns. Structural assignment of the separated compounds is done by online LC-MS and capillary HPLC-NMR.

  19. 1H, 13C, and 15N resonance assignments of the N-terminal domain of human TIG3.

    Science.gov (United States)

    Wang, Lei; Yu, Wenyu; Ren, Xiaobai; Lin, Jian; Jin, Changwen; Xia, Bin

    2012-10-01

    Human TIG3 protein is a member of H-REV107 protein family which belongs to the type II tumor suppressor family. TIG3 can induce apoptosis in cancer cells, and it also possesses Ca(2+)-independent phospholipase A(1/2) activity. The NMR assignments of the N-terminal domain of TIG3 are essential for its solution structure determination.

  20. Integrated assignment and path planning

    Science.gov (United States)

    Murphey, Robert A.

    2005-11-01

    A surge of interest in unmanned systems has exposed many new and challenging research problems across many fields of engineering and mathematics. These systems have the potential of transforming our society by replacing dangerous and dirty jobs with networks of moving machines. This vision is fundamentally separate from the modern view of robotics in that sophisticated behavior is realizable not by increasing individual vehicle complexity, but instead through collaborative teaming that relies on collective perception, abstraction, decision making, and manipulation. Obvious examples where collective robotics will make an impact include planetary exploration, space structure assembly, remote and undersea mining, hazardous material handling and clean-up, and search and rescue. Nonetheless, the phenomenon driving this technology trend is the increasing reliance of the US military on unmanned vehicles, specifically, aircraft. Only a few years ago, following years of resistance to the use of unmanned systems, the military and civilian leadership in the United States reversed itself and have recently demonstrated surprisingly broad acceptance of increasingly pervasive use of unmanned platforms in defense surveillance, and even attack. However, as rapidly as unmanned systems have gained acceptance, the defense research community has discovered the technical pitfalls that lie ahead, especially for operating collective groups of unmanned platforms. A great deal of talent and energy has been devoted to solving these technical problems, which tend to fall into two categories: resource allocation of vehicles to objectives, and path planning of vehicle trajectories. An extensive amount of research has been conducted in each direction, yet, surprisingly, very little work has considered the integrated problem of assignment and path planning. This dissertation presents a framework for studying integrated assignment and path planning and then moves on to suggest an exact

  1. Assigning historic responsibility for extreme weather events

    Science.gov (United States)

    Otto, Friederike E. L.; Skeie, Ragnhild B.; Fuglestvedt, Jan S.; Berntsen, Terje; Allen, Myles R.

    2017-11-01

    Recent scientific advances make it possible to assign extreme events to human-induced climate change and historical emissions. These developments allow losses and damage associated with such events to be assigned country-level responsibility.

  2. NMR-based milk metabolomics

    DEFF Research Database (Denmark)

    Sundekilde, Ulrik; Larsen, Lotte Bach; Bertram, Hanne Christine S.

    2013-01-01

    and processing capabilities of bovine milk is closely associated to milk composition. Metabolomics is ideal in the study of the low-molecular-weight compounds in milk, and this review focuses on the recent nuclear magnetic resonance (NMR)-based metabolomics trends in milk research, including applications linking...... the milk metabolite profiling with nutritional aspects, and applications which aim to link the milk metabolite profile to various technological qualities of milk. The metabolite profiling studies encompass the identification of novel metabolites, which potentially can be used as biomarkers or as bioactive...... compounds. Furthermore, metabolomics applications elucidating how the differential regulated genes affects milk composition are also reported. This review will highlight the recent advances in NMR-based metabolomics on milk, as well as give a brief summary of when NMR spectroscopy can be useful for gaining...

  3. Further development of deuterium NMR

    International Nuclear Information System (INIS)

    Al-azzawi, N.A.Y.

    1983-01-01

    In this work dichlorotris (triphenylphosphine) ruthenium (11) (RuCl 2 (PPh 3 ) 3 ) coupled with the deuterium source D 2 O was used as a catalyst for the study of the isotopic exchange reaction in alcohols and amines deuterium labelling of several primary and secondary alcohols have been made, and the position of labelling in the molecule was established by comparison of the 1 H NMR and 2 H NMR spectra while the relative distribution of deuterium was obtained from 2 H NMR spectrum. An oxidation-reduction mechanism was proposed for the hydrogen-deuterium exchange process, since in case of secondary alcohol the anticipated intermediate product (Ketone) was separated and identified. The relative distribution of deuterium was found to be time-dependent. Moreover the labelling in the B. Position was found to increase up on the addition of sodium hydroxide to the reaction mixture. 80 tabs.; 290 figs.; 124 refs

  4. Flow NMR of complex systems

    Energy Technology Data Exchange (ETDEWEB)

    Scheler, U.; Bagusat, F. [Leibniz-Inst. fuer Polymerforschung Dresden e.V., Dresden (Germany)

    2007-07-01

    A combination of NMR imaging and pulsed field gradient (PFG) NMR is applied to investigate flow. NMR longitudinal relaxation is used to generate contrast in a binary system of oil and water. The spatial distribution of each component and its flow pattern are measured separately. As a model a Couette cell with an additional area of high shear is used as model geometry. While a flat smooth interface is found at rest, the interface become bent under rotation, finally emulgation starts because of the velocity differences between the components. Flow from a submillimeter tube into a wide box and out of the box is investigated as well to understand shear-induced mixing and demixing. (orig.)

  5. Investigating sorption on iron-oxyhydroxide soil minerals by solid-state NMR spectroscopy: a 6Li MAS NMR study of adsorption and absorption on goethite

    DEFF Research Database (Denmark)

    Nielsen, Ulla Gro; Paik, Younkee; Julmis, Keinia

    2005-01-01

    High-resolution 2H MAS NMR spectra can be obtained for nanocrystalline particles of goethite (alpha-FeOOH, particle size approximately 4-10 nm) at room temperature, facilitating NMR studies of sorption under environmentally relevant conditions. Li sorption was investigated as a function of pH, th...... on the goethite surface. Even larger Li hyperfine shifts (289 ppm) were observed for Li+-exchanged goethite, which contains lithium ions in the tunnels of the goethite structure, confirming the Li assignment of the 145 ppm Li resonance to the surface sites. Udgivelsesdato: 2005-Oct-6...

  6. 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. Lexical Stress Assignment in Italian Developmental Dyslexia

    Science.gov (United States)

    Paizi, Despina; Zoccolotti, Pierluigi; Burani, Cristina

    2011-01-01

    Stress assignment to Italian polysyllabic words is unpredictable, because stress is neither marked nor predicted by rule. Stress assignment, especially to low frequency words, has been reported to be a function of stress dominance and stress neighbourhood. Two experiments investigate stress assignment in sixth-grade, skilled and dyslexic, readers.…

  8. Assigning Homework to Couples and Families

    Science.gov (United States)

    Dattilio, Frank M.; Dickson, Jan

    2007-01-01

    Homework assignments, or "out-of-session assignments," have gained popularity among couple and family therapists due to their potential to solidify the work achieved during the course of therapy and to help clients take responsibility for their own change. Homework assignments also serve as a testing ground in therapy to determine what works and…

  9. RFAC, a program for automated NMR R-factor estimation

    International Nuclear Information System (INIS)

    Gronwald, Wolfram; Kirchhoefer, Renate; Goerler, Adrian; Kremer, Werner; Ganslmeier, Bernhard; Neidig, Klaus-Peter; Kalbitzer, Hans Robert

    2000-01-01

    A computer program (RFAC) has been developed, which allows the automated estimation of residual indices (R-factors) for protein NMR structures and gives a reliable measure for the quality of the structures. The R-factor calculation is based on the comparison of experimental and simulated 1 H NOESY NMR spectra. The approach comprises an automatic peak picking and a Bayesian analysis of the data, followed by an automated structure based assignment of the NOESY spectra and the calculation of the R-factor. The major difference to previously published R-factor definitions is that we take the non-assigned experimental peaks into account as well. The number and the intensities of the non-assigned signals are an important measure for the quality of an NMR structure. It turns out that for different problems optimally adapted R-factors should be used which are defined in the paper. The program allows to compute a global R-factor, different R-factors for the intra residual NOEs, the inter residual NOEs, sequential NOEs, medium range NOEs and long range NOEs. Furthermore, R-factors can be calculated for various user defined parts of the molecule or it is possible to obtain a residue-by-residue R-factor. Another possibility is to sort the R-factors according to their corresponding distances. The summary of all these different R-factors should allow the user to judge the structure in detail. The new program has been successfully tested on two medium sized proteins, the cold shock protein (TmCsp) from Termotoga maritima and the histidine containing protein (HPr) from Staphylococcus carnosus. A comparison with a previously published R-factor definition shows that our approach is more sensitive to errors in the calculated structure

  10. NMR spectroscopic study and DFT calculations of GIAO NMR ...

    African Journals Online (AJOL)

    1H, 13C NMR chemical shifts and 1JCH coupling constants of danon have been calculated by means of B3LYP density functional method with 6-311++G(d,p) basis set. Comparison between the experimental and the theoretical results indicates that density functional B3LYP method is able to provide satisfactory results for ...

  11. 13C solid state NMR investigation of natural resins components

    International Nuclear Information System (INIS)

    Tavares, Maria I.B.; Bathista, Andre L.B.S.; Silva, Emerson O.; Priante Filho, Nicolau; Nogueira, Jose S.

    2001-01-01

    The objective of this work is to establish and analytical methodology as a routine using solid state nuclear magnetic resonance (NMR) techniques to investigate the mainly chemical components presented in natural resins in bulk. And also to evaluate the molecular behaviour of these resins. The routine solid state techniques allow us to assign the main compounds presented in the resins. Therefore, applying specialised techniques, like variable contact time, delayed contact time, dephasing time and proton spin lattice relaxation time in the rotating frame (T 1 H ρ), more information about chemical structure and molecular dynamic is available

  12. Push-through Direction Injectin NMR Automation

    Science.gov (United States)

    Nuclear magnetic resonance (NMR) and mass spectrometry (MS) are the two major spectroscopic techniques successfully used in metabolomics studies. The non-invasive, quantitative and reproducible characteristics make NMR spectroscopy an excellent technique for detection of endogeno...

  13. Developments in Solid-State NMR

    Indian Academy of Sciences (India)

    reso/020/11/1040-1052. Keywords. NMR; solid state; anisotropy; magic angle spinning dipolar coupling; quadrupolar coupling; chemical shift. Author Affiliations. K V Ramanathan1. NMR Research Center, Indian Institute of Science, Bengaluru ...

  14. Understanding NMR: self-learning manual

    International Nuclear Information System (INIS)

    Kastler, B.

    2000-01-01

    This initiation to the principles of nuclear magnetic resonance (NMR) imaging allows to understand the essential basic physical principles for the realization and the interpretation of an NMR examination. (J.S.)

  15. Influence of N-15 enrichment on neutronics, costs and C-14 production in nitride fuel cycle scenarios

    International Nuclear Information System (INIS)

    Wallenius, Janne; Arai, Yasuo; Minato, Kazuo

    2004-01-01

    The C-14 production for different closed fuel cycle scenarios has been investigated. If nitride fuel is used in fast reactors and ADSs dedicated to management of plutonium and minor actinides, an N-15 enrichment level of about 99% is required for the nitride cores to produce the same amount of C-14 as the oxide cores in the power park. The corresponding cost penalty for fuel fabrication is estimated to be larger than 25%. If reprocessing is included in the costs for fuel operations, the penalty is of the order of 5-10%, provided that a closed gas cycle is implemented for the fabrication. If nitride fuels are used only for minor actinide management in ADS, the required enrichment level is about 93%, and the cost penalty is less than 10%. (author)

  16. Biological nitrogen fixation by faba bean, pea and vetch, using isotopic techniques (N-15) and two reference crops

    International Nuclear Information System (INIS)

    Calvache, Marcelo; Bernal, Gustavo

    1991-01-01

    A field experiment was carried out on a Typic Dystrandept soil at Santa Catalina Experimental Station, Cutuglagua, Pichincha, Ecuador. The objectives were to quantify faba bean (Vicia faba) pea (Pisum sativum) and vetch (Vicia sativa) biological nitrogen fixation using N-15 isotopic technique and to evaluate suitability of reference crops for such quantification. Higher values of biological nitrogen fixation were obtained using maize (Zea mays L.) than using wheat (Triticum vurgare) as reference crops. The average values were 85 and 81 per cent for vetch; 73 and 69 per cent for faba bean; and 34 and 18 per cent for pea, respectively. It was assumed that nitrogen use efficiency should be the same for fixing and no fixing crop, but it was observed that a reference crop with low nitrogen use efficiency underestimates legume biological nitrogen fixation. Results suggest that greater caution is needed when selecting reference crops for legumes with low nitrogen fixation

  17. Bulk carbohydrate grain filling of barley ß-glucan mutants studied by 1H HR MAS NMR

    DEFF Research Database (Denmark)

    Seefeldt, Helene Fast; Larsen, Flemming Hofmann; Viereck, Nanna

    2008-01-01

    ) during grain filling. For the first time, 1H HR MAS NMR spectra of flour from immature barley seeds are analyzed. Spectral assignments are made using two-dimensional (2D) NMR methods. Both α- and β-glucan biosynthesis were characterized by inspection of the spectra as well as by calibration......Temporal and genotypic differences in bulk carbohydrate accumulation in three barley genotypes differing in the content of mixed linkage β-(1→3),(1→4)-D-glucan (β-glucan) and starch were investigated using proton high-resolution, magic angle spinning, nuclear magnetic resonance (1H HR MAS NMR...

  18. Fourier transform n.m.r. spectroscopy

    International Nuclear Information System (INIS)

    Shaw, D.

    1976-01-01

    This book is orientated to techniques rather than applications. The basic theory of n.m.r. is dealt with in a unified approach to the Fourier theory. The middle section of the book concentrates on the practical aspects of Fourier n.m.r., both instrumental and experimental. The final chapters briefly cover general application of n.m.r., but concentrate strongly on those areas where Fourier n.m.r. can give information which is not available by conventional techniques

  19. High resolution NMR theory and chemical applications

    CERN Document Server

    Becker, Edwin D

    1969-01-01

    High Resolution NMR: Theory and Chemical Applications focuses on the applications of nuclear magnetic resonance (NMR), as well as chemical shifts, lattices, and couplings. The book first offers information on the theory of NMR, including nuclear spin and magnetic moment, spin lattice relaxation, line widths, saturation, quantum mechanical description of NMR, and ringing. The text then ponders on instrumentation and techniques and chemical shifts. Discussions focus on the origin of chemical shifts, reference compounds, empirical correlations of chemical shifts, modulation and phase detection,

  20. 7-epi-griffonilide, a new lactone from Bauhinia pentandra: complete {sup 1}H and {sup 13}C chemical shift assignments

    Energy Technology Data Exchange (ETDEWEB)

    Almeida, Macia C.S. de; Souza, Luciana G.S.; Ferreira, Daniele A.; Pinto, Francisco C.L.; Santiago, Gilvandete M.P.; Monte, Francisco J.Q.; Lemos, Telma L.G., E-mail: fmonte@dqoi.ufc.br [Universidade Federal do Ceara (UFC), Fortaleza, CE (Brazil); Oliveira, Debora R. de; Braz-Filho, Raimundo [Universidade Federal Rural do Rio de Janeiro (UFRRJ), Seropedica, RJ (Brazil). Departamento de Quimica

    2017-09-01

    A new lactone, 7-epi-griffonilide (1), and six known compounds, 2, 3a - 3c, 4a and 4b, were isolated from the leaves of Bauhinia pentandra (Fabaceae). The structures elucidation of 1 and 2 were based on detailed 2D NMR techniques and spectral comparison with related compounds, leading to complete assignment of the {sup 1}H and {sup 13}C NMR spectra. (author)

  1. Authentication of animal origin of heparin and low molecular weight heparin including ovine, porcine and bovine species using 1D NMR spectroscopy and chemometric tools.

    Science.gov (United States)

    Monakhova, Yulia B; Diehl, Bernd W K; Fareed, Jawed

    2018-02-05

    High resolution (600MHz) nuclear magnetic resonance (NMR) spectroscopy is used to distinguish heparin and low-molecular weight heparins (LMWHs) produced from porcine, bovine and ovine mucosal tissues as well as their blends. For multivariate analysis several statistical methods such as principal component analysis (PCA), factor discriminant analysis (FDA), partial least squares - discriminant analysis (PLS-DA), linear discriminant analysis (LDA) were utilized for the modeling of NMR data of more than 100 authentic samples. Heparin and LMWH samples from the independent test set (n=15) were 100% correctly classified according to its animal origin. Moreover, by using 1 H NMR coupled with chemometrics and several batches of bovine heparins from two producers were differentiated. Thus, NMR spectroscopy combined with chemometrics is an efficient tool for simultaneous identification of animal origin and process based manufacturing difference in heparin products. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Structures of Biomolecules by NMR Spectroscopy

    Indian Academy of Sciences (India)

    IAS Admin

    solution makes NMR more suitable for studying the dynamic behavior of macromolecules. The first high resolution protein structure by NMR spectroscopy was carried out in mid-1980s [3]. Before the beginning of this millennium, NMR spectroscopy was limited to solving 3D struc- tures of proteins with molecular masses less ...

  3. Nitrogen content and delta N-15 of marine algae and associated waters of Maui, Hawaii, from 2012-07-28 to 2014-04-01 (NCEI Accession 0156294)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set includes nutrient data related to algal and water samples collected between 2012 and 2014 on Maui, Hawaii. Algal tissue N%, C:N ratios, and delta N-15...

  4. Polymers under mechanical stress- an NMR investigation

    Energy Technology Data Exchange (ETDEWEB)

    Boehme, Ute; Scheler, Ulrich [Leibniz Institute of Polymer Research Dresden (Germany); Xu, Bo; Leisen, Johannes; Beckham, Haskell W. [Georgia Institute of Technology, Atlanta, Georgia (United States)

    2010-07-01

    Low-field NMR using permanent magnets in Halbach arrangements permit NMR investigation without the limits present in high-field NMR. The lower field in conjunction with confined stray field permit the application of NMR, in particular relaxation NMR in a stretching apparatus and a rheometer. Crystalline and amorphous fraction of semi-crystalline polymers are distinguished by their transverse relaxation times. Upon mechanical load the relaxation times of the amorphous fraction changes as seen in in-situ measurements on polypropylene rods. During the formation of a neck the crystalline fraction becomes more prominent.

  5. Solid State NMR Studies of the Aluminum Hydride Phases

    Science.gov (United States)

    Hwang, Son-Jong; Bowman, R. C., Jr.; Graetz, Jason; Reilly, J. J.

    2006-01-01

    Several solid state NMR techniques including magic-angle-spinning (MAS) and multiple-quantum (MQ) MAS experiments have been used to characterize various AlH3 samples. MAS-NMR spectra for the 1H and 27Al nuclei have been obtained on a variety of AlH3 samples that include the (beta)- and (gamma)- phases as well as the most stable (alpha)-phase. While the dominant components in these NMR spectra correspond to the aluminum hydride phases, other species were found that include Al metal, molecular hydrogen (H2), as well as peaks that can be assigned to Al-O species in different configurations. The occurrence and concentration of these extraneous components are dependent upon the initial AlH3 phase composition and preparation procedures. Both the (beta)-AlH3 and (gamma)-AlH3 phases were found to generate substantial amounts of Al metal when the materials were stored at room temperature while the (alpha)-phase materials do not exhibit these changes.

  6. 1H NMR Fingerprinting of Soybean Extracts, with Emphasis on Identification and Quantification of Isoflavones

    Directory of Open Access Journals (Sweden)

    Vincenzo Brandolini

    2010-02-01

    Full Text Available 1H NMR spectra were recorded of methanolic extracts of seven soybean varieties (Glycine max., cultivated using traditional and organic farming techniques. It was possible to identify signals belonging to the groups of amino acids, carbohydrates, organic acids and aromatic substances in the spectra. In the aromatic zone, the isoflavone signals were of particular interest: genistein, daidzein, genistin, daidzin, malonylgenistin, acetylgenistin, malonyldaidzin signals were assigned and these compounds were quantified, resulting in accordance with published data, and further demonstrating the potential of the NMR technique in food science.

  7. Uniform and selective deuteration in two-dimensional NMR of proteins

    International Nuclear Information System (INIS)

    LeMaster, D.M.

    1990-01-01

    This paper reports on the practicality of isotopic labeling, particularly deuteration, that has received considerable impetus from advances in molecular biology, which have allowed ready production of NMR quantities of labeled proteins. Protein expression in Escherichia coli allows use of the considerable metabolic genetics known for the organism in shaping the biosynthetic process to meet the labeling demands of the NMR experiments. In addition to deuteration's common use in spectral assignment problems, it also offers considerable potential for enhancing the quality of the nuclear Overhauser effect (NOE) distance and dihedral angle constraints used for solution structural analysis of proteins. Recent reviews emphasize the sample preparation and spectral benefits of protein deuteration

  8. Theoretical and experimental NMR studies on muscimol from fly agaric mushroom (Amanita muscaria)

    Science.gov (United States)

    Kupka, Teobald; Wieczorek, Piotr P.

    2016-01-01

    In this article we report results of combined theoretical and experimental NMR studies on muscimol, the bioactive alkaloid from fly agaric mushroom (Amanita muscaria). The assignment of 1H and 13C NMR spectra of muscimol in DMSO-d6 was supported by additional two-dimensional heteronuclear correlated spectra (2D NMR) and gauge independent atomic orbital (GIAO) NMR calculations using density functional theory (DFT). The effect of solvent in theoretical calculations was included via polarized continuum model (PCM) and the hybrid three-parameter B3LYP density functional in combination with 6-311++G(3df,2pd) basis set enabled calculation of reliable structures of non-ionized (neutral) molecule and its NH and zwitterionic forms in the gas phase, chloroform, DMSO and water. GIAO NMR calculations, using equilibrium and rovibrationally averaged geometry, at B3LYP/6-31G* and B3LYP/aug-cc-pVTZ-J levels of theory provided muscimol nuclear magnetic shieldings. The theoretical proton and carbon chemical shifts were critically compared with experimental NMR spectra measured in DMSO. Our results provide useful information on its structure in solution. We believe that such data could improve the understanding of basic features of muscimol at atomistic level and provide another tool in studies related to GABA analogs.

  9. NMR imaging of human atherosclerosis

    International Nuclear Information System (INIS)

    Toussaint, J.F.

    1995-01-01

    Diagnosis and prognosis of atherosclerosis can no longer be evaluated with morphological parameters only. A description of atherosclerotic plaque composition is necessary to study the mechanisms of plaque rupture, which depends on collagenous cap and lipid core thicknesses. NMR, as a biochemical imaging technique, allows visualization of these components using T1 contrast (mobile lipids), T2 contrast (cap vs. core), spin density (calcifications), diffusion imaging, 1H and 13C spectroscopy. Today, these imaging sequences allow to study in vitro the effects of interventional techniques such as angioplasty or atherectomy. Clinical investigations begin, which will attempt to develop in vivo microscopy and test the ability of NMR to predict plaque rupture. (author). 13 refs., 7 figs

  10. Effect of Organic and Inorganic nitrogen Fertilizers on Salinity tolerance in Sorghum Plants Grown in sandy Soil Using N-15

    International Nuclear Information System (INIS)

    Ismail, M.M.

    2011-01-01

    A pot experiment was carried out in the green house to study the effect of compost, farmyard manure (FYM) and/or ammonium sulphate on salinity tolerance and nutrients-uptake by sorghum plants grown on sandy soil using N-15. Nitrogen was added at full dose of 100 mg N/kg soil. In general, dry matter accumulation as well as N, P and K-uptake by root and stalk of sorghum plants were significantly fluctuated between decrease and increase as influenced by the combined effect of water salinity levels and organic nitrogen source. The data showed that the application of organic sources decreased the adverse effect of salinity on dry matter yield of root and stalk of sorghum plants. The lowest dry matter yield was recorded when the plant received mineral fertilizer combined with irrigation of high concentration of diluted sea water. In the same time, root and stalk of sorghum plants were more dependent on N derived from organic sources than those derived from fertilizer. Fertilizer use efficiency (FUE %) was negatively affected by increasing water salinity levels under all treatments of organic and inorganic nitrogen fertilizer

  11. Biological nitrogen fixation in common beans(kidney); under fungicidal effects(vitavox), using N-15 isotopic methodology

    International Nuclear Information System (INIS)

    Gomez, Marco; Arahana, Venancio; Bernal, Gustavo

    1991-01-01

    This research was conducted in the EXPERIMENTAL EDUCATIONAL FIELD L a Tola , located in Tumbaco, Pichincha. The purpose was to evaluate the fixative efficiency of five strains of Rhizobium leguminosarum Bv. phaseoli under the effect of fungicidy, using the N-15 isotopic methodology. The experimental utilized desing was that of split plot with four replications. The area of the experimental plot in the assay was 2.4 Sq. m. (1.2 m x 2 m) and had three 0.60 m. appart furrows. The analized variables were: combined dry weight of stem and leaves and pods; total nitrogen of steam and leaves and pod; percentage and amount of fixed nitrogen (NFx per cent, QNFx); and the yield. The strains of greater nitrogen fixation were 1073 and 1020, with 40 NFx per cent and 31.0 kg NFx per ha. vitavax fungicidy had influence on all analized variables and did not affect the fixation of nitrogen of the strains for the yield of the Cargabello variety of bean

  12. 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…

  13. 7 CFR 784.15 - Assignments.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 7 2010-01-01 2010-01-01 false Assignments. 784.15 Section 784.15 Agriculture Regulations of the Department of Agriculture (Continued) FARM SERVICE AGENCY, DEPARTMENT OF AGRICULTURE SPECIAL PROGRAMS 2004 EWE LAMB REPLACEMENT AND RETENTION PAYMENT PROGRAM § 784.15 Assignments. Any person...

  14. 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

  15. 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…

  16. 24 CFR 221.770 - Assignment option.

    Science.gov (United States)

    2010-04-01

    ... MODERATE INCOME MORTGAGE INSURANCE-SAVINGS CLAUSE Contract Rights and Obligations-Moderate Income Projects... mortgagee's approved underwriter on or before November 30, 1983) has the option to assign, transfer and... direct the mortgagee to assign, transfer and deliver the original credit instrument, and the mortgage...

  17. Frequency assignment for satellite multilevel SCPC systems

    Science.gov (United States)

    Lau, Yuk-Hong; Skellern, D. J.

    1991-01-01

    A method for searching the frequency assignment for satellite multilevel SCPC systems is proposed based on the method for the case of equal carrier systems. The quality of assignment improves significantly on published results. The method requires only very short computations times.

  18. Solid-state NMR of inorganic semiconductors.

    Science.gov (United States)

    Yesinowski, James P

    2012-01-01

    Studies of inorganic semiconductors by solid-state NMR vary widely in terms of the nature of the samples investigated, the techniques employed to observe the NMR signal, and the types of information obtained. Compared with the NMR of diamagnetic non-semiconducting substances, important differences often result from the presence of electron or hole carriers that are the hallmark of semiconductors, and whose theoretical interpretation can be involved. This review aims to provide a broad perspective on the topic for the non-expert by providing: (1) a basic introduction to semiconductor physical concepts relevant to NMR, including common crystal structures and the various methods of making samples; (2) discussions of the NMR spin Hamiltonian, details of some of the NMR techniques and strategies used to make measurements and theoretically predict NMR parameters, and examples of how each of the terms in the Hamiltonian has provided useful information in bulk semiconductors; (3) a discussion of the additional considerations needed to interpret the NMR of nanoscale semiconductors, with selected examples. The area of semiconductor NMR is being revitalized by this interest in nanoscale semiconductors, the great improvements in NMR detection sensitivity and resolution that have occurred, and the current interest in optical pumping and spintronics-related studies. Promising directions for future research will be noted throughout.

  19. [Adenovirus-mediated killing of hepatocellular carcinoma HepG2 cells by heterogeneous fusion gene NT4p53(N15)Ant].

    Science.gov (United States)

    Li, Yue-ping; Qiu, Shu-dong; Song, Li-ping; Wang, Quan-ying; Yang, Guang-xiao

    2007-07-01

    OBJECTIVE To construct a recombinant adenovirus Ad.NT4p53(N15)Ant and explore its cytotoxic effect against hepatocellular carcinoma HepG2 cells in vitro. The recombinant adenovirus containing the fusion gene of neurotrophin 4 (NT4)signal peptide, N-terminal residues (12-26) of p53 and 17 amino acid Drosophila homeobox protein Antennapedia (Ant) was constructed by gene cloning protocol. The effect of this fusion gene on HepG2 cells was evaluated by MTT assay, PI staining and flow cytometry. The fusion gene Ad.NT4p53(N15)Ant was successfully constructed, as verified by restriction endonuclease digestion and PCR. Ad.NT4p53(N15)Ant could strongly suppress the growth of HepG2 cells (with a growth inhibition rate of 63.3% 48 h after infection) without affecting NIH-3T3 cells. Flow cytometry showed that Ad.NT4p53(N15)Ant could induce obvious apoptosis of HepG2 cells. The recombinant adenovirus containing NT4p53(N15)Ant fusion gene can inhibit the growth the of HepG2 cells in vitro partially by inducing cell apoptosis.

  20. 1H, 13C, and 15N resonance assignments for human regenerating family Iα protein.

    Science.gov (United States)

    Ho, Meng-Ru; Chen, Chinpan

    2012-10-01

    Human regenerating (Reg) genes belong to the C-type lectin superfamily and express secretory proteins in various tissues. Reg Iα, also named lithostathine, has multiple roles in numerous biological events such as cytokines, anti-apoptotic factors and the calcium carbonate crystals inhibitor. Under physiological pH, Reg Iα becomes largely insoluble after a self-proteolysis process, and the N-terminally truncated form readily polymerizes into fibrils, which leads to neurodegenerative diseases. Reg Iα may form protofibril via lateral hydrophobic interactions with a native-like conformation. The structural basis from the native to fibril form, as well as the carbohydrate binding sites on Reg Iα, remain unknown. Here we present the NMR backbone and side-chain assignments of Reg Iα for use in further NMR investigations.

  1. Optimal processor assignment for pipeline computations

    Science.gov (United States)

    Nicol, David M.; Simha, Rahul; Choudhury, Alok N.; Narahari, Bhagirath

    1991-01-01

    The availability of large scale multitasked parallel architectures introduces the following processor assignment problem for pipelined computations. Given a set of tasks and their precedence constraints, along with their experimentally determined individual responses times for different processor sizes, find an assignment of processor to tasks. Two objectives are of interest: minimal response given a throughput requirement, and maximal throughput given a response time requirement. These assignment problems differ considerably from the classical mapping problem in which several tasks share a processor; instead, it is assumed that a large number of processors are to be assigned to a relatively small number of tasks. Efficient assignment algorithms were developed for different classes of task structures. For a p processor system and a series parallel precedence graph with n constituent tasks, an O(np2) algorithm is provided that finds the optimal assignment for the response time optimization problem; it was found that the assignment optimizing the constrained throughput in O(np2log p) time. Special cases of linear, independent, and tree graphs are also considered.

  2. Dynamic pulsed-field-gradient NMR

    CERN Document Server

    Sørland, Geir Humborstad

    2014-01-01

    Dealing with the basics, theory and applications of dynamic pulsed-field-gradient NMR NMR (PFG NMR), this book describes the essential theory behind diffusion in heterogeneous media that can be combined with NMR measurements to extract important information of the system being investigated. This information could be the surface to volume ratio, droplet size distribution in emulsions, brine profiles, fat content in food stuff, permeability/connectivity in porous materials and medical applications currently being developed. Besides theory and applications it will provide the readers with background knowledge on the experimental set-ups, and most important, deal with the pitfalls that are numerously present in work with PFG-NMR. How to analyze the NMR data and some important basic knowledge on the hardware will be explained, too.

  3. The Assignment Game : The Reduced Game

    OpenAIRE

    Guillermo OWEN

    1992-01-01

    Let v be an assignment game. For a given reference payoff vector (x; y), and a coalition S, bargaining within the coalition can be represented by either the reduced game or the derived game. It is known that the reduced game need not be an assignment game (in fact, it need not be super additive) while the derived game is another assignment game, with modified reservation prices. We prove that, when the reference vector is in the core of the game, the derived game is the super additive cover o...

  4. Comprehensive NMR analysis of compositional changes of black garlic during thermal processing.

    Science.gov (United States)

    Liang, Tingfu; Wei, Feifei; Lu, Yi; Kodani, Yoshinori; Nakada, Mitsuhiko; Miyakawa, Takuya; Tanokura, Masaru

    2015-01-21

    Black garlic is a processed food product obtained by subjecting whole raw garlic to thermal processing that causes chemical reactions, such as the Maillard reaction, which change the composition of the garlic. In this paper, we report a nuclear magnetic resonance (NMR)-based comprehensive analysis of raw garlic and black garlic extracts to determine the compositional changes resulting from thermal processing. (1)H NMR spectra with a detailed signal assignment showed that 38 components were altered by thermal processing of raw garlic. For example, the contents of 11 l-amino acids increased during the first step of thermal processing over 5 days and then decreased. Multivariate data analysis revealed changes in the contents of fructose, glucose, acetic acid, formic acid, pyroglutamic acid, cycloalliin, and 5-(hydroxymethyl)furfural (5-HMF). Our results provide comprehensive information on changes in NMR-detectable components during thermal processing of whole garlic.

  5. Alternating spin chain compound AgVOAsO4 probed by 75As NMR

    Science.gov (United States)

    Ahmed, N.; Khuntia, P.; Ranjith, K. M.; Rosner, H.; Baenitz, M.; Tsirlin, A. A.; Nath, R.

    2017-12-01

    75As NMR measurements were performed on a polycrystalline sample of spin-1/2 alternating spin chain Heisenberg antiferromagnet AgVOAsO4. The temperature-dependent NMR shift K (T ) , which is a direct measure of the intrinsic spin susceptibility, agrees very well with the spin-1/2 alternating-chain model, justifying the assignment of the spin lattice. From the analysis of K (T ) , magnetic exchange parameters were estimated as follows: the leading exchange J /kB≃38.4 K and the alternation ratio α =J'/J ≃0.69 . The transferred hyperfine coupling between the 75As nucleus and V4 + spins obtained by comparing the NMR shift with the bulk susceptibility amounts to Ahf≃3.3 TμB. The effect of interchain couplings on the low-temperature activated behavior of K (T ) and the spin-lattice relaxation rate 1 /T1 is identified.

  6. Solid-state NMR studies of form I of atorvastatin calcium.

    Science.gov (United States)

    Wang, Wei David; Gao, Xudong; Strohmeier, Mark; Wang, Wei; Bai, Shi; Dybowski, Cecil

    2012-03-22

    Solid-state (13)C, (19)F, and (15)N magic angle spinning NMR studies of Form I of atorvastatin calcium are reported, including chemical shift tensors of all resolvable carbon sites and fluorine sites. The complete (13)C and (19)F chemical shift assignments are given based on an extensive analysis of (13)C-(1)H HETCOR and (13)C-(19)F HETCOR results. The solid-state NMR data indicate that the asymmetric unit of this material contains two atorvastatin molecules. A possible structure of Form I of atorvastatin calcium (ATC-I), derived from solid-state NMR data and density functional theory calculations of various structures, is proposed for this important active pharmaceutical ingredient (API).

  7. Identification of phosphorylethanolamine in 31P-NMR spectra of human peripheral blood lymphocytes.

    Science.gov (United States)

    Petersen, A; Hørder, M; Jacobsen, J P

    1986-10-10

    The 31P-NMR spectrum of intact human peripheral blood lymphocytes contains a large unidentified peak in the phosphomonoester region. The pH dependency of the 31P-NMR chemical shift of this peak in perchloric acid extracts of peripheral blood lymphocytes was recorded. It was compared to the pH dependency of the chemical shift of phosphorylethanolamine, phosphorylcholine, and ribose 5-phosphate in model solutions. An excellent agreement was found between the behavior of phosphorylethanolamine and the unidentified peak. To further substantiate this assignment phosphorylethanolamine was added to extracts and the pH titrations were repeated. The added phosphorylethanolamine gave exactly the same chemical shift as the unidentified peak and no difference was observed with pH titrations. The concentration of phosphorylethanolamine in human peripheral blood lymphocytes was estimated by 31P NMR to be 2.4 mumol/10(9) cells (range 0.9-4.3/10(9) cells, n = 4).

  8. An Inversion Recovery NMR Kinetics Experiment

    OpenAIRE

    Williams, Travis J.; Kershaw, Allan D.; Li, Vincent; Wu, Xinping

    2011-01-01

    A convenient laboratory experiment is described in which NMR magnetization transfer by inversion recovery is used to measure the kinetics and thermochemistry of amide bond rotation. The experiment utilizes Varian spectrometers with the VNMRJ 2.3 software, but can be easily adapted to any NMR platform. The procedures and sample data sets in this article will enable instructors to use inversion recovery as a laboratory activity in applied NMR classes and provide research students with a conveni...

  9. Fourier Analysis and Structure Determination. Part II: Pulse NMR and NMR Imaging.

    Science.gov (United States)

    Chesick, John P.

    1989-01-01

    Uses simple pulse NMR experiments to discuss Fourier transforms. Studies the generation of spin echoes used in the imaging procedure. Shows that pulse NMR experiments give signals that are additions of sinusoids of differing amplitudes, frequencies, and phases. (MVL)

  10. Solution NMR structure determination of proteins revisited

    International Nuclear Information System (INIS)

    Billeter, Martin; Wagner, Gerhard; Wuethrich, Kurt

    2008-01-01

    This 'Perspective' bears on the present state of protein structure determination by NMR in solution. The focus is on a comparison of the infrastructure available for NMR structure determination when compared to protein crystal structure determination by X-ray diffraction. The main conclusion emerges that the unique potential of NMR to generate high resolution data also on dynamics, interactions and conformational equilibria has contributed to a lack of standard procedures for structure determination which would be readily amenable to improved efficiency by automation. To spark renewed discussion on the topic of NMR structure determination of proteins, procedural steps with high potential for improvement are identified

  11. NMR spectroscopy using liquid crystal solvents

    CERN Document Server

    Emsley, JW

    2013-01-01

    NMR Spectroscopy using Liquid Crystal Solvents covers the importance of using a liquid crystal solvent in NMR to derive nuclear dipolar spin-spin coupling constants. This book is composed of ten chapters, and begins with a brief description of the features and benefits of liquid crystal in NMR spectroscopic analysis. The succeeding chapters deal with the mode of operation of nuclear spin Hamiltonian for partially oriented molecules and the analysis of NMR spectra of partially oriented molecules, as well as the determination of rigid molecule structure. These topics are followed by discussions

  12. NMR in structure-based drug design.

    Science.gov (United States)

    Carneiro, Marta G; Ab, Eiso; Theisgen, Stephan; Siegal, Gregg

    2017-11-08

    NMR spectroscopy is a powerful technique that can provide valuable structural information for drug discovery endeavors. Here, we discuss the strengths (and limitations) of NMR applications to structure-based drug discovery, highlighting the different levels of resolution and throughput obtainable. Additionally, the emerging field of paramagnetic NMR in drug discovery and recent developments in approaches to speed up and automate protein-observed NMR data collection and analysis are discussed. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  13. NMR characterization of pituitary tumors

    International Nuclear Information System (INIS)

    Osbakken, M.; Gonzales, J.; Page, R.

    1984-01-01

    Twelve patients (5 male, 7 female, mean age 37.9 +- 20) with pituitary tumors were extensively evaluated with NMR imaging using a 1.5K gauss resistive magnet. Saturation recovery (SR), inversion recovery (IR) and spin echo (SE) pulse sequences were used for qualitative characterization of the lesions. T/sub 1/ calculations were also performed for brain and pituitary. Tumor histology and endocrine status were correlated with NMR data. All tumors were large with suprasellar extension (6 with prolactin secretion, 6 without). Pituitary T/sub 1/'s ranged from .2 to .64, the mean T/sub 1/ being longer than that of brain (Brain = .4 +- .04; Pit = .48 +- .14). 3 patients with histological evidence of homogeneous adenomas had long T/sub 1/'s (0.58 +- .05). 3 patients with evidence of recent or old hemorhage into the pituitary had much shorter T/sub 1/'s (0.29 +- .12). There was no relationship between prolactin secretion and T/sub 1/. Qualitative T/sub 1/ and T/sub 2/ information can be obtained by using a combination of SR, IR, and SE images. Using this method in the patients, homogeneous adenomas had similar T/sub 1/'s and longer T/sub 2/'s compared to the brain, while patients with bleeds had shorter T/sub 1/'s and T/sub 2/'s. Image T/sub 1/ characteristics correlated well with the calculated T/sub 1/ values. The range of T/sub 1/ (and potentially T/sub 2/) values which occur in apparently similar lesions are most likely due to anatomical and pathophysiological variations in these lesions. It may be ultimately possible to separate different types of pathological processes based on NMR image T/sub 1/ and T/sub 2/ characteristics after careful comparative studies of NMR and histological data are completed. The combination of calculated T/sub 1/ and T/sub 2/ with image T/sub 1/ and T/sub 2/ information may also be useful in further characterization of lesions

  14. Investigating the reactivity of pMDI with wood cell walls using high-resolution solution-state NMR spectroscopy

    Science.gov (United States)

    Daniel J. Yelle; John Ralph; Charles R. Frihart

    2009-01-01

    The objectives of this study are the following: (1) Use solution-state NMR to assign contours in HSQC spectra of the reaction products between pMDI model compounds and: (a) lignin model compounds, (b) milled-wood lignin, (c) ball-milled wood, (d) microtomed loblolly pine; (2) Determine where and to what degree urethane formation occurs with loblolly pine cell wall...

  15. Inositol phosphates from barley low-phytate grain mutants analysed by metal-dye detection HPLC and NMR

    DEFF Research Database (Denmark)

    Hatzack, F.; Hübel, F.; Zhang, W.

    2001-01-01

    Inositolphosphates from barley low-phytate grain mutants and their parent variety were analysed by metal-dye detection HPLC and NMR. Compound assignment was carried out by comparison of retention times using a chemical hydrolysate of phytate [Ins(1,2,3,4,5,6)P(6)] as a reference; Co...

  16. Homework assignments in couple and family therapy.

    Science.gov (United States)

    Dattilio, Frank M

    2002-05-01

    Homework has been cited as an integral part of a number of theoretical orientations and therapy formats; unfortunately, very little has been written about its use with couples and families. This is despite the fact that many couple and family therapists espouse the use of homework or out-of-session assignments in order to help the effects of therapy jell. This article reviews some of the empirical literature on homework assignments and their effectiveness in the domain of therapy for families and couples. It also highlights the effectiveness of and the need for out-of-session assignments in treatment. A case illustration is used to demonstrate how homework assignments may be used as a significant change agent in couple and family treatment. Copyright 2002 Wiley Periodicals, Inc.

  17. 12 CFR 25.28 - Assigned ratings.

    Science.gov (United States)

    2010-01-01

    ... of discriminatory or other illegal credit practices in any geography by the bank or in any assessment...) of this section on the bank's assigned rating, the OCC considers the nature, extent, and strength of...

  18. 12 CFR 228.28 - Assigned ratings.

    Science.gov (United States)

    2010-01-01

    ... evidence of discriminatory or other illegal credit practices in any geography by the bank or in any... described in paragraph (c)(1) of this section on the bank's assigned rating, the Board considers the nature...

  19. 12 CFR 345.28 - Assigned ratings.

    Science.gov (United States)

    2010-01-01

    ... credit practices in any geography by the bank or in any assessment area by any affiliate whose loans have... section on the bank's assigned rating, the FDIC considers the nature, extent, and strength of the evidence...

  20. 12 CFR 563e.28 - Assigned ratings.

    Science.gov (United States)

    2010-01-01

    ... practices in any geography by the savings association or in any assessment area by any affiliate whose loans...) of this section on the savings association's assigned rating, the OTS considers the nature, extent...

  1. Genetic algorithms for air traffic assignment

    OpenAIRE

    Delahaye , Daniel; Alliot , Jean-Marc; Schoenauer , Marc; Farges , Jean-Loup

    1994-01-01

    International audience; In this paper, we show how genetic algorithms can be used to compute automatically a traffic assignment of aircraft on the air network to increase Air Traffic Control capacity in high density areas.

  2. 12C/13C and 14N/15N isotopic ratios in HCN in the middle atmosphere of Titan from Cassini/CIRS data

    Science.gov (United States)

    Mathé, Christophe; Vinatier, Sandrine; Bézard, Bruno; Nixon, Conor A.

    2017-10-01

    Our study aims at constraining the 12C/13C and 14N/15N isotopic ratios in HCN, the most abundant nitrile in Titan’s atmosphere, which can provide information on physical and chemical process occurring during the formation and/or destruction of this molecule.Over the last decade, several estimations of the 12C/13C and 14N/15N isotopic ratios in HCN were performed from ground-based, Herschel and Cassini observations (Bézard et al,2014). The 14N/15N ratio lies in the range 56-76, which corresponds to half of the 14N/15N ratio in N2 (major N-bearing molecule in Titan’s atmosphere). This nitrogen isotopic fractionation mostly originates from the photodissociation of N2 (Liang et al, 2007). The 12C/13C ratio lies in the range 75-108, in agreement with the 12C/13C ratio in CH4 (major C-bearing molecule). Recent disk-averaged ALMA observations indicate 12C/13C and 14N/15N ratios equal to ˜90 and ˜72, respectively (Molter et al, 2016).Vinatier et al (2007) derived 14N/15N and 12C/13C ratios in two different regions (equator and north pole) from Cassini/CIRS (Composite InfraRed Spectrometer) observations at the beginning of the Cassini mission. 14N/15N was similar for both latitudes while the 12C/13C ratio displayed a possible enhancement at the equator.We present here a new study of the 12C/13C and 14N/15N isotopic ratios in HCN from CIRS. We analyzed limb observations (0.5 cm-1 resolution) from northern winter to early spring at poles, mid-latitudes and equator in order to investigate potential spatial and seasonal changes of these isotopic ratios in Titan’s middle atmosphere. These preliminary results will be presented and compared with previous observations.References:Bézard et al., Cambrigde University Press, 2014Liang et al., The Astrophysical Jounral Letters, 2007Molter et al., The Astronomical Journal, 2016Vinatier et al., Icarus, 2007

  3. Changes in mechanical properties of the OKh16N15M3B steel in the temperature range of radiation-induced swelling

    International Nuclear Information System (INIS)

    Neustroev, V.S.; Golovanov, V.N.; Povstyanko, A.V.; Shamardin, V.K.

    1986-01-01

    Presented are the results of investigations of both swelling and mechanical properties of the fuel element cans of BOR-60 reactor of the 0Kh16N15M3B steel after austenitization. The dose-temperature dependences have been plotted swelling and radiation-induced porosity parameters as well as for mechanical properties of the above steel. Interpretation of changes in some 0Kh16N15M3B steel mechanical properties with dose and temperature has been proposed based on Orovan's mechanism and on that for crack nucleation with voids present

  4. 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

  5. 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...

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

    Science.gov (United States)

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

    2012-10-01

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

  7. 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.

  8. Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR

    NARCIS (Netherlands)

    Van Der Schot, Gijs; Bonvin, Alexandre M J J

    We present here the performance of the WeNMR CS-Rosetta3 web server in CASD-NMR, the critical assessment of automated structure determination by NMR. The CS-Rosetta server uses only chemical shifts for structure prediction, in combination, when available, with a post-scoring procedure based on

  9. Access to NMR Spectroscopy for Two-Year College Students: The NMR Site at Trinity University

    Science.gov (United States)

    Mills, Nancy S.; Shanklin, Michael

    2011-01-01

    Students at two-year colleges and small four-year colleges have often obtained their exposure to NMR spectroscopy through "canned" spectra because the cost of an NMR spectrometer, particularly a high-field spectrometer, is prohibitive in these environments. This article describes the design of a NMR site at Trinity University in which…

  10. ABACUS, a direct method for protein NMR structure computation via assembly of fragments.

    Science.gov (United States)

    Grishaev, A; Steren, C A; Wu, B; Pineda-Lucena, A; Arrowsmith, C; Llinás, M

    2005-10-01

    The ABACUS algorithm obtains the protein NMR structure from unassigned NOESY distance restraints. ABACUS works as an integrated approach that uses the complete set of available NMR experimental information in parallel and yields spin system typing, NOE spin pair identities, sequence specific resonance assignments, and protein structure, all at once. The protocol starts from unassigned molecular fragments (including single amino acid spin systems) derived from triple-resonance (1)H/(13)C/(15)N NMR experiments. Identifications of connected spin systems and NOEs precede the full sequence specific resonance assignments. The latter are obtained iteratively via Monte Carlo-Metropolis and/or probabilistic sequence selections, molecular dynamics structure computation and BACUS filtering (A. Grishaev and M. Llinás, J Biomol NMR 2004;28:1-10). ABACUS starts from scratch, without the requirement of an initial approximate structure, and improves iteratively the NOE identities in a self-consistent fashion. The procedure was run as a blind test on data recorded on mth1743, a 70-amino acid genomic protein from M. thermoautotrophicum. It converges to a structure in ca. 15 cycles of computation on a 3-GHz processor PC. The calculated structures are very similar to the ones obtained via conventional methods (1.22 A backbone RMSD). The success of ABACUS on mth1743 further validates BACUS as a NOESY identification protocol. (c) 2005 Wiley-Liss, Inc.

  11. 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. NMR studies of oriented molecules

    Energy Technology Data Exchange (ETDEWEB)

    Sinton, S.W.

    1981-11-01

    Deuterium and proton magnetic resonance are used in experiments on a number of compounds which either form liquid crystal mesophases themselves or are dissolved in a liquid crystal solvent. Proton multiple quantum NMR is used to simplify complicated spectra. The theory of nonselective multiple quantum NMR is briefly reviewed. Benzene dissolved in a liquid crystal are used to demonstrate several outcomes of the theory. Experimental studies include proton and deuterium single quantum (..delta..M = +-1) and proton multiple quantum spectra of several molecules which contain the biphenyl moiety. 4-Cyano-4'-n-pentyl-d/sub 11/-biphenyl (5CB-d/sub 11/) is studied as a pure compound in the nematic phase. The obtained chain order parameters and dipolar couplings agree closely with previous results. Models for the effective symmetry of the biphenyl group in 5CB-d/sub 11/ are tested against the experimental spectra. The dihedral angle, defined by the planes containing the rings of the biphenyl group, is found to be 30 +- 2/sup 0/ for 5DB-d/sub 11/. Experiments are also described for 4,4'-d/sub 2/-biphenyl, 4,4' - dibromo-biphenyl, and unsubstituted biphenyl.

  13. New techniques in NMR spectroscopy

    International Nuclear Information System (INIS)

    Hughes, C.E.

    1998-10-01

    In 1989, Soerensen introduced a method, the unitary bound, for calculating the maximum efficiencies of coherence transfer processes in NMR. This thesis applies this method to quadrupolar nuclei, an area not investigated by Soerensen. In doing so, several questions are raised, and answered, as to the implications of the unitary bound for coherence transfer processes in all areas of NMR. These include discussions of when such processes can be reversed without loss of signal and when sequential coherence transfer steps can be carried out with both steps having the maximum efficiency. One area of NMR of quadrupolar nuclei which has attracted some interest over the past few years has been the selective excitation of 23 Na nuclei in ordered environments. This was hinted at by Jaccard et al. in 1986 and demonstrated in biological systems by Eliav et al. in 1992, who achieved the selective excitation using a double-quantum filtration (DQF) experiment. The following year, Kemp-Harper and Wimperis demonstrated that the Jeener-Broekaert experiment could be used to achieve the same selectivity through excitation of quadrupolar order. The unitary bound shows that neither of these experiments achieve the maximum coherence transfer efficiency. This thesis sets out to improve upon the efficiency of these two experiments. Two multiple-pulse experiments are investigated. One seeks to improve upon the efficiency of the Jeener-Broekaert experiment for spin I = 3/2 nuclei by 33% to achieve the unitary bound efficiency. The other seeks to improve the efficiency of the selective DQF experiment by 41% to achieve the bound for spin I= 3/2 nuclei. 23 Na NMR spectra of cartilage and a lyotropic liquid crystal are presented which show that, although the new version of the Jeener-Broekaert experiment achieves no greater efficiency in practical application than the original, the new DQF experiment produces up to half of the expected improvement in efficiency. Alternative techniques to the

  14. FLAMEnGO 2.0: an enhanced fuzzy logic algorithm for structure-based assignment of methyl group resonances.

    Science.gov (United States)

    Chao, Fa-An; Kim, Jonggul; Xia, Youlin; Milligan, Michael; Rowe, Nancy; Veglia, Gianluigi

    2014-08-01

    We present an enhanced version of the FLAMEnGO (Fuzzy Logic Assignment of Methyl Group) software, a structure-based method to assign methyl group resonances in large proteins. FLAMEnGO utilizes a fuzzy logic algorithm coupled with Monte Carlo sampling to obtain a probability-based assignment of the methyl group resonances. As an input, FLAMEnGO requires either the protein X-ray structure or an NMR structural ensemble including data such as methyl-methyl NOESY, paramagnetic relaxation enhancement (PRE), methine-methyl TOCSY data. Version 2.0 of this software (FLAMEnGO 2.0) has a user-friendly graphic interface and presents improved modules that enable the input of partial assignments and additional NMR restraints. We tested the performance of FLAMEnGO 2.0 on maltose binding protein (MBP) as well as the C-subunit of the cAMP-dependent protein kinase A (PKA-C). FLAMEnGO 2.0 can be used as a standalone method or to assist in the completion of partial resonance assignments and can be downloaded at www.chem.umn.edu/groups/veglia/forms/flamengo2-form.html. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. Physician in Triage Versus Rotational Patient Assignment.

    Science.gov (United States)

    Traub, Stephen J; Bartley, Adam C; Smith, Vernon D; Didehban, Roshanak; Lipinski, Christopher A; Saghafian, Soroush

    2016-05-01

    Physician in triage and rotational patient assignment are different front-end processes that are designed to improve patient flow, but there are little or no data comparing them. To compare physician in triage with rotational patient assignment with respect to multiple emergency department (ED) operational metrics. Design-Retrospective cohort review. Patients-Patients seen on 23 days on which we utilized a physician in triage with those patients seen on 23 matched days when we utilized rotational patient assignment. There were 1,869 visits during physician in triage and 1,906 visits during rotational patient assignment. In a simple comparison, rotational patient assignment was associated with a lower median length of stay (LOS) than physician in triage (219 min vs. 233 min; difference of 14 min; 95% confidence interval [CI] 5-27 min). In a multivariate linear regression incorporating multiple confounders, there was a nonsignificant reduction in the geometric mean LOS in rotational patient assignment vs. physician in triage (204 min vs. 217 min; reduction of 6.25%; 95% CI -3.6% to 15.2%). There were no significant differences between groups for left before being seen, left subsequent to being seen, early (within 72 h) returns, early returns with admission, or complaint ratio. In a single-site study, there were no statistically significant differences in important ED operational metrics between a physician in triage model and a rotational patient assignment model after adjusting for confounders. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. Flexible taxonomic assignment of ambiguous sequencing reads

    Directory of Open Access Journals (Sweden)

    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.

  17. Spin Choreography: Basic Steps in High Resolution NMR (by Ray Freeman)

    Science.gov (United States)

    Minch, Michael J.

    1998-02-01

    There are three orientations that NMR courses may take. The traditional molecular structure course focuses on the interpretation of spectra and the use of chemical shifts, coupling constants, and nuclear Overhauser effects (NOE) to sort out subtle details of structure and stereochemistry. Courses can also focus on the fundamental quantum mechanics of observable NMR parameters and processes such a spin-spin splitting and relaxation. More recently there are courses devoted to the manipulation of nuclear spins and the basic steps of one- and two-dimensional NMR experiments. Freeman's book is directed towards the latter audience. Modern NMR methods offer a myriad ways to extract information about molecular structure and motion by observing the behavior of nuclear spins under a variety of conditions. In Freeman's words: "We can lead the spins through an intricate dance, carefully programmed in advance, to enhance, simplify, correlate, decouple, edit or assign NMR spectra." This is a carefully written, well-illustrated account of how this dance is choreographed by pulse programming, double resonance, and gradient effects. Although well written, this book is not an easy read; every word counts. It is recommended for graduate courses that emphasize the fundamentals of magnetic resonance. It is not a text on interpretation of spectra.

  18. Assessment of structural changes of human teeth by low-field nuclear magnetic resonance (NMR)

    International Nuclear Information System (INIS)

    Ni, Qingwen; Chen, Shuo

    2010-01-01

    A technique of low-field pulsed proton nuclear magnetic resonance (NMR) spin relaxation is described for assessment of age-related structural changes (dentin and pulp) of human teeth in vitro. The technique involves spin–spin relaxation measurement and inversion spin–spin spectral analysis methods. The spin–spin relaxation decay curve is converted into a T 2 distribution spectrum by a sum of single exponential decays. The NMR spectra from the extracted dentin-portion-only and dental pulp-cells-only were compared with the whole extracted teeth spectra, for the dentin and pulp peak assignments. While dentin and pulp are highly significant parameters in determining tooth quality, variations in these parameters with age can be used as an effective tool for estimating tooth quality. Here we propose an NMR calibration method—the ratio of the amount of dentin to the amount of pulp obtained from NMR T 2 distribution spectra can be used for measuring the age-related structural changes in teeth while eliminating any variations in size of teeth. Eight teeth (third molars) extracted from humans, aged among 17–67 years old, were tested in this study. It is found that the intensity ratio of dentin to pulp sensitively changes from 0.48 to 3.2 approaching a linear growth with age. This indicates that age-related structural changes in human teeth can be detected using the low-field NMR technique

  19. 27 Al MAS NMR Studies of HBEA Zeolite at Low to High Magnetic Fields

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Jian Z.; Wan, Chuan; Vjunov, Aleksei; Wang, Meng; Zhao, Zhenchao; Hu, Mary Y.; Camaioni, Donald M.; Lercher, Johannes A.

    2017-06-01

    27Al single pulse (SP) MAS NMR spectra of HBEA zeolites with high Si/Al ratios of 71 and 75 were obtained at three magnetic field strengths of 7.05, 11.75 and 19.97 T. High field 27Al MAS NMR spectra acquired at 19.97 T show significantly improved spectral resolution, resulting in at least two well-resolved tetrahedral-Al NMR peaks. Based on the results obtained from 27Al MAS and MQMAS NMR acquired at 19.97 T, four different quadrupole peaks are used to deconvolute the 27Al SP MAS spectra acquired at vari-ous fields by using the same set of quadrupole coupling constants, asymmetric parameters and relative integrated peak intensities for the tetrahedral Al peaks. The line shapes of individual peaks change from typical quadrupole line shape at low field to essentially symmetrical line shapes at high field. We demonstrate that for fully hydrated HBEA zeolites the effect of second order quadrupole interaction can be ignored and quantitative spectral analysis can be performed by directly fitting the high field spectra using mixed Gaussian/Lorentzian line shapes. Also, the analytical steps described in our work allow direct assignment of spectral intensity to individual Al tetrahedral sites (T-sites) of zeolite HBEA. Finally, the proposed concept is suggested generally applicable to other zeo-lite framework types, thus, allowing a direct probing of Al distributions by NMR spectroscopic methods in zeolites with high confi-dence.

  20. Complex Mixture Analysis of Organic Compounds in Yogurt by NMR Spectroscopy

    Science.gov (United States)

    Lu, Yi; Hu, Fangyu; Miyakawa, Takuya; Tanokura, Masaru

    2016-01-01

    NMR measurements do not require separation and chemical modification of samples and therefore rapidly and directly provide non-targeted information on chemical components in complex mixtures. In this study, one-dimensional (1H, 13C, and 31P) and two-dimensional (1H-13C and 1H-31P) NMR spectroscopy were conducted to analyze yogurt without any pretreatment. 1H, 13C, and 31P NMR signals were assigned to 10 types of compounds. The signals of α/β-lactose and α/β-galactose were separately observed in the 1H NMR spectra. In addition, the signals from the acyl chains of milk fats were also successfully identified but overlapped with many other signals. Quantitative difference spectra were obtained by subtracting the diffusion ordered spectroscopy (DOSY) spectra from the quantitative 1H NMR spectra. This method allowed us to eliminate interference on the overlaps; therefore, the correct intensities of signals overlapped with those from the acyl chains of milk fat could be determined directly without separation. Moreover, the 1H-31P HMBC spectra revealed for the first time that N-acetyl-d-glucosamine-1-phosphate is contained in yogurt. PMID:27322339

  1. Sudan dyes in adulterated saffron (Crocus sativus L.): Identification and quantification by (1)H NMR.

    Science.gov (United States)

    Petrakis, Eleftherios A; Cagliani, Laura R; Tarantilis, Petros A; Polissiou, Moschos G; Consonni, Roberto

    2017-02-15

    Saffron, the dried red stigmas of Crocus sativus L., is considered as one of the most expensive spices worldwide, and as such, it is prone to adulteration. This study introduces an NMR-based approach to identify and determine the adulteration of saffron with Sudan I-IV dyes. A complete (1)H and (13)C resonance assignment for Sudan I-IV, achieved by two-dimensional homonuclear and heteronuclear NMR experiments, is reported for the first time. Specific different proton signals for the identification of each Sudan dye in adulterated saffron can be utilised for quantitative (1)H NMR (qHNMR), a well-established method for quantitative analysis. The quantification of Sudan III, as a paradigm, was performed in varying levels (0.14-7.1g/kg) by considering the NMR signal occurring at 8.064ppm. The high linearity, accuracy and rapidity of investigation enable high resolution (1)H NMR spectroscopy to be used for evaluation of saffron adulteration with Sudan dyes. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. High-resolution solid-state NMR study of isotactic polypropylenes

    Directory of Open Access Journals (Sweden)

    O. Fricova

    2012-03-01

    Full Text Available The high-resolution solid-state 13C NMR spectra were recorded for metallocene (m and Ziegler-Natta (ZN isotactic polypropylenes (iPP in pelletized form using cross polarization (CP and magic angle spinning (MAS techniques within the temperature range of 20–160°C. Besides the CP MAS experiments also the MAS 13C NMR spectra (without CP, MAS 1H NMR spectra and rotating frame spin-lattice relaxation times T1ρ (13C were measured at elevated temperatures. With the rise of temperature the splitting of CH2, CH and CH3 signals into two components was detected in 13C NMR spectra and assigned to amorphous and crystalline phases. The temperature dependences of chemical shifts and integral intensities obtained from the deconvoluted spectra provided information on the main chain and CH3 groups motions in amorphous and crystalline regions of studied samples. While T1ρ (13C values show that the rate of segmental motion in amorphous regions in m-iPP and ZN-iPP is virtually the same, larger linewidths in 13C and 1H NMR spectra indicate somewhat larger restraints of the motion in amorphous regions of ZN-iPP.

  3. Effects of NaCl salinity on N-15-nitrate fluxes and specific root length in the halophyte Plantago maritima L.

    NARCIS (Netherlands)

    Rubinigg, M; Posthumus, F; Ferschke, M; Elzenga, JTM; Stulen, [No Value

    The effect of salinity on nitrate influx, efflux, nitrate net uptake rate and net nitrogen translocation to the shoot was assessed in a N-15 steady state labelling experiment in the halophyte Plantago maritima L. raised for 14 days on solution supplied with 50, 100 and 200 mol m(-3) sodium chloride

  4. Genesis herschreven en geïnterpreteerd in het boek Jubileeën, nader toegelicht met een vergelijking van Genesis 17 en Jubileeën 15

    NARCIS (Netherlands)

    Ruiten, Jacques T.A.G.M. van

    2010-01-01

    Jacques T.A.G.M. van Ruiten, “Genesis herschreven en geïnterpreteerd in het boek Jubileeën, nader toegelicht met een vergelijking van Genesis 17 en Jubileeën 15,” Nederlands theologisch tijdschrift 64 (2010): 32-50.

  5. NMR Analysis of Some Pentacycloundecanedione Derivatives

    African Journals Online (AJOL)

    NJD

    was used to assist with the elucidation of the asymmetric ketal structure. KEYWORDS. NMR elucidation, pentacycloundecane, 2D NMR. 1. Introduction. The chemistry ... intermediate for the diol 413,14 which is used in the synthesis of various crown ethers13,15–17 and macrocycles.11,18. 2. Experimental. The four products ...

  6. A Guided Inquiry Approach to NMR Spectroscopy

    Science.gov (United States)

    Parmentier, Laura E.; Lisensky, George C.; Spencer, Brock

    1998-04-01

    We present a novel way to introduce NMR spectroscopy into the general chemistry curriculum as part of a week-long aspirin project in our one-semester introductory course. Aspirin is synthesized by reacting salicylic acid and acetic anhydride. Purity is determined by titration and IR and NMR spectroscopy. Students compare IR and NMR spectra of their aspirin product to a series of reference spectra obtained by the class. Students are able to interpret the IR spectra of their aspirin using IR data from previous experiments. NMR is introduced by having students collect 1H NMR spectra of a series of reference compounds chosen to include some of the structural features of aspirin and compare spectra and structures of the reference compounds to develop a correlation chart for chemical shifts. This process is done in small groups using shared class data and is guided by a series of questions designed to relate the different kinds of hydrogen atoms to number and position of peaks in the NMR spectrum. Students then identify the peaks in the NMR spectrum of their aspirin product and relate percent purity by titration with spectral results and percent yield. This is an enjoyable project that combines the synthesis of a familiar material with a guided inquiry-based introduction to NMR spectroscopy.

  7. Early history of NMR at Los Alamos

    International Nuclear Information System (INIS)

    Jackson, J.A.

    1985-11-01

    Nuclear magnetic resonance (NMR) spectroscopy has developed into an important research tool in chemistry. More recently, NMR imaging and in vivo spectroscopy promise to produce a revolution in medicine and biochemistry. Early experiments at Los Alamos led to DOE programs involving stable isotopes of importance to biology and to medicine. These events are briefly recounted. 2 refs

  8. Using Cloud Storage for NMR Data Distribution

    Science.gov (United States)

    Soulsby, David

    2012-01-01

    An approach using Google Groups as method for distributing student-acquired NMR data has been implemented. We describe how to configure NMR spectrometer software so that data is uploaded to a laboratory section specific Google Group, thereby removing bottlenecks associated with printing and processing at the spectrometer workstation. Outside of…

  9. Nitrogen Use Efficiency and Carbon Isotope Discrimination Study on NMR151 and NMR152 Mutant Lines Rice at Field Under Different Nitrogen Rates and Water Potentials

    International Nuclear Information System (INIS)

    Ahmad Nazrul Abdul Wahid; Shyful Azizi Abdul Rahman; Abdul Rahim Harun; Latiffah Nordin; Abdul Razak Ruslan; Hazlina Abdullah; Khairuddin Abdul Rahim

    2016-01-01

    This study was conducted to evaluate the nitrogen use efficiency and 13 C isotope discrimination of rice mutant lines viz. NMR151 and NMR152. Both cultivars are developed under rice radiation mutagenesis programme for adaptability to aerobic conditions. In the present study, NMR151 and NMR152 were grown under conditions of varying water potentials and nitrogen levels in a field. Two water potentials and three nitrogen rates in a completely randomized design with three replications were carried out. The rice mutants were grown for 110 days under two water potentials, (i) Field capacity from 0 to 110 DAS [FC], and (ii) Field capacity from 0 to 40 DAS and 30 % dry of field capacity from 41 to 110 DAS [SS] and three nitrogen rates, (i) 0 kg N/ ha (0N), (ii) 60 kg N/ ha (60N), and (iii) 120 kg N/ ha (120N). 15 N isotopic tracer technique was used in this study, whereby the 15 N labeled urea fertilizer 5.20 % atom excess (a.e) was utilized as a tracer for nitrogen use efficiency (NUE) study. 15 N isotope presence in the samples was determined using emission spectrometry and percentage of total nitrogen was determined by the Kjeldahl method. 15 N a.e values of the samples were used in the determination of the NUE. The value of 13 C isotope discrimination (Δ 13 C) in the sample was determined using isotope ratio mass spectrometry (IRMS). The 13 C isotope discrimination technique was used as a tool to identify drought resistance rice cultivars with improves water use efficiency. The growth and agronomy data, viz. plant height, number of tillers, grain yield, straw yield, and 1000 grain weight also were recorded. Results from this study showed nitrogen rates imparted significant effects on yield (grain and straw) plant height, number of tillers and 1000 grain weight. Water potentials had significant effects only on 1000 grain weight and Δ 13 C. The NUE for both mutant lines rice showed no significant different between treatments. Both Rice mutant lines rice NMR151 and NMR

  10. Carbon-13 NMR spectroscopy of biological systems

    CERN Document Server

    Beckmann, Nicolau

    1995-01-01

    This book is intended to provide an in-depth understanding of 13C NMR as a tool in biological research. 13C NMR has provided unique information concerning complex biological systems, from proteins and nucleic acids to animals and humans. The subjects addressed include multidimensional heteronuclear techniques for structural studies of molecules in the liquid and solid states, the investigation of interactions in model membranes, the elucidation of metabolic pathwaysin vitro and in vivo on animals, and noninvasive metabolic studies performed on humans. The book is a unique mix of NMR methods and biological applications which makes it a convenient reference for those interested in research in this interdisciplinary area of physics, chemistry, biology, and medicine.Key Features* An interdisciplinary text with emphasis on both 13C NMR methodology and the relevant biological and biomedical issues* State-of-the-art 13C NMR techniques are described; Whenever possible, their advantages over other approaches are empha...

  11. Resonance assignments for the substrate binding domain of Hsp70 chaperone Ssa1 from Saccharomyces cerevisiae.

    Science.gov (United States)

    Hu, Wanhui; Wu, Huiwen; Zhang, Hong; Gong, Weibin; Perrett, Sarah

    2015-10-01

    Hsp70 chaperone proteins play crucial roles in the cell. Extensive structural and functional studies have been performed for bacterial and mammalian Hsp70s. Ssa1 from Saccharomyces cerevisiae is a member of the Hsp70 family. In vivo and biochemical studies on Ssa1 have revealed that it regulates prion propagation and the cell cycle. However, no structural data has been obtained for Ssa1 up to now. Here we report the almost complete (96 %) (1)H, (13)C, (15)N backbone and side chain NMR assignment of the 18.8 kDa Ssa1 substrate binding domain. The construct includes residues 382-554, which corresponds to the entire substrate binding domain and two following α-helices in homologous structures. The secondary structure predicted from the assigned chemical shifts is consistent with that of homologous Hsp70 substrate binding domains.

  12. The Airport Gate Assignment Problem: A Survey

    Science.gov (United States)

    Ghaleb, Mageed A.; Salem, Ahmed M.

    2014-01-01

    The airport gate assignment problem (AGAP) is one of the most important problems operations managers face daily. Many researches have been done to solve this problem and tackle its complexity. The objective of the task is assigning each flight (aircraft) to an available gate while maximizing both conveniences to passengers and the operational efficiency of airport. This objective requires a solution that provides the ability to change and update the gate assignment data on a real time basis. In this paper, we survey the state of the art of these problems and the various methods to obtain the solution. Our survey covers both theoretical and real AGAP with the description of mathematical formulations and resolution methods such as exact algorithms, heuristic algorithms, and metaheuristic algorithms. We also provide a research trend that can inspire researchers about new problems in this area. PMID:25506074

  13. Proton Nuclear Magnetic Resonance (1H NMR) Spectroscopy-Based Analysis of Lipid Components in Serum/Plasma of Patients with Duchenne Muscular Dystrophy (DMD).

    Science.gov (United States)

    Srivastava, Niraj Kumar

    2018-01-01

    Proton nuclear magnetic resonance spectroscopy ( 1 H NMR) is a useful tool for the analysis of lipid components in biofluids such as serum/plasma. Such tool is applied for the analysis of lipid components in serum/plasma of patients with Duchenne muscular dystrophy (DMD). The practical approach of sampling, storage, lipid extraction procedure, sample preparation before performing the 1 H NMR spectroscopy experiments is presented. All the experimental parameters of NMR spectroscopy are also described. Details of the assignments of lipid components (qualitative analysis) and quantification of particular lipid components (quantitative analysis) are explained.

  14. Hetero Diels-Alder Reaction with Aqueous Glyoxylic Acid: An Experiment in Organic Synthesis and 2-D NMR Analysis for Advanced Undergraduate Students

    Science.gov (United States)

    Augé, Jacques; Lubin-Germain, Nadège

    1998-10-01

    As an application of the use of water as solvent in organic synthesis, a convenient synthesis of a-hydroxy-g-lactones from an aqueous solution of glyoxylic acid is described. The mechanism of the reaction leading to the lactones goes through cycloadducts which rearrange in situ. The NMR analysis of the diastereomeric lactones is particularly interesting; such an analysis illustrates the importance of modern techniques including 2-D NMR spectroscopy. Complete assignments of the signals are mentioned and NOESY spectra are enclosed. The full experiment is addressed to advanced undergraduate students who are trained in organic synthesis and NMR spectroscopy.

  15. A new Schiff base compound N,N'-(2,2-dimetylpropane)-bis(dihydroxylacetophenone): synthesis, experimental and theoretical studies on its crystal structure, FTIR, UV-visible, 1H NMR and 13C NMR spectra.

    Science.gov (United States)

    Saheb, Vahid; Sheikhshoaie, Iran

    2011-10-15

    The Schiff base compound, N,N'-(2,2-dimetylpropane)-bis(dihydroxylacetophenone) (NDHA) is synthesized through the condensation of 2-hydroxylacetophenone and 2,2-dimethyl 1,3-amino propane in methanol at ambient temperature. The yellow crystalline precipitate is used for X-ray single-crystal determination and measuring Fourier transform infrared (FTIR), UV-visible, (1)H NMR and (13)C NMR spectra. Electronic structure calculations at the B3LYP, PBEPBE and PW91PW91 levels of theory are performed to optimize the molecular geometry and to calculate the FTIR, (1)H NMR and (13)C NMR spectra of the compound. Time-dependent density functional theory (TDDFT) method is used to calculate the UV-visible spectrum of NDHA. Vibrational frequencies are determined experimentally and compared with those obtained theoretically. Vibrational assignments and analysis of the fundamental modes of the compound are also performed. All theoretical methods can well reproduce the structure of the compound. The (1)H NMR and (13)C NMR chemical shifts calculated by all DFT methods are consistent with the experimental data. However, the NMR shielding tensors computed at the B3LYP/6-31+G(d,p) level of theory are in better agreement with experimental (1)H NMR and (13)C NMR spectra. The electronic absorption spectrum calculated at the B3LYP/6-31+G(d,p) level by using TD-DFT method is in accordance with the observed UV-visible spectrum of NDHA. In addition, some quantum descriptors of the molecule are calculated and conformational analysis is performed and the results were compared with the crystallographic data. Copyright © 2011 Elsevier B.V. All rights reserved.

  16. 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.

  17. Protein NMR Structure Refinement based on Bayesian Inference

    Science.gov (United States)

    Ikeya, Teppei; Ikeda, Shiro; Kigawa, Takanori; Ito, Yutaka; Güntert, Peter

    2016-03-01

    Nuclear Magnetic Resonance (NMR) spectroscopy is a tool to investigate threedimensional (3D) structures and dynamics of biomacromolecules at atomic resolution in solution or more natural environments such as living cells. Since NMR data are principally only spectra with peak signals, it is required to properly deduce structural information from the sparse experimental data with their imperfections and uncertainty, and to visualize 3D conformations by NMR structure calculation. In order to efficiently analyse the data, Rieping et al. proposed a new structure calculation method based on Bayes’ theorem. We implemented a similar approach into the program CYANA with some modifications. It allows us to handle automatic NOE cross peak assignments in unambiguous and ambiguous usages, and to create a prior distribution based on a physical force field with the generalized Born implicit water model. The sampling scheme for obtaining the posterior is performed by a hybrid Monte Carlo algorithm combined with Markov chain Monte Carlo (MCMC) by the Gibbs sampler, and molecular dynamics simulation (MD) for obtaining a canonical ensemble of conformations. Since it is not trivial to search the entire function space particularly for exploring the conformational prior due to the extraordinarily large conformation space of proteins, the replica exchange method is performed, in which several MCMC calculations with different temperatures run in parallel as replicas. It is shown with simulated data or randomly deleted experimental peaks that the new structure calculation method can provide accurate structures even with less peaks, especially compared with the conventional method. In particular, it dramatically improves in-cell structures of the proteins GB1 and TTHA1718 using exclusively information obtained in living Escherichia coli (E. coli) cells.

  18. Assignment Procedure Biases in Randomised Policy Experiments

    DEFF Research Database (Denmark)

    Aldashev, Gani; Kirchsteiger, Georg; Sebald, Alexander

    2017-01-01

    's propensity to act reciprocally. When people are motivated by reciprocity, the choice of assignment procedure influences the RCTs’ findings. We show that even credible and explicit randomisation procedures do not guarantee an unbiased prediction of the impact of policy interventions; however, they minimise......Randomised controlled trials (RCT) have gained ground as the dominant tool for studying policy interventions in many fields of applied economics. We analyse theoretically encouragement and resentful demoralisation in RCTs and show that these might be rooted in the same behavioural trait – people...... any bias relative to other less transparent assignment procedures....

  19. Optimization of Rated Officer Staff Assignments

    Science.gov (United States)

    2007-06-01

    determinant +1, -1 or 0, which holds for the assignment problem (Bazaraa et al., 1990). The Unimodularity Theorem states for an integer matrix A with...The constraints of the assignment problem, in matrix notation, are defined as in part (b) of the Unimodularity Theorem , therefore since the coefficient...ABM Match Flow output for cA Ac C∈ N = 1 2( , ),NCN N ,...,N where is the navigator Match Flow output for cN Nc C∈ P = 1 2( , ), PCP P ,...,P

  20. 13C CPMAS NMR Studies of Anthocyanidins and their Glucosides

    International Nuclear Information System (INIS)

    Wolniak, M.; Wawer, I.

    2005-01-01

    Anthocyanins are responsible for red, purple or blue colours of flower petals and can be found in red or black fruits and berries. Many foods, especially red grapes and wines, aronia or blueberries contain large amounts of anthocyanins. Their health beneficial effects are related to antioxidant and radical scavenging properties. Structural analysis of anthocyanins by NMR are few, owing to the difficulty in obtaining analysable spectra for unstable, interconverting compounds, available in small amounts. Compounds studied by us were isolated from fruits and berries. 13 C CPMAS NMR spectra were recorded on a Bruker DSX-400 spectrometer for solid chlorides of: cyanidin, cyanidin 3-O-glucoside, cyanidin 3,5-O-diglucoside, pelargonidin and pelargonidin 3-O-glucoside. Dipolar dephased and short contact pulse sequences were used as an aid in the assignment of resonances in CPMAS spectra of solids. Inspection of the spectra indicates that anthocyanidins are in the form of flavylium (cationic) and not in form of the chalcone.: the resonance of C2 appears at ca. 160 ppm and C3 at ca. 135 ppm, whereas C ring opening produces C2 = O, for which chemical shift of ca. 180 ppm can be expected. A comparison of experimental (CPMAS) and predicted (GIAO DFT) shielding constants for cyanidin provided information about the orientation of OH groups, twist angle of aromatic ring B and the localization of the chloride anion.(author)

  1. Automated probabilistic method for assigning backbone resonances of (13C,15N)-labeled proteins

    Energy Technology Data Exchange (ETDEWEB)

    Lukin, Jonathan A. [Carnegie Mellon University, Department of Biological Sciences (United States); Gove, Andrew P.; Talukdar, Sarosh N. [Carnegie Mellon University, Robotics Institute (United States); Ho Chien [Carnegie Mellon University, Department of Biological Sciences (United States)

    1997-02-15

    We present a computer algorithm for the automated assignment of polypeptide backbone and 13C{beta} resonances of a protein of known primary sequence. Input to the algorithm consists of cross peaks from several 3D NMR experiments: HNCA, HN(CA)CO, HN(CA)HA,HNCACB, COCAH, HCA(CO)N, HNCO, HN(CO)CA, HN(COCA)HA, and CBCA(CO)NH. Data from these experiments performed on glutamine-binding protein are analyzed statistically using Bayes' theorem to yield objective probability scoring functions for matching chemical shifts. Such scoring is used in the first stage of the algorithm to combine cross peaks from the first five experiments to form intraresidue segments of chemical shifts{l_brace}Ni,HiN,Ci{alpha},Ci{beta},C'i{r_brace}, while the latter five are combined into interresidue segments {l_brace}Ci{alpha},Ci{beta},C'i,Ni+1,HNi+1{r_brace}. Given a tentative assignment of segments,the second stage of the procedure calculates probability scores based on the likelihood of matching the chemical shifts of each segment with (i) overlapping segments; and (ii) chemical shift distributions of the underlying amino acid type (and secondary structure, if known). This joint probability is maximized by rearranging segments using a simulated annealing program,optimized for efficiency. The automated assignment program was tested using CBCANH and CBCA(CO)NH cross peaks of the two previously assigned proteins, calmodulin and CheA.The agreement between the results of our method and the published assignments was excellent. Our algorithm was also applied to the observed cross peaks of glutamine-binding protein of Escherichia coli, yielding an assignment in excellent agreement with that obtained by time-consuming, manual methods. The chemical shift assignment procedure described here should be most useful for NMR studies of large proteins, which are now feasible with the use of pulsed-field gradients and random partial deuteration of samples.

  2. AEM and NMR: Tools for the Future of Groundwater Management

    Science.gov (United States)

    Abraham, J. D.; Cannia, J. C.; Lawrie, K.

    2012-12-01

    nuclear magnetization of the hydrogen (protons) in the water. These measurements are the basis of the familiar MRI (magnetic resonance imaging) in medical applications. NMR is also widely used in logging applications within the petroleum industry. Effective porosity values were derived directly from the borehole and surface NMR data, and hydraulic conductivity values were calculated using empirical relationships calibrated and verified with few laboratory permeameter and aquifer tests. NMR provides measurements of the effective porosity and hydraulic conductivity at a resolution not possible using traditional methods. Unlike aquifer tests, NMR logs are not unique in design and are applied in similar fashion from borehole to borehole providing a standard way of measuring hydraulic properties. When the hydraulic properties from the NMR are integrated with hydrogeological framework interpretations of AEM data large areas can be characterized. This allows a much more robust method for conceptualizing groundwater models then simply using previously published data for assigning effective porosity and hydraulic conductivity. Examples from the North Platte River Basin in Nebraska and the Murray Darling Basin of Australia illustrate that borehole and surface NMR allows superior, rapid measurements of the complexities of aquifers within when integrated with AEM.

  3. /sup 13/C-NMR studies of selectively carboxymethylated (methyl-/sup 13/C)methionine-labeled bacterial dihydrofolate reductase. [Streptococcus faecium

    Energy Technology Data Exchange (ETDEWEB)

    London, R.E.; Wageman, W.E.; Blakley, R.L.

    1983-08-01

    The /sup 13/C-labeled Streptococcus faecium enzyme was prepared under relatively mild conditions for NMR studies by reaction of unlabeled iodoacetate with the enzyme containing biosynthetically incorporated (methyl-/sup 13/C)methionine. The compound produced by this unique strategy was used as a part of a continuing study of the enzyme dihydrofolate reductase. The NMR studies provided assignment of resonance data for two of the methionine residues. Additionally, the specificity of the carboxymethylation provides a useful basis for resonance assignment.

  4. Repeatable Writing Assignments to Enhance Student Writing.

    Science.gov (United States)

    Wiebold, W. J.; And Others

    1990-01-01

    Discussed is the use of two short writing assignments and a peer review system in an undergraduate agronomy course to improve writing skills and the learning of agronomic principles. Provided is a course description and procedures used in the course. Student evaluation in the course is reviewed. (CW)

  5. Strategy-Proof Assignment Of Multiple Resources

    DEFF Research Database (Denmark)

    Erlanson, Albin; Szwagrzak, Karol

    2015-01-01

    We examine the strategy-proof allocation of multiple resources; an application is the assignment of packages of tasks, workloads, and compensations among the members of an organization. In the domain of multidimensional single-peaked preferences, we find that any allocation mechanism obtained by ...

  6. Accounting for Sustainability: An Active Learning Assignment

    Science.gov (United States)

    Gusc, Joanna; van Veen-Dirks, Paula

    2017-01-01

    Purpose: Sustainability is one of the newer topics in the accounting courses taught in university teaching programs. The active learning assignment as described in this paper was developed for use in an accounting course in an undergraduate program. The aim was to enhance teaching about sustainability within such a course. The purpose of this…

  7. 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... requests for return of members to the United States for delivery to civilian authorities when the request...) Requests for return of members to the United States for delivery to civilian authorities when the request...

  8. Statistical aspects of optimal treatment assignment

    NARCIS (Netherlands)

    van der Linden, Willem J.

    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

  9. Influence Of Agricultural Education Students Home Assignments ...

    African Journals Online (AJOL)

    Four courses offered in the first semester were used and their raw scores in homework /assignments and class tests made up the data. Performance of students was relatively high in homework. However, there was no significant relationship in performance in homework and class test, since the correlation was almost ...

  10. 5 CFR 870.901 - Assignments permitted.

    Science.gov (United States)

    2010-01-01

    ..., corporations, or trustees, the insured individual must specify percentage shares, rather than dollar amounts or... increased insurance coverage under § 870.506 or during an open enrollment period, the increased coverage is considered included in the already existing assignment. The right to increase coverage remains with the...

  11. 7 CFR 1437.104 - Assigned production.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Assigned production. 1437.104 Section 1437.104 Agriculture Regulations of the Department of Agriculture (Continued) COMMODITY CREDIT CORPORATION, DEPARTMENT OF AGRICULTURE LOANS, PURCHASES, AND OTHER OPERATIONS NONINSURED CROP DISASTER ASSISTANCE PROGRAM...

  12. Enhanced functional and structural domain assignments using ...

    Indian Academy of Sciences (India)

    The most populated families in MTB are involved in lipid metabolism, entry and survival of the bacillus in host. Interestingly, for 353 proteins, which we refer to as MTB-specific, no homologues have been identified. Numerous, previously unannotated, hypothetical proteins have been assigned domains and some of these ...

  13. income tax assignment under the ethiopian constitution

    African Journals Online (AJOL)

    eliasn

    Constitution from an income tax point of view. And finally, the article ends with some concluding remarks. 1. Theories of Fiscal Federalism In Income Tax Assignment. Few countries pursue the course of decentralization on grounds of its perceived economic efficiency or equity. Political, social, cultural or historical forces are.

  14. Enhanced functional and structural domain assignments using ...

    Indian Academy of Sciences (India)

    Unknown

    Superfamily relationships between families of unknown and known structures have increased structural in- formation by ~ 11%. Remote similarity detection methods have enabled domain assignments for 1325 'hypo- thetical proteins'. The most populated families in MTB are involved in lipid metabolism, entry and survival of.

  15. Dynamic traffic assignment on parallel computers

    Energy Technology Data Exchange (ETDEWEB)

    Nagel, K.; Frye, R.; Jakob, R.; Rickert, M.; Stretz, P.

    1998-12-01

    The authors describe part of the current framework of the TRANSIMS traffic research project at the Los Alamos National Laboratory. It includes parallel implementations of a route planner and a microscopic traffic simulation model. They present performance figures and results of an offline load-balancing scheme used in one of the iterative re-planning runs required for dynamic route assignment.

  16. Tabu search for target-radar assignment

    DEFF Research Database (Denmark)

    Hindsberger, Magnus; Vidal, Rene Victor Valqui

    2000-01-01

    In the paper the problem of assigning air-defense illumination radars to enemy targets is presented. A tabu search metaheuristic solution is described and the results achieved are compared to those of other heuristic approaches, implementation and experimental aspects are discussed. It is argued...

  17. 48 CFR 208.7002 - Assignment authority.

    Science.gov (United States)

    2010-10-01

    ... (MIPR) by a requiring activity and its acceptance by the contracting activity of another department, even though based on an oral communication, constitutes a one-time agreement. (ii) Consider repetitive... activities concerned. (b) Under the Integrated Materiel Management Program, assignments are made by the...

  18. Verifiable Task Assignment and Scheduling Controller

    Science.gov (United States)

    2017-07-01

    AFRL-RH-WP-TR-2017-0045 Verifiable Task Assignment and Scheduling Controller Clayton Rothwell Infoscitex Corporation...Chief, Supervisory Control Cognition Branch Supervisory Control and Cognition Branch Warfighter Interface Division //signed// KRISTOFFER A...information if it does not display a currently valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS. 1. REPORT DATE (DD-MM

  19. Generalised Assignment Matrix Methodology in Linear Programming

    Science.gov (United States)

    Jerome, Lawrence

    2012-01-01

    Discrete Mathematics instructors and students have long been struggling with various labelling and scanning algorithms for solving many important problems. This paper shows how to solve a wide variety of Discrete Mathematics and OR problems using assignment matrices and linear programming, specifically using Excel Solvers although the same…

  20. Teaching Historical Analysis through Creative Writing Assignments

    Science.gov (United States)

    Peterson, Janine Larmon; Graham, Lea

    2015-01-01

    Incorporating creative writing exercises in history courses can heighten students' critical reading and analytical skills in an active learning model. We identify and define two types of possible assignments that use model texts as their locus: centripetal, which focuses on specific context and disciplinary terms, and centrifugal, which address…

  1. NMR reaction monitoring in flow synthesis

    Directory of Open Access Journals (Sweden)

    M. Victoria Gomez

    2017-02-01

    Full Text Available Recent advances in the use of flow chemistry with in-line and on-line analysis by NMR are presented. The use of macro- and microreactors, coupled with standard and custom made NMR probes involving microcoils, incorporated into high resolution and benchtop NMR instruments is reviewed. Some recent selected applications have been collected, including synthetic applications, the determination of the kinetic and thermodynamic parameters and reaction optimization, even in single experiments and on the μL scale. Finally, software that allows automatic reaction monitoring and optimization is discussed.

  2. The characterisation of polymers using pulsed NMR

    International Nuclear Information System (INIS)

    Charlesby, A.

    1983-01-01

    Broad line pulsed NMR is applied to obtain information on radiation-induced polymer changes and other aspects of polymer science based on the interpretation of spin-spin relaxation curves. Calculations are made to determine the molecular weight, the crosslink density of simple, low molecular weight, flexible polymers. For higher molecular weight polymers, a conclusion can be drawn on the concentrations of entangled and crosslinked units by means of pulsed NMR. Some typical applications of the technique are illustrated by the examples of polyethylenes, rubbers, filled polymeric systems and aqueous polyethylene oxide solutions. The morphology of polymers can be followed by pulsed NMR. (V.N.)

  3. Graphical programming for pulse automated NMR experiments

    Energy Technology Data Exchange (ETDEWEB)

    Belmonte, S.B. [Universidade do Estado, Rio de Janeiro, RJ (Brazil); Oliveira, I.S.; Guimaraes, A.P. [Centro Brasileiro de Pesquisas Fisicas (CBPF), Rio de Janeiro, RJ (Brazil)

    1999-01-01

    We describe a software program designed to control a broadband pulse Nuclear Magnetic Resonance (NMR) spectrometer used in zero-field NMR studies of magnetic metals. The software is written in the graphical language LabVIEW. This type of programming allows modifications and the inclusion of new routines to be easily made by the non-specialist, without changing the basic structure of the program. The program corrects for differences in the gain of the two acquisition channels [U (phase) and V (quadrature)], and automatic baseline subtraction. We present examples of measurements of NMR spectra, spin-echo decay (T{sub 2}), and quadrupolar oscillations, performed in magnetic intermetallic compounds. (author)

  4. MAS NMR of HIV-1 protein assemblies

    Science.gov (United States)

    Suiter, Christopher L.; Quinn, Caitlin M.; Lu, Manman; Hou, Guangjin; Zhang, Huilan; Polenova, Tatyana

    2015-04-01

    The negative global impact of the AIDS pandemic is well known. In this perspective article, the utility of magic angle spinning (MAS) NMR spectroscopy to answer pressing questions related to the structure and dynamics of HIV-1 protein assemblies is examined. In recent years, MAS NMR has undergone major technological developments enabling studies of large viral assemblies. We discuss some of these evolving methods and technologies and provide a perspective on the current state of MAS NMR as applied to the investigations into structure and dynamics of HIV-1 assemblies of CA capsid protein and of Gag maturation intermediates.

  5. Solid-state NMR of polymers

    International Nuclear Information System (INIS)

    Mirau, P.

    2001-01-01

    Nuclear magnetic resonance (NMR) spectroscopy has emerged as one of the most important methods for the solid-state characterisation of polymers. The popularity of NMR is due to the fact that many molecular level features can be measured from the NMR spectra, including the polymer chain conformation, the morphology and the dynamics. The spectral features and relaxation times are affected by local interactions, so they provide information about the structure of polymers on a length scale (2-200 A) that is difficult to measure by other methods. In favourable cases, the NMR experiments provide a molecular-level explanation for the transitions observed by differential scanning calorimetry (DSC) and other methods, and the NMR properties can often be related to the bulk properties. Solid-state NMR has long been of interest in polymer science, and the first solid-state NMR studies of polymers were reported approximately a year after the discovery of nuclear resonance in bulk matter. It was reported in this initial study that the proton line width for natural rubber at room temperature is more like that of a mobile liquid than of a solid, but that the resonance broadens near the glass transition temperature (T g ). This was recognised as being related to a change in chain dynamics above and below the T g . NMR methods developed rapidly after these initial observations, first for polymers in solution and, more recently, for polymers in the solid-state. Solid-state NMR studies of polymers were developed more slowly than their solution-state counterparts because solid-state NMR requires more specialised equipment. Solid-state NMR is now such an important tool that most modern spectrometers are capable of performing these studies. The interest in the NMR of solid polymers is due in part to the fact that most polymers are used in the solid state, and in many cases the NMR properties can be directly related to the macroscopic properties. Polymers have restricted mobility in

  6. J-UNIO protocol used for NMR structure determination of the 206-residue protein NP-346487.1 from Streptococcus pneumoniae TIGR4

    Energy Technology Data Exchange (ETDEWEB)

    Jaudzems, Kristaps [Latvian Institute of Organic Synthesis (Latvia); Pedrini, Bill [Paul Scherrer Institute (PSI), SwissFEL Project (Switzerland); Geralt, Michael; Serrano, Pedro; Wüthrich, Kurt, E-mail: wuthrich@scripps.edu [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States)

    2015-01-15

    The NMR structure of the 206-residue protein NP-346487.1 was determined with the J-UNIO protocol, which includes extensive automation of the structure determination. With input from three APSY-NMR experiments, UNIO-MATCH automatically yielded 77 % of the backbone assignments, which were interactively validated and extended to 97 %. With an input of the near-complete backbone assignments and three 3D heteronuclear-resolved [{sup 1}H,{sup 1}H]-NOESY spectra, automated side chain assignment with UNIO-ATNOS/ASCAN resulted in 77 % of the expected assignments, which was extended interactively to about 90 %. Automated NOE assignment and structure calculation with UNIO-ATNOS/CANDID in combination with CYANA was used for the structure determination of this two-domain protein. The individual domains in the NMR structure coincide closely with the crystal structure, and the NMR studies further imply that the two domains undergo restricted hinge motions relative to each other in solution. NP-346487.1 is so far the largest polypeptide chain to which the J-UNIO structure determination protocol has successfully been applied.

  7. (13)C NMR-based metabolomics for the classification of green coffee beans according to variety and origin.

    Science.gov (United States)

    Wei, Feifei; Furihata, Kazuo; Koda, Masanori; Hu, Fangyu; Kato, Rieko; Miyakawa, Takuya; Tanokura, Masaru

    2012-10-10

    (13)C NMR-based metabolomics was demonstrated as a useful tool for distinguishing the species and origins of green coffee bean samples of arabica and robusta from six different geographic regions. By the application of information on (13)C signal assignment, significantly different levels of 14 metabolites of green coffee beans were identified in the classifications, including sucrose, caffeine, chlorogenic acids, choline, amino acids, organic acids, and trigonelline, as captured by multivariate analytical models. These studies demonstrate that the species and geographical origin can be quickly discriminated by evaluating the major metabolites of green coffee beans quantitatively using (13)C NMR-based metabolite profiling.

  8. 1H and 13C NMR studies of palladium(2) and platinium(2) complexes with S-Methyl-L-Cysteine

    International Nuclear Information System (INIS)

    Allain, A.; Jezowska-Trzebiatowska, B.; Kozlowski, H.

    1979-01-01

    Our recent 1 H NMR studies on Pd(2)-S-Methyl-L-Cysteine(SMC) complexes have shown that the use of a conformational analysis to establish the complexed species existing in solution may provide clearer results than considering the proton chemical shift only. However, the use of the vicinal coupling constant of ABC spectrum of αCH-βCH 2 proton unit to estimate the rotational isomer fractions, may contain some ambiguity, especially on the proton assignment of the methylene group. For this reason 13 C NMR method has been applied to study these systems. (author)

  9. Isolation and NMR Characterization of Fumonisin B-2 and a New Fumonisin B-6 from Aspergillus niger

    DEFF Research Database (Denmark)

    Månsson, Maria; Klejnstrup, Marie Louise; Phipps, Richard Kerry

    2010-01-01

    A new fumonisin, fumonisin B-6 (1), has been isolated by cation-exchange and reverse-phase chromatography, together with fumonisin B-2 (2), from,stationary cultures of the fungus Aspergillus niger NRRL 326. Analysis of mass spectrometric and NMR data determined that FB6 is a positional isomer...... of FBI and iso-FB1, having hydroxyl functions at C3, C4, and C5. Analysis of the NMR data for FB2 showed very similar chemical shift values when compared to an authentic Fusarium FB2 standard, strongly indicating identical molecules despite that an absolute stereochemical assignment of FB2 from A. niger...

  10. NMR analysis of male fathead minnow urinary metabolites: A potential approach for studying impacts of chemical exposures

    Energy Technology Data Exchange (ETDEWEB)

    Ekman, D.R. [Ecosystems Research Division, U.S. EPA, 960 College Station Road, Athens, GA 30605 (United States)], E-mail: ekman.drew@epa.gov; Teng, Q. [Ecosystems Research Division, U.S. EPA, 960 College Station Road, Athens, GA 30605 (United States); Jensen, K.M.; Martinovic, D.; Villeneuve, D.L.; Ankley, G.T. [Mid-Continent Ecology Division, U.S. EPA, 6201 Congdon Boulevard, Duluth, MN 55804 (United States); Collette, T.W. [Ecosystems Research Division, U.S. EPA, 960 College Station Road, Athens, GA 30605 (United States)

    2007-11-30

    The potential for profiling metabolites in urine from male fathead minnows (Pimephales promelas) to assess chemical exposures was explored using nuclear magnetic resonance (NMR) spectroscopy. Both one-dimensional (1D) and two-dimensional (2D) NMR spectroscopy was used for the assignment of metabolites in urine from unexposed fish. Because fathead minnow urine is dilute, we lyophilized these samples prior to analysis. Furthermore, 1D {sup 1}H NMR spectra of unlyophilized urine from unexposed male fathead minnow and Sprague-Dawley rat were acquired to qualitatively compare rat and fish metabolite profiles and to provide an estimate of the total urinary metabolite pool concentration difference. As a small proof-of-concept study, lyophilized urine samples from male fathead minnows exposed to three different concentrations of the antiandrogen vinclozolin were analyzed by 1D {sup 1}H NMR to assess exposure-induced changes. Through a combination of principal components analysis (PCA) and measurements of {sup 1}H NMR peak intensities, several metabolites were identified as changing with statistical significance in response to exposure. Among those changes occurring in response to exposure to the highest concentration (450 {mu}g/L) of vinclozolin were large increases in taurine, lactate, acetate, and formate. These increases coincided with a marked decrease in hippurate, a combination potentially indicative of hepatotoxicity. The results of these investigations clearly demonstrate the potential utility of an NMR-based approach for assessing chemical exposures in male fathead minnow, using urine collected from individual fish.

  11. Structural investigations of substituted indolizine derivatives by NMR studies

    International Nuclear Information System (INIS)

    Furdui, Bianca; Dinica, Rodica; Demeunynck, Martine; Druta, Ioan

    2008-01-01

    Owing to the increasing importance of indolizine heterocycles in the field of biology and pharmacology we have synthesized and investigated the obtained heterocycles by NMR techniques. In order to investigate the substituent effects on the spectroscopic properties, a series of indolizine derivatives were studied by 1 H-NMR, 13 C-NMR and 2D NMR (GCOSY, GHMBC and GHMQC spectra). (authors)

  12. Simultaneous acquisition of three NMR spectra in a single ...

    Indian Academy of Sciences (India)

    reduce the acquisition time of high-dimensional NMR spectra for metabolomics.8 The different fast NMR methods and their combinations developed during the past decade for proteins and nucleic acids such as single-scan NMR spectroscopy (ultrafast NMR),9–13. HADMARD encoding,14 reduced dimensional (RD). 1091 ...

  13. Bayesian Peak Picking for NMR Spectra

    KAUST Repository

    Cheng, Yichen

    2014-02-01

    Protein structure determination is a very important topic in structural genomics, which helps people to understand varieties of biological functions such as protein-protein interactions, protein–DNA interactions and so on. Nowadays, nuclear magnetic resonance (NMR) has often been used to determine the three-dimensional structures of protein in vivo. This study aims to automate the peak picking step, the most important and tricky step in NMR structure determination. We propose to model the NMR spectrum by a mixture of bivariate Gaussian densities and use the stochastic approximation Monte Carlo algorithm as the computational tool to solve the problem. Under the Bayesian framework, the peak picking problem is casted as a variable selection problem. The proposed method can automatically distinguish true peaks from false ones without preprocessing the data. To the best of our knowledge, this is the first effort in the literature that tackles the peak picking problem for NMR spectrum data using Bayesian method.

  14. Cultural Heritage Studies with Mobile NMR.

    Science.gov (United States)

    Rehorn, Christian; Blümich, Bernhard

    2018-03-30

    Nuclear Magnetic Resonance (NMR) provides in-situ information about selected isotope densities in samples and objects, while also providing contrast through rotational and translational molecular dynamics. These parameters are probed not only in magnetic resonance spectroscopy and imaging but also in nondestructive materials testing by mobile stray-field NMR whose unique perks are valuable in cultural heritage studies. We present recent progress in the analysis of cultural heritage with mobile 1H NMR stray-field sensors, for which the detection zone is outside of the NMR magnet. Prominent applications include the analysis of stratigraphies in paintings and frescoes, and the assessment of material states changing under the impact of aging, conservation and restoration. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Development of Two-Dimensional NMR

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 20; Issue 11. Development of Two-Dimensional NMR: Strucure Determination of Biomolecules in Solution. Anil Kumar. General Article Volume 20 Issue 11 November 2015 pp 995-1002 ...

  16. NMR study of Albemoschus esculentus characterization

    International Nuclear Information System (INIS)

    Bathista, A.L.B.S; Silva, E.O.; Nogueira, Jose de S.; Tavares, M.I.B.

    2001-01-01

    The investigation of the main compounds presented in the Albemoschus esculentus has been carried out employing nuclear magnetic resonance spectroscopy (NMR), using solution and solid state NMR when it one was necessary. The evaluation of NMR data allowed us to characterize the main type of components presented in this kind of sample. It was necessary to use a total information from solid state NMR and also the solution response. From these information we could get that four main components were presented in this sample. One in the shell, that is cellulose, another one between the shell and seeds that is a polysaccharide and in the seed two components were found one is a starch and the second one is an oil, a triacylglycerol. These components are responsible by its physical chemistry properties. (author)

  17. NMR analysis of compositional heterogeneity in polysaccharides

    Science.gov (United States)

    Many copolysaccharides are compositionally heterogeneous, and the composition determined by the usual analytical or spectroscopic methods provides only an average value. For some polysaccharides, the NMR data contain copolymer sequence information, such as diad, triad, and tetrad sequence intensiti...

  18. Bayesian Peak Picking for NMR Spectra

    Directory of Open Access Journals (Sweden)

    Yichen Cheng

    2014-02-01

    Full Text Available Protein structure determination is a very important topic in structural genomics, which helps people to understand varieties of biological functions such as protein-protein interactions, protein–DNA interactions and so on. Nowadays, nuclear magnetic resonance (NMR has often been used to determine the three-dimensional structures of protein in vivo. This study aims to automate the peak picking step, the most important and tricky step in NMR structure determination. We propose to model the NMR spectrum by a mixture of bivariate Gaussian densities and use the stochastic approximation Monte Carlo algorithm as the computational tool to solve the problem. Under the Bayesian framework, the peak picking problem is casted as a variable selection problem. The proposed method can automatically distinguish true peaks from false ones without preprocessing the data. To the best of our knowledge, this is the first effort in the literature that tackles the peak picking problem for NMR spectrum data using Bayesian method.

  19. Relaxation time estimation in surface NMR

    Science.gov (United States)

    Grunewald, Elliot D.; Walsh, David O.

    2017-03-21

    NMR relaxation time estimation methods and corresponding apparatus generate two or more alternating current transmit pulses with arbitrary amplitudes, time delays, and relative phases; apply a surface NMR acquisition scheme in which initial preparatory pulses, the properties of which may be fixed across a set of multiple acquisition sequence, are transmitted at the start of each acquisition sequence and are followed by one or more depth sensitive pulses, the pulse moments of which are varied across the set of multiple acquisition sequences; and apply processing techniques in which recorded NMR response data are used to estimate NMR properties and the relaxation times T.sub.1 and T.sub.2* as a function of position as well as one-dimensional and two-dimension distributions of T.sub.1 versus T.sub.2* as a function of subsurface position.

  20. WaVPeak: Picking NMR peaks through wavelet-based smoothing and volume-based filtering

    KAUST Repository

    Liu, Zhi

    2012-02-10

    Motivation: Nuclear magnetic resonance (NMR) has been widely used as a powerful tool to determine the 3D structures of proteins in vivo. However, the post-spectra processing stage of NMR structure determination usually involves a tremendous amount of time and expert knowledge, which includes peak picking, chemical shift assignment and structure calculation steps. Detecting accurate peaks from the NMR spectra is a prerequisite for all following steps, and thus remains a key problem in automatic NMR structure determination. Results: We introduce WaVPeak, a fully automatic peak detection method. WaVPeak first smoothes the given NMR spectrum by wavelets. The peaks are then identified as the local maxima. The false positive peaks are filtered out efficiently by considering the volume of the peaks. WaVPeak has two major advantages over the state-of-the-art peak-picking methods. First, through wavelet-based smoothing, WaVPeak does not eliminate any data point in the spectra. Therefore, WaVPeak is able to detect weak peaks that are embedded in the noise level. NMR spectroscopists need the most help isolating these weak peaks. Second, WaVPeak estimates the volume of the peaks to filter the false positives. This is more reliable than intensity-based filters that are widely used in existing methods. We evaluate the performance of WaVPeak on the benchmark set proposed by PICKY (Alipanahi et al., 2009), one of the most accurate methods in the literature. The dataset comprises 32 2D and 3D spectra from eight different proteins. Experimental results demonstrate that WaVPeak achieves an average of 96%, 91%, 88%, 76% and 85% recall on 15N-HSQC, HNCO, HNCA, HNCACB and CBCA(CO)NH, respectively. When the same number of peaks are considered, WaVPeak significantly outperforms PICKY. The Author(s) 2012. Published by Oxford University Press.

  1. Solving Quadratic Assignment Problem with Fixed Assignment (QAPFA) using Branch and Bound Approach

    Science.gov (United States)

    Shuthairah Syed-Abdullah, Sharifah; Abdul-Rahman, Syariza; Mauziah Benjamin, Aida; Wibowo, Antoni; Ku-Mahamud, Ku-Ruhana

    2018-01-01

    Quadratic Assignment Problem (QAP) has been a very popular problem to be solved among researchers due to its practical applications. Several variants of QAP have been proposed by researchers in the past in order to reflect the real situations of QAP. One of the real problems of QAP is related with facilities which are required to be assigned to certain locations due to its function. In solving this problem, a fixed assignment has to be made thus allowing for the complexity of the problem to be reduced. Hence, this study introduces Quadratic Assignment Problem with Fixed Assignment (QAPFA) with the objective to minimize the assignment cost between the facility and location. This assignment takes into account the flow and distance between facility and location. QAPFA represents the real-world situation of the problem especially in dealing with specific requirement of some facilities to specific locations. Dataset of QAPFA is introduced and is solved using branch and bound approach. As for validation, the results of QAPFA are compared with QAP in terms of objective function and running time. The computational results show that the solution quality of QAPFA is lower when compared with the QAP, while the running time for QAPFA is lower than the QAP. Since the complexity of the problem is reduced by fixing the assignment, thus there is possibility that QAPFA has lower quality than QAP due to the fixed assignment. Nevertheless, in terms of running time QAPFA is better than QAP. It can be concluded that this problem reflect the real problem and practical to be used.

  2. Frontiers of NMR in Molecular Biology

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-08-25

    NMR spectroscopy is expanding the horizons of structural biology by determining the structures and describing the dynamics of blobular proteins in aqueous solution, as well as other classes of proteins including membrane proteins and the polypeptides that form the aggregates diagnostic of prion and amyloid diseases. Significant results are also emerging on DNA and RNA oligomers and their complexes with proteins. This meeting focused attention on key structural questions emanating from molecular biology and how NMR spectroscopy can be used to answer them.

  3. NMR spectroscopy in the characterization of asphalt

    Energy Technology Data Exchange (ETDEWEB)

    Jennings, P.W.; Desando, M.A.; Raub, M.F.; Hoberg, J.O.; Moats, R.; Stewart, F.F. (Montana State Univ., Bozeman (United States))

    1990-07-01

    NMR spectrometry represents a probe which can provide many details regarding the structure and functionality of asphalts. This is particularly true if it is combined with chromatography and/or chemical modifications. In this project {sup 1}H, {sup 2}H, {sup 13}C, {sup 19}F, {sup 29}Si, {sup 31}P nuclei and a variety of NMR techniques (1D, 2D, DEPT) have been used to describe a few chemical characteristics of the asphalts and chromatographic fractions therefrom.

  4. Assignation of limited resources in pediatrics

    Directory of Open Access Journals (Sweden)

    Garduño Espinosa Armando

    2014-07-01

    Full Text Available Limited resources assignation is fundamental in the development of health services and since they will never be enough, justice is- sues arise. Many distributive justice theories are discussed: liberal, equilable and utilitarian, as well as ethic principles and cost-benefit relation, that is, the consequences. Palliative medicine is suggested as a strategy to reduce the cost of hospitable care and to enhance its designation.

  5. Structural Encoding of Static Single Assignment Form

    DEFF Research Database (Denmark)

    Gal, Andreas; Probst, Christian; Franz, Michael

    2005-01-01

    Static Single Assignment (SSA) form is often used as an intermediate representation during code optimization in Java Virtual Machines. Recently, SSA has successfully been used for bytecode verification. However, constructing SSA at the code consumer is costly. SSAbased mobile code transport formats...... Java bytecode. While the resulting bytecode sequence can still be directly executed by traditional Virtual Machines, our novel VM can infer SSA form and confirm its safety with virtually no overhead....

  6. 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....

  7. Careerism, Committee Assignments and the Electoral Connection

    OpenAIRE

    Katz, Jonathan N.; Sala, Brian R.

    1996-01-01

    Most scholars agree that members of Congress are strongly motivated by their desire for reelection. This assumption implies that members of Congress adopt institutions, rules, and norms of behavior in part to serve their electoral interests. Direct tests of the electoral connection are rare, however, because significant, exogenous changes in the electoral environment are difficult to identify. We develop and test an electoral rationale for the norm of committee assignment "property rights...

  8. NMR of dielectrically oriented molecules

    International Nuclear Information System (INIS)

    Ruessink, B.H.

    1986-01-01

    General information on experimental aspects of EFNMR is given. It is shown that the complete 14 N quadrupole tensor (qct) of pyridine and pyrimidine in the liquid state is accessible to EFNMR. Information obtained about 17 O qct in liquid nitromethane, is compared with results from other techniques. The 33 S qct in liquid sulfolane is investigated. The EFNMR results, combined with those from spin-lattice relaxation time measurements and from Hartree-Fock-Slater MO calculations, allowed the complete assignment of the 33 S qct. The quadrupole coupling of both 10 B and 11 B in a carborane compound is investigated and, together with the results of spin-lattice relaxation time measurements, detailed information about the assignment of the boron qct's could be derived. EFNMR studies of apolar molecules are described. A limitation in EFNMR is the inhomogeneity (delta B) of the magnetic field, which is introduced by the use of non-spinning sample cells. A way out is the detection of zero quantum transitions, their widths being independent of delta B. The results and prospectives of this approach are shown for the simple three spin 1/2 system of acrylonitrile in which the small dipolar proton-proton couplings could be revealed via zero quantum transitions. (Auth.)

  9. Effects of individualized assignments on biology achievement

    Science.gov (United States)

    Kremer, Philip L.

    A pretest-posttest, randomized, two groups, experimental, factorial design compared effects of detailed and nondetailed assignments on biology achievement over seven and a half months. Detailed assignments (favoring field independence and induction) employed block diagrams and stepwise directions. Nondetailed assignments (favoring field dependence and deduction) virtually lacked these. The accessible population was 101 tenth grade preparatory school male students. The 95 students enrolled in first year biology constituted the sample. Two by three ANOVA was done on residualized posttest score means of the students. Totally, the detailed students achieved significantly higher than the nondetailed students. This significantly higher achievement was only true of detailed students in the middle thirds of the deviation intelligence quotient (DIQ) range and of the grade point average (G.P.A.) range after the breakdown into upper, middle, and lower thirds of intellectual capability (ability and achievement). The upper third detailed DIQ grouping indirectly achieved higher than its peers, whereas the lower detailed DIQ third achieved lower than its peers. Thus, high capability students apparently benefit from flow and block diagrams, inductions, field independence, and high structure, whereas low capability students may be hindered by these.

  10. Capacity constrained assignment in spatial databases

    DEFF Research Database (Denmark)

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

    2008-01-01

    once) in M, (ii) the size of M is maximized (i.e., it comprises min{|P|, P q2Q q.k} pairs), and (iii) the total assignment cost (i.e., the sum of Euclidean distances within all pairs) is minimized. Thus, the CCA problem is to identify the assignment with the optimal overall quality; intuitively......, the quality of q's service to p in a given (q, p) pair is anti-proportional to their distance. Although max-flow algorithms are applicable to this problem, they require the complete distance-based bipartite graph between Q and P. For large spatial datasets, this graph is expensive to compute and it may be too...... 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...

  11. Influence of the O-phosphorylation of serine, threonine and tyrosine in proteins on the amidic N-15 chemical shielding anisotropy tensors

    Czech Academy of Sciences Publication Activity Database

    Emmer, Jiří; Vavrinská, A.; Sychrovský, V.; Benda, L.; Kříž, Z.; Koča, J.; Boelens, R.; Sklenář, V.; Trantírek, L.

    2013-01-01

    Roč. 55, č. 1 (2013), s. 59-70 ISSN 0925-2738 Institutional support: RVO:60077344 Keywords : csa * Phosphorylation * Amidic nitrogen * Serine * Threonine * Tyrosine * Protein * nmr Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biochemistry and molecular biology Impact factor: 3.305, year: 2013

  12. A novel tridentate Schiff base dioxo-molybdenum(VI) complex: synthesis, experimental and theoretical studies on its crystal structure, FTIR, UV-visible, ¹H NMR and ¹³C NMR spectra.

    Science.gov (United States)

    Saheb, Vahid; Sheikhshoaie, Iran; Stoeckli-Evans, Helen

    2012-09-01

    A new dioxo-molybdenum(VI) complex [MoO(2)(L)(H(2)O)] has been synthesized, using 5-methoxy 2-[(2-hydroxypropylimino)methyl]phenol as tridentate ONO donor Schiff base ligand (H(2)L) and MoO(2)(acac)(2). The yellow crystals of the compound are used for single-crystal X-ray analysis and measuring Fourier Transform Infrared (FTIR), UV-visible, (1)H NMR and (13)C NMR spectra. Electronic structure calculations at the B3LYP and PW91PW91 levels of theory are performed to optimize the molecular geometry and to calculate the UV-visible, FTIR, (1)H NMR and (13)C NMR spectra of the compound. Vibrational assignments and analysis of the fundamental modes of the compound are performed. Time-dependent density functional theory (TDDFT) method is used to calculate the electronic transitions of the complex. All theoretical methods can well reproduce the structure of the compound. The (1)H NMR shielding tensors computed at the B3LYP/DGDZVP level of theory is in agreement with experimental (1)H NMR spectra. However, the (13)C NMR shielding tensors computed at the B3LYP level, employing a combined basis set of DGDZVP for Mo and 6-31+G(2df,p) for other atoms, are in better agreement with experimental (13)C NMR spectra. The electronic transitions calculated at the B3LYP/DGDZVP level by using TD-DFT method is in accordance with the observed UV-visible spectrum of the compound. Copyright © 2012 Elsevier B.V. All rights reserved.

  13. NMRbox: A Resource for Biomolecular NMR Computation.

    Science.gov (United States)

    Maciejewski, Mark W; Schuyler, Adam D; Gryk, Michael R; Moraru, Ion I; Romero, Pedro R; Ulrich, Eldon L; Eghbalnia, Hamid R; Livny, Miron; Delaglio, Frank; Hoch, Jeffrey C

    2017-04-25

    Advances in computation have been enabling many recent advances in biomolecular applications of NMR. Due to the wide diversity of applications of NMR, the number and variety of software packages for processing and analyzing NMR data is quite large, with labs relying on dozens, if not hundreds of software packages. Discovery, acquisition, installation, and maintenance of all these packages is a burdensome task. Because the majority of software packages originate in academic labs, persistence of the software is compromised when developers graduate, funding ceases, or investigators turn to other projects. To simplify access to and use of biomolecular NMR software, foster persistence, and enhance reproducibility of computational workflows, we have developed NMRbox, a shared resource for NMR software and computation. NMRbox employs virtualization to provide a comprehensive software environment preconfigured with hundreds of software packages, available as a downloadable virtual machine or as a Platform-as-a-Service supported by a dedicated compute cloud. Ongoing development includes a metadata harvester to regularize, annotate, and preserve workflows and facilitate and enhance data depositions to BioMagResBank, and tools for Bayesian inference to enhance the robustness and extensibility of computational analyses. In addition to facilitating use and preservation of the rich and dynamic software environment for biomolecular NMR, NMRbox fosters the development and deployment of a new class of metasoftware packages. NMRbox is freely available to not-for-profit users. Copyright © 2017 Biophysical Society. All rights reserved.

  14. O-17 NMR measurement of water

    International Nuclear Information System (INIS)

    Fukazawa, Nobuyuki

    1990-01-01

    Recently, attention has been paid to the various treatment of water and the utilization of water by magnetic treatment, electric field treatment and so on. It has been said that by these treatments, the change in the properties of water arises. The state of this treated water cannot be explained by the properties of water from conventional physical and chemical standpoints. In addition, the method of measurement of whether the change arose or not is not yet determined. It is necessary to establish the method of measurement for the basic state of water. In this study, O-17 NMR which observes the state of water directly at molecular or atomic level was investigated as the method of measuring water. The measurement of O-17 NMR was carried out with a JNR 90Q FT NMR of Fourier transformation type of JEOL Ltd. The experimental method and the results are reported. The result of measurement of the O-17 NMR spectrum for distilled ion exchange water is shown. It is know that it has very wide line width as compared with the NMR spectra of protons and C-13. The relative sensitivity of O-17 observation is about 1/100,000 of that of protons. As to the information on the state of water obtained by O-17 NMR, there are chemical shift and line width. As temperature rose, the line width showed decrease, which seemed to be related to the decrease of hydrogen combination. (K.I.)

  15. 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.

  16. 33S NMR cryogenic probe for taurine detection

    Science.gov (United States)

    Hobo, Fumio; Takahashi, Masato; Maeda, Hideaki

    2009-03-01

    With the goal of a S33 nuclear magnetic resonance (NMR) probe applicable to in vivo NMR on taurine-biological samples, we have developed the S33 NMR cryogenic probe, which is applicable to taurine solutions. The NMR sensitivity gain relative to a conventional broadband probe is as large as 3.5. This work suggests that improvements in the preamplifier could allow NMR measurements on 100 μM taurine solutions, which is the level of sensitivity necessary for biological samples.

  17. Basics of spectroscopic instruments. Hardware of NMR spectrometer

    International Nuclear Information System (INIS)

    Sato, Hajime

    2009-01-01

    NMR is a powerful tool for structure analysis of small molecules, natural products, biological macromolecules, synthesized polymers, samples from material science and so on. Magnetic Resonance Imaging (MRI) is applicable to plants and animals Because most of NMR experiments can be done by an automation mode, one can forget hardware of NMR spectrometers. It would be good to understand features and performance of NMR spectrometers. Here I present hardware of a modern NMR spectrometer which is fully equipped with digital technology. (author)

  18. 19F-NMR study on separation and identification of stereoisomers of nerve agents

    International Nuclear Information System (INIS)

    Miao Zhenchun; Li Hua; Zhou Yongxin; Feng Rui; Li Guangyu

    1999-01-01

    Objective: To separate and identify the stereoisomers of nerve agents. Methods: 19 F-NMR shift difference was induced by chiral shift reagent. Results and Conclusion: 19 F-NMR spectra of eleven nerve agents were recorded at a frequency of 376 MHz in the Fourier transform mode. A convenient and effective NMR method was developed for the separation of stereoisomers of nerve agents containing P-F bond. It relies on the acquisition of the chemical shift difference between enantiomers, caused by the optically active europium shift reagent tris (3-trifluoromethyl-hydrox-methylene-d-camphorato) europium (III) [Eu(tfc) 3 ] in deutero-benzene. In all cases, a downfield shift induced by chiral shift reagent was observed. The shift increased with increasing molar ratio chiral shift reagent/nerve agent. The optimum molar ratio that should be used for the separation of the stereoisomers of nerve agents 1-11 was found to be in the range of 1.5-2.5. 19 F-NMR spectra of the stereoisomers were assigned by means of stereospecificity, observed upon partial breakdown of the nerve agent in rat blood at 37 degree C

  19. Use of NMR and NMR Prediction Software to Identify Components in Red Bull Energy Drinks

    Science.gov (United States)

    Simpson, Andre J.; Shirzadi, Azadeh; Burrow, Timothy E.; Dicks, Andrew P.; Lefebvre, Brent; Corrin, Tricia

    2009-01-01

    A laboratory experiment designed as part of an upper-level undergraduate analytical chemistry course is described. Students investigate two popular soft drinks (Red Bull Energy Drink and sugar-free Red Bull Energy Drink) by NMR spectroscopy. With assistance of modern NMR prediction software they identify and quantify major components in each…

  20. NMR Spectra through the Eyes of a Student: Eye Tracking Applied to NMR Items

    Science.gov (United States)

    Topczewski, Joseph J.; Topczewski, Anna M.; Tang, Hui; Kendhammer, Lisa K.; Pienta, Norbert J.

    2017-01-01

    Nuclear magnetic resonance spectroscopy (NMR) plays a key role in introductory organic chemistry, spanning theory, concepts, and experimentation. Therefore, it is imperative that the instruction methods for NMR are both efficient and effective. By utilizing eye tracking equipment, the researchers were able to monitor how second-semester organic…

  1. Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR.

    Science.gov (United States)

    van der Schot, Gijs; Bonvin, Alexandre M J J

    2015-08-01

    We present here the performance of the WeNMR CS-Rosetta3 web server in CASD-NMR, the critical assessment of automated structure determination by NMR. The CS-Rosetta server uses only chemical shifts for structure prediction, in combination, when available, with a post-scoring procedure based on unassigned NOE lists (Huang et al. in J Am Chem Soc 127:1665-1674, 2005b, doi: 10.1021/ja047109h). We compare the original submissions using a previous version of the server based on Rosetta version 2.6 with recalculated targets using the new R3FP fragment picker for fragment selection and implementing a new annotation of prediction reliability (van der Schot et al. in J Biomol NMR 57:27-35, 2013, doi: 10.1007/s10858-013-9762-6), both implemented in the CS-Rosetta3 WeNMR server. In this second round of CASD-NMR, the WeNMR CS-Rosetta server has demonstrated a much better performance than in the first round since only converged targets were submitted. Further, recalculation of all CASD-NMR targets using the new version of the server demonstrates that our new annotation of prediction quality is giving reliable results. Predictions annotated as weak are often found to provide useful models, but only for a fraction of the sequence, and should therefore only be used with caution.

  2. New methods for the correction of 31P NMR spectra in in vivo NMR spectroscopy

    International Nuclear Information System (INIS)

    Starcuk, Z.; Bartusek, K.; Starcuk, Z. jr.

    1994-01-01

    The new methods for the correction of 31 P NMR spectra in vivo NMR spectroscopy have been performed. A method for the baseline correction of the spectra which represents a combination of time-domain and frequency-domain has been discussed.The method is very fast and efficient for minimization of base line artifacts of biological tissues impact

  3. 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…

  4. 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...

  5. The core and related solution concepts for infinite assignment games

    NARCIS (Netherlands)

    Llorca, Natividad; Sanchez-Soriano, Joaquin; Tijs, Stef; Timmer, Judith B.

    2004-01-01

    Assignment problems where both sets of agents that have to be matched are countably infinite, the so-called infinite assignment problems, are studied as well as the related cooperative assignment games. Further, several solution concepts for these assignment games are studied. The first one is the

  6. Strategy-Proof Assignment Of Multiple Resources

    DEFF Research Database (Denmark)

    Erlanson, Albin; Szwagrzak, Karol

    2015-01-01

    by maximizing a separably concave function over a polyhedral extension of the set of Pareto-efficient allocations is strategy-proof. Moreover, these are the only strategy-proof, unanimous, consistent, and resource-monotonic mechanisms. These mechanisms generalize the parametric rationing mechanisms (Young, 1987......We examine the strategy-proof allocation of multiple resources; an application is the assignment of packages of tasks, workloads, and compensations among the members of an organization. In the domain of multidimensional single-peaked preferences, we find that any allocation mechanism obtained...

  7. Symmetric Logic Synthesis with Phase Assignment

    OpenAIRE

    Benschop, N. F.

    2001-01-01

    Decomposition of any Boolean Function BF_n of n binary inputs into an optimal inverter coupled network of Symmetric Boolean functions SF_k (k \\leq n) is described. Each SF component is implemented by Threshold Logic Cells, forming a complete and compact T-Cell Library. Optimal phase assignment of input polarities maximizes local symmetries. The "rank spectrum" is a new BF_n description independent of input ordering, obtained by mapping its minterms onto an othogonal n \\times n grid of (transi...

  8. General method of preparation of uniformly 13C, 15N-labeled DNA fragments for NMR analysis of DNA structures

    International Nuclear Information System (INIS)

    Rene, Brigitte; Masliah, Gregoire; Zargarian, Loussine; Mauffret, Olivier; Fermandjian, Serge

    2006-01-01

    Summary 13 C, 15 N labeling of biomolecules allows easier assignments of NMR resonances and provides a larger number of NMR parameters, which greatly improves the quality of DNA structures. However, there is no general DNA-labeling procedure, like those employed for proteins and RNAs. Here, we describe a general and widely applicable approach designed for preparation of isotopically labeled DNA fragments that can be used for NMR studies. The procedure is based on the PCR amplification of oligonucleotides in the presence of labeled deoxynucleotides triphosphates. It allows great flexibility thanks to insertion of a short DNA sequence (linker) between two repeats of DNA sequence to study. Size and sequence of the linker are designed as to create restriction sites at the junctions with DNA of interest. DNA duplex with desired sequence and size is released upon enzymatic digestion of the PCR product. The suitability of the procedure is validated through the preparation of two biological relevant DNA fragments

  9. Recent progress in heteronuclear long-range NMR of complex carbohydrates: 3D H2BC and clean HMBC

    DEFF Research Database (Denmark)

    Meier, Sebastian; Petersen, Bent O.; Duus, Jens Øllgaard

    2009-01-01

    carbohydrates whose structure has been determined by NMR, not least due to the enhanced resolution offered by the third dimension in 3D H2BC and the improved spectral quality due to artifact suppression in clean HMBC. Hence these new experiments set the scene to take advantage of the sensitivity boost achieved...... by the latest generation of cold probes for NMR structure determination of even larger and more complex carbohydrates in solution.......The new NMR experiments 3D H2BC and clean HMBC are explored for challenging applications to a complex carbohydrate at natural abundance of 13C. The 3D H2BC experiment is crucial for sequential assignment as it yields heteronuclear one- and two-bond together with COSY correlations for the 1H spins...

  10. Solution NMR characterization of Sgf73(1-104) indicates that Zn ion is required to stabilize zinc finger motif

    International Nuclear Information System (INIS)

    Lai, Chaohua; Wu, Minhao; Li, Pan; Shi, Chaowei; Tian, Changlin; Zang, Jianye

    2010-01-01

    Zinc finger motif contains a zinc ion coordinated by several conserved amino acid residues. Yeast Sgf73 protein was identified as a component of SAGA (Spt/Ada/Gcn5 acetyltransferase) multi-subunit complex and Sgf73 protein was known to contain two zinc finger motifs. Sgf73(1-104), containing the first zinc finger motif, was necessary to modulate the deubiquitinase activity of SAGA complex. Here, Sgf73(1-104) was over-expressed using bacterial expression system and purified for solution NMR (nuclear magnetic resonance) structural studies. Secondary structure and site-specific relaxation analysis of Sgf73(1-104) were achieved after solution NMR backbone assignment. Solution NMR and circular dichroism analysis of Sgf73(1-104) after zinc ion removal using chelation reagent EDTA (ethylene-diamine-tetraacetic acid) demonstrated that zinc ion was required to maintain stable conformation of the zinc finger motif.

  11. Enantiotopic discrimination in the NMR spectrum of prochiral solutes in chiral liquid crystals.

    Science.gov (United States)

    Lesot, Philippe; Aroulanda, Christie; Zimmermann, Herbert; Luz, Zeev

    2015-04-21

    review, various important aspects of enantiodiscrimination by NMR are presented. Thus the possibility to reveal enantiotopic recognition using residual dipolar couplings or to determine the absolute configuration of enantiotopic NMR signals is discussed. The various kinds of chiral mesophases able to reveal enantiotopic discrimination in guest prochiral molecules are also described and compared with each other. Finally to illustrate the high analytical potentialities of NMR in CLCs, several and various applications involving the enantiodiscrimination phenomenon are described. A strategy for assigning the NMR signals of meso compound in a meso-threo mixture of cyclic molecules is first discussed. This is followed by a description of advantages of the method for the determination of (D/H) natural isotopic fractionation in biocompounds.

  12. ORTHO-TO-PARA ABUNDANCE RATIO (OPR) OF AMMONIA IN 15 COMETS: OPRs OF AMMONIA VERSUS 14N/15N RATIOS IN CN

    International Nuclear Information System (INIS)

    Shinnaka, Yoshiharu; Kawakita, Hideyo; Kobayashi, Hitomi; Jehin, Emmanuel; Manfroid, Jean; Hutsemekers, Damien; Arpigny, Claude

    2011-01-01

    The ortho-to-para abundance ratio (OPR) of cometary molecules is considered to be one of the primordial characteristics of cometary ices. We present OPRs of ammonia (NH 3 ) in 15 comets based on optical high-dispersion spectroscopic observations of NH 2 , which is a photodissociation product of ammonia in the gaseous coma. The observations were mainly carried out with the VLT/UVES. The OPR of ammonia is estimated from the OPR of NH 2 based on the observations of the NH 2 (0, 9, 0) vibronic band. The absorption lines by the telluric atmosphere are corrected and the cometary C 2 emission lines blended with NH 2 lines are removed in our analysis. The ammonia OPRs show a cluster between 1.1 and 1.2 (this corresponds to a nuclear spin temperature of ∼30 K) for all comets in our sample except for 73P/Schwassmann-Wachmann 3 (73P/SW3). Comet 73P/SW3 (both B- and C-fragments) shows the OPR of ammonia consistent with nuclear spin statistical weight ratio (1.0) that indicates a high-temperature limit as nuclear spin temperature. We compared the ammonia OPRs with other properties ( 14 N/ 15 N ratios in CN, D/H ratios of water, and mixing ratios of volatiles). Comet 73P/SW3 is clearly different from the other comets in the plot of ammonia OPRs versus 14 N/ 15 N ratios in CN. The ammonia OPRs of 1.0 and lower 15 N-fractionation of CN in comet 73P/SW3 imply that icy materials in this comet formed under warmer conditions than other comets. Comets may be classified into two groups in the plot of ammonia OPRs against 14 N/ 15 N ratios in CN.

  13. Chemical characterization of a prominent phosphomonoester resonance from mammalian brain. 31P and 1H NMR analysis at 4.7 and 14.1 tesla

    Science.gov (United States)

    Pettegrew, J. W.; Kopp, S. J.; Dadok, J.; Minshew, N. J.; Feliksik, J. M.; Glonek, T.; Cohen, M. M.

    A prominent 31P NMR resonance at 3.84 ppm in mammalian brain has been identified as ethanolamine phosphate. The identification was based on 1H and 31P NMR findings (including pH titrations) at 4.7 and 14.1 T, as well as thin-layer chromatography studies. We previously incorrectly assigned the 3.84 ppm resonance to ribose-5-phosphate. The incorrect assignment occurred because the two compounds have very similar 31P chemical shifts, and because we did not carefully consider the effects of counter ions and ionic strengths when interpreting the 31P chemical shifts. In separate preliminary studies we have demonstrated ethanolamine phosphate to be high in immature developing brain and in the degenerating brain of Alzheimer's and Huntington's disease patients. Ethanolamine phosphate may therefore serve as a sensitive marker of membrane phospholipid turnover for both in vitro and in vivo31P NMR studies.

  14. High resolution NMR spectroscopy of synthetic polymers in bulk

    International Nuclear Information System (INIS)

    Komorski, R.A.

    1986-01-01

    The contents of this book are: Overview of high-resolution NMR of solid polymers; High-resolution NMR of glassy amorphous polymers; Carbon-13 solid-state NMR of semicrystalline polymers; Conformational analysis of polymers of solid-state NMR; High-resolution NMR studies of oriented polymers; High-resolution solid-state NMR of protons in polymers; and Deuterium NMR of solid polymers. This work brings together the various approaches for high-resolution NMR studies of bulk polymers into one volume. Heavy emphasis is, of course, given to 13C NMR studies both above and below Tg. Standard high-power pulse and wide-line techniques are not covered

  15. NMR techniques in the study of cardiovascular structure and functions

    International Nuclear Information System (INIS)

    Osbakken, M.; Haselgrove, J.

    1987-01-01

    The chapter titles of this book are: Introduction to NMR Techniques;Theory of NMR Probe Design;Overview of Magnetic Resonance Imaging to Study the Cardiovascular System;Vascular Anatomy and Physiology Studied with NMR Techniques;Assessment of Myocardial Ischemia and Infarction by Nuclear Magnetic Resonance Imaging;The Use of MRI in Congenital Heart Disease;Cardiomyopathies and Myocarditis Studied with NMR Techniques;Determination of Myocardial Mechanical Function with Magnetic Resonance Imaging Techniques;Determination of Flow Using NMR Techniques;The Use of Contrast Agents in Cardiac MRI;Can Cardiovascular Disease Be Effectively Evaluated with NMR Spectroscopy? NMR Studies of ATP Synthesis Reactions in the Isolated Heart;Studies of Intermediary Metabolism in the Heart by 13C NMR Spectroscopy;23Na and 39K NMR Spectroscopic Studies of the Intact Beating Heart;and Evaluation of Skeletal Muscle Metabolism in Patients with Congestive Heart Failure Using Phosphorus Nuclear Magnetic Resonance

  16. High-resolution /sup 1/H NMR study of the solution structure of delta-hemolysin

    Energy Technology Data Exchange (ETDEWEB)

    Tappin, M.J.; Pastore, A.; Norton, R.S.; Freer, J.H.; Campbell, I.D.

    1988-03-08

    The 26-residue toxin from Staphylococcus aureus delta-hemolysin, is thought to act by traversing the plasma membrane. The structure of this peptide, in methanol solution, has been investigated by using high-resolution NMR in combination with molecular dynamics calculations. The /sup 1/H NMR spectrum has been completely assigned, and it is shown that residues 2-20 form a relatively stable helix while the residues at the C-terminal end appear to be more flexible. The structures were calculated only from nuclear Overhauser effect data and standard bond lengths. It is shown that the results are consistent with /sup 3/J/sub NH-..cap alpha..CH/ coupling constants and amide hydrogen exchange rates.

  17. Spin-State-Dependent Ion-Molecule Chemistry as the Origin of N-15 and D Isotopic Anomalies in Primitive Matter.

    Science.gov (United States)

    Wirstrom, E. S.; Charnley, S. B.; Cordiner, M. A.; Milam, S. N.

    2012-01-01

    Many meteoritic and interplanetary dust particle (IDP) samples contain bulk enhancements and hotspots rich in N-15. Similarly low C(14)N/C(15)N ratios have been observed in numerous comets, An almost constant enrichment factor in comets from disti'nct formation zones in the nebular disk (i.e. both Jupiter Family and Oort Cloud comets), strongly suggests that this fractionation is primordial and was set in the protsolar cloud core. Deuterium enrichment is observed in both meteorites and IDPs

  18. 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...

  19. A cost-effective protocol for the parallel production of libraries of 13CH3-specifically labeled mutants for NMR studies of high molecular weight proteins.

    Science.gov (United States)

    Crublet, Elodie; Kerfah, Rime; Mas, Guillaume; Noirclerc-Savoye, Marjolaine; Lantez, Violaine; Vernet, Thierry; Boisbouvier, Jerome

    2014-01-01

    There is increasing interest in applying NMR spectroscopy to the study of large protein assemblies. Development of methyl-specific labeling protocols combined with improved NMR spectroscopy enable nowadays studies of proteins complexes up to 1 MDa. For such large complexes, the major interest lies in obtaining structural, dynamic and interaction information in solution, which requires sequence-specific resonance assignment of NMR signals. While such analysis is quite standard for small proteins, it remains one of the major bottlenecks when the size of the protein increases. Here, we describe implementation and latest improvements of SeSAM, a fast and user-friendly approach for assignment of methyl resonances in large proteins using mutagenesis. We have improved culture medium to boost the production of methyl-specifically labeled proteins, allowing us to perform small-scale parallel production and purification of a library of (13)CH3-specifically labeled mutants. This optimized protocol is illustrated by assignment of Alanine, Isoleucine, and Valine methyl groups of the homododecameric aminopeptidase PhTET2. We estimated that this improved method allows assignment of ca. 100 methyl cross-peaks in 2 weeks, including 4 days of NMR time and less than 2 k€ of isotopic materials.

  20. Chemical shift assignments of RHE_RS02845, a NTF2-like domain-containing protein from Rhizobium etli.

    Science.gov (United States)

    Li, Tao; Li, Shuangli; Liang, Chunjie; Zhu, Jiang; Liu, Maili; Yang, Yunhuang

    2018-03-23

    The nuclear transport factor 2 (NTF2) like superfamily includes members of the NTF2 family, delta-5-3-ketosteroid isomerases, and the beta subunit of ring hydroxygenases. This family plays important roles in both eukaryotic and prokaryotic cells, and is taken as a classic example of divergent evolution because proteins in this family exhibit diverse biological functions, although share common structural features. We cloned the gene RHE_RS02845 encoding a predicted NTF2-like domain-containing protein in Rhizobium etli, and prepared U- 13 C/ 15 N-labeled protein samples for its three-dimensional NMR structural determination. Here, chemical shift assignments for both backbone and side-chain atoms are reported, which is prerequisite for further structural calculation and functional research using NMR spectroscopy.

  1. Chemical constituents of Ottonia corcovadensis Miq. from Amazon forest: 1H and 13C chemical shift assignments

    International Nuclear Information System (INIS)

    Facundo, Valdir A.; Morais, Selene M.; Braz Filho, Raimundo

    2004-01-01

    In an ethanolic extract of leaves of Ottonia corcovadensis (Piperaceae) were identified sixteen terpenoids of essential oil and the three flavonoids 3',4',5,5',7-penta methoxyflavone (1), 3',4',5,7-tetra methoxyflavone (2) and 5-hydroxy-3',4',5',7-tetra methoxyflavone (3) and cafeic acid (4). Two amides (5 and 6) were isolated from an ethanolic extract of the roots. The structures were established by spectral analysis, meanly NMR (1D and 2D) and mass spectra. Extensive NMR analysis was also used to complete 1 H and 13 C chemical shift assignments of the flavonoids and amides. The components of the essential oil were identified by computer library search, retention indices and visual interpretation of mass spectra. (author)

  2. Optimization of demand assigned SCPC satellite networks

    Science.gov (United States)

    Laborde, E.

    1985-09-01

    This paper investigates various system aspects and price tradeoffs involved in providing cost-effective Demand Assignment (DA) satellite channel service. Those network characteristics which significantly affect the ultimate cost-based decision are discussed. The number of stations participating in the DA or PA system, the number of satellite channels, and the traffic are kept parametric within expected limits, covering most of the present and future applications. In particular, the interrelationships between the network requirements (e.g., grade of service) and network elements, and the impacts of different blocking assignment allocations on the number of modems in the network is examined. A cost model is then derived that allows the evaluation and comparison of both DA and PA networks. Absolute and differential costing of PA and DA networks is permitted using economic quantities available to the system planner. These include modem cost, satellite channel cost, network size, and defined efficiency factors. Based on the differential cost comparisons for several DA and PA network strategies, tradeoffs have been derived to aid the system designer in configuring the most cost-effective DA network.

  3. Assigned value improves memory of proper names.

    Science.gov (United States)

    Festini, Sara B; Hartley, Alan A; Tauber, Sarah K; Rhodes, Matthew G

    2013-01-01

    Names are more difficult to remember than other personal information such as occupations. The current research examined the influence of assigned point value on memory and metamemory judgements for names and occupations to determine whether incentive can improve recall of proper names. In Experiment 1 participants studied face-name and face-occupation pairs assigned 1 or 10 points, made judgements of learning, and were given a cued recall test. High-value names were recalled more often than low-value names. However, recall of occupations was not influenced by value. In Experiment 2 meaningless nonwords were used for both names and occupations. The name difficulty disappeared, and value influenced recall of both names and occupations. Thus value similarly influenced names and occupations when meaningfulness was held constant. In Experiment 3 participants were required to use overt rote rehearsal for all items. Value did not boost recall of high-value names, suggesting that differential processing could not be implemented to improve memory. Thus incentives may improve memory for proper names by motivating people to engage in selective rehearsal and effortful elaborative processing.

  4. NMR assignment of intrinsically disordered self-processing module of the FrpC protein of Neisseria meningitidis

    Czech Academy of Sciences Publication Activity Database

    Kubáň, V.; Nováček, J.; Bumba, Ladislav; Žídek, L.

    2015-01-01

    Roč. 9, č. 2 (2015), s. 435-440 ISSN 1874-2718 R&D Projects: GA ČR(CZ) GAP207/11/0717 Institutional support: RVO:61388971 Keywords : FrpC * Self-processing module * Neisseria meningitidis Subject RIV: EE - Microbiology, Virology Impact factor: 0.687, year: 2015

  5. NMR studies of cation transport across membranes

    Energy Technology Data Exchange (ETDEWEB)

    Shochet, N.R.

    1985-01-01

    /sup 23/Na NMR Studies of cation transport across membranes were conducted both on model and biological membranes. Two ionophores, the carrier monensin and the channel-former gramicidin, were chosen to induce cation transport in large unilamellar phosphatidylcholine vesicles. The distinction between the NMR signals arising from the two sides of the membrane was achieved by the addition of an anionic paramagnetic shift reagent to the outer solution. The kinetics of the cation transport across the membrane was observed simultaneously monitoring the changes in the /sup 23/Na NMR signals of both compartments. Two mathematical models were developed for the estimation of the transport parameters of the monensin- and gramicidin-induced cation transport. The models were able to fit the experimental data very well. A new method for the estimation of the volume trapped inside the vesicles was developed. The method uses the relative areas of the intra- and extravesicular NMR signals arising from a suspension of vesicles bathed in the same medium they contain, as a measure for the relative volumes of these compartments. Sodium transport across biological membranes was studied by /sup 23/ NMR, using suspensions of cultured nerve cells. The sodium influx through voltage-gated channels was studied using the channel modifier batrachotoxin in combination with scorpion toxin.

  6. Nuclear magnetic resonance (NMR): principles and applications

    International Nuclear Information System (INIS)

    Quibilan, E.I.

    The basis for the phenomenon of nuclear magnetic resonance (NMR) is the ability of certain nuclei possessing both intrinsic angular momentum or ''spin'' I and magnetic moment to absorb electromagnetic energy in the radio frequency range. In principle, there are approximately 200 nuclei which may be investigated using the NMR technique. The NMR spectrum consists of intensity peaks along an axis calibrated in terms of the steady magnetic field or the frequency of the radiofrequency electromagnetic radiation. Analysis of the number, spacing, position and intensity of the lines in an NMR spectrum consists of intensity peaks along an axis calibrated in terms of the steady magnetic field or the frequency of the radiofrequency electromagnetic radiation. Analysis of the number, spacing, position and intensity of the lines in an NMR spectrum provides a variety of qualitative and quantitative analytical applications. The most obvious applications consist of the measurements of nuclear properties, such as spin number and nuclear magnetic moment. In liquids, the fine structure of resonance spectra provides a tool for chemical identification and molecular structure analysis. Other applications include the measurements of self-diffusion coefficients, magnetic fields and field homogeneity, inter-nuclear distances, and, in some cases, the water content of biological materials. (author)

  7. Identifying critical unrecognized sugar-protein interactions in GH10 xylanases from Geobacillus stearothermophilus using STD NMR.

    Science.gov (United States)

    Balazs, Yael S; Lisitsin, Elina; Carmiel, Oshrat; Shoham, Gil; Shoham, Yuval; Schmidt, Asher

    2013-09-01

    (1)H solution NMR spectroscopy is used synergistically with 3D crystallographic structures to map experimentally significant hydrophobic interactions upon substrate binding in solution under thermodynamic equilibrium. Using saturation transfer difference spectroscopy (STD NMR), a comparison is made between wild-type xylanase XT6 and its acid/base catalytic mutant E159Q--a non-active, single-heteroatom alteration that has been previously utilized to measure binding thermodynamics across a series of xylooligosaccharide-xylanase complexes [Zolotnitsky et al. (2004) Proc Natl Acad Sci USA 101, 11275-11280). In this study, performing STD NMR of one substrate screens binding interactions to two proteins, avoiding many disadvantages inherent to the technique and clearly revealing subtle changes in binding induced upon mutation of the catalytic Glu. To visualize and compare the binding epitopes of xylobiose-xylanase complexes, a 'SASSY' plot (saturation difference transfer spectroscopy) is used. Two extraordinarily strong, but previously unrecognized, non-covalent interactions with H2-5 of xylobiose were observed in the wild-type enzyme but not in the E159Q mutant. Based on the crystal structure, these interactions were assigned to tryptophan residues at the -1 subsite. The mutant selectively binds only the β-xylobiose anomer. The (1)H solution NMR spectrum of a xylotriose-E159Q complex displays non-uniform broadening of the NMR signals. Differential broadening provides a unique subsite assignment tool based on structural knowledge of face-to-face stacking with a conserved tyrosine residue at the +1 subsite. The results obtained herein by substrate-observed NMR spectroscopy are discussed further in terms of methodological contributions and mechanistic understanding of substrate-binding adjustments upon a charge change in the E159Q construct. © 2013 FEBS.

  8. Influence of the O-phosphorylation of serine, threonine and tyrosine in proteins on the amidic N-15 chemical shielding anisotropy tensors

    Czech Academy of Sciences Publication Activity Database

    Emmer, J.; Vavrinská, A.; Sychrovský, Vladimír; Benda, Ladislav; Kříž, Z.; Koča, J.; Boelens, R.; Sklenář, V.; Trantírek, L.

    2013-01-01

    Roč. 55, č. 1 (2013), s. 59-70 ISSN 0925-2738 R&D Projects: GA ČR GAP205/10/0228 Grant - others:CEITEC(XE) CZ.1.05/1.1.00/02.0068 Institutional support: RVO:61388963 Keywords : CSA * phosphorylation * amidic nitrogen * serine * threonine * tyrosine * protein * NMR Subject RIV: CE - Biochemistry Impact factor: 3.305, year: 2013

  9. 1H, 15N and 13C backbone resonance assignments of pentaerythritol tetranitrate reductase from Enterobacter cloacae PB2.

    Science.gov (United States)

    Iorgu, Andreea I; Baxter, Nicola J; Cliff, Matthew J; Waltho, Jonathan P; Hay, Sam; Scrutton, Nigel S

    2018-04-01

    Pentaerythritol tetranitrate reductase (PETNR) is a flavoenzyme possessing a broad substrate specificity and is a member of the Old Yellow Enzyme family of oxidoreductases. As well as having high potential as an industrial biocatalyst, PETNR is an excellent model system for studying hydrogen transfer reactions. Mechanistic studies performed with PETNR using stopped-flow methods have shown that tunneling contributes towards hydride transfer from the NAD(P)H coenzyme to the flavin mononucleotide (FMN) cofactor and fast protein dynamics have been inferred to facilitate this catalytic step. Herein, we report the near-complete 1 H, 15 N and 13 C backbone resonance assignments of PETNR in a stoichiometric complex with the FMN cofactor in its native oxidized form, which were obtained using heteronuclear multidimensional NMR spectroscopy. A total of 97% of all backbone resonances were assigned, with 333 out of a possible 344 residues assigned in the 1 H- 15 N TROSY spectrum. This is the first report of an NMR structural study of a flavoenzyme from the Old Yellow Enzyme family and it lays the foundation for future investigations of functional dynamics in hydride transfer catalytic mechanism.

  10. (1)H, (13)C and (15)N assignments of CdnL, an essential protein in Myxococcus xanthus.

    Science.gov (United States)

    Mirassou, Yasmina; Elías-Arnanz, Montserrat; Padmanabhan, S; Jiménez, M Angeles

    2013-04-01

    CdnL, an essential protein in Myxococcus xanthus and several other bacteria, is a member of the large CarD_TRCF family of bacterial proteins that interact with RNA polymerase. Structural analyses of the 164-residue M. xanthus CdnL by NMR is complicated because of broadening, and hence overlap, of the signals due to the self-association and the monomer-dimer equilibrium that occurs in solution. Here, we report (1)H, (13)C and (15)N assignments for CdnL achieved by analyzing its NMR spectra on the basis of the complete assignment obtained in this study for the 68-residue N-terminal fragment of CdnL (CdnLNt) together with those we described previously for the stable, protease-resistant, 110-residue C-terminal domain (CdnLCt). This approach relied on our observation that many of the CdnLNt and CdnLCt chemical shifts matched closely with those of the equivalent residues in the full-length protein. Our assignments provide the crucial first step in the structural analysis of CdnL and this functionally important family of bacterial proteins.

  11. High resolution 4D HPCH experiment for sequential assignment of {sup 13}C-labeled RNAs via phosphodiester backbone

    Energy Technology Data Exchange (ETDEWEB)

    Saxena, Saurabh; Stanek, Jan [University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre (Poland); Cevec, Mirko; Plavec, Janez [National Institute of Chemistry, Slovenian NMR Centre (Slovenia); Koźmiński, Wiktor, E-mail: kozmin@chem.uw.edu.pl [University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre (Poland)

    2015-11-15

    The three-dimensional structure determination of RNAs by NMR spectroscopy requires sequential resonance assignment, often hampered by assignment ambiguities and limited dispersion of {sup 1}H and {sup 13}C chemical shifts, especially of C4′/H4′. Here we present a novel through-bond 4D HPCH NMR experiment involving phosphate backbone where C4′–H4′ correlations are resolved along the {sup 1}H3′–{sup 31}P spectral planes. The experiment provides high peak resolution and effectively removes ambiguities encountered during assignments. Enhanced peak dispersion is provided by the inclusion of additional {sup 31}P and {sup 1}H3′ dimensions and constant-time evolution of chemical shifts. High spectral resolution is obtained by using non-uniform sampling in three indirect dimensions. The experiment fully utilizes the isotopic {sup 13}C-labeling with evolution of C4′ carbons. Band selective {sup 13}C inversion pulses are used to achieve selectivity and prevent signal dephasing due to the C4′–C3′ and C4′–C5′ homonuclear couplings. Multiple quantum line narrowing is employed to minimize sensitivity loses. The 4D HPCH experiment is verified and successfully applied to a non-coding 34-nt RNA consisting typical structure elements and a 14-nt RNA hairpin capped by cUUCGg tetraloop.

  12. Heterologous Expression of Hen Egg White Lysozyme and Resonance Assignment of Tryptophan Side Chains in its Non-native States

    International Nuclear Information System (INIS)

    Schloerb, Christian; Ackermann, Katrin; Richter, Christian; Wirmer, Julia; Schwalbe, Harald

    2005-01-01

    A new protocol is described for the isotope ( 15 N and 13 C, 15 N) enrichment of hen egg white lysozyme. Hen egg white lysozyme and an all-Ala-mutant of this protein have been expressed in E. coli. They formed inclusion bodies from which mg quantities of the proteins were purified and prepared for NMR spectroscopic investigations. 1 H, 13 C and 15 N main chain resonances of disulfide reduced and S-methylated lysozyme were assigned and its residual structure in water pH 2 was characterized by chemical shift perturbation analysis. A new NMR experiment has been developed to assign tryptophan side chain indole resonances by correlation of side chain and backbone NH resonances with the C γ resonances of these residues. Assignment of tryptophan side chains enables further residue specific investigations on structural and dynamical properties, which are of significant interest for the understanding of non-natives states of lysozyme stabilized by hydrophobic interactions between clusters of tryptophan residues

  13. Two dimensional NMR of liquids and oriented molecules

    Energy Technology Data Exchange (ETDEWEB)

    Gochin, M.

    1987-02-01

    Chapter 1 discusses the quantum mechanical formalism used for describing the interaction between magnetic dipoles that dictates the appearance of a spectrum. The NMR characteristics of liquids and liquid crystals are stressed. Chapter 2 reviews the theory of multiple quantum and two dimensional NMR. Properties of typical spectra and phase cycling procedures are discussed. Chapter 3 describes a specific application of heteronuclear double quantum coherence to the removal of inhomogeneous broadening in liquids. Pulse sequences have been devised which cancel out any contribution from this inhomogeneity to the final spectrum. An interpretation of various pulse sequences for the case of /sup 13/C and /sup 1/H is given, together with methods of spectral editing by removal or retention of the homo- or heteronuclear J coupling. The technique is applied to a demonstration of high resolution in both frequency and spatial dimensions with a surface coil. In Chapter 4, multiple quantum filtered 2-D spectroscopy is demonstrated as an effective means of studying randomly deuterated molecules dissolved in a nematic liquid crystal. Magnitudes of dipole coupling constants have been determined for benzene and hexane, and their signs and assignments found from high order multiple quantum spectra. For the first time, a realistic impression of the conformation of hexane can be estimated from these results. Chapter 5 is a technical description of the MDB DCHIB-DR11W parallel interface which has been set up to transfer data between the Data General Nova 820 minicomputer, interfaced to the 360 MHz spectrometer, and the Vax 11/730. It covers operation of the boards, physical specifications and installation, and programs for testing and running the interface.

  14. Two dimensional NMR of liquids and oriented molecules

    International Nuclear Information System (INIS)

    Gochin, M.

    1987-02-01

    Chapter 1 discusses the quantum mechanical formalism used for describing the interaction between magnetic dipoles that dictates the appearance of a spectrum. The NMR characteristics of liquids and liquid crystals are stressed. Chapter 2 reviews the theory of multiple quantum and two dimensional NMR. Properties of typical spectra and phase cycling procedures are discussed. Chapter 3 describes a specific application of heteronuclear double quantum coherence to the removal of inhomogeneous broadening in liquids. Pulse sequences have been devised which cancel out any contribution from this inhomogeneity to the final spectrum. An interpretation of various pulse sequences for the case of 13 C and 1 H is given, together with methods of spectral editing by removal or retention of the homo- or heteronuclear J coupling. The technique is applied to a demonstration of high resolution in both frequency and spatial dimensions with a surface coil. In Chapter 4, multiple quantum filtered 2-D spectroscopy is demonstrated as an effective means of studying randomly deuterated molecules dissolved in a nematic liquid crystal. Magnitudes of dipole coupling constants have been determined for benzene and hexane, and their signs and assignments found from high order multiple quantum spectra. For the first time, a realistic impression of the conformation of hexane can be estimated from these results. Chapter 5 is a technical description of the MDB DCHIB-DR11W parallel interface which has been set up to transfer data between the Data General Nova 820 minicomputer, interfaced to the 360 MHz spectrometer, and the Vax 11/730. It covers operation of the boards, physical specifications and installation, and programs for testing and running the interface

  15. Remote tuning of NMR probe circuits.

    Science.gov (United States)

    Kodibagkar, V D; Conradi, M S

    2000-05-01

    There are many circumstances in which the probe tuning adjustments cannot be located near the rf NMR coil. These may occur in high-temperature NMR, low-temperature NMR, and in the use of magnets with small diameter access bores. We address here circuitry for connecting a fixed-tuned probe circuit by a transmission line to a remotely located tuning network. In particular, the bandwidth over which the probe may be remotely tuned while keeping the losses in the transmission line acceptably low is considered. The results show that for all resonant circuit geometries (series, parallel, series-parallel), overcoupling of the line to the tuned circuit is key to obtaining a large tuning bandwidth. At equivalent extents of overcoupling, all resonant circuit geometries have nearly equal remote tuning bandwidths. Particularly for the case of low-loss transmission line, the tuning bandwidth can be many times the tuned circuit's bandwidth, f(o)/Q. Copyright 2000 Academic Press.

  16. Determination of solid fat content by NMR

    International Nuclear Information System (INIS)

    Kawada, Tsukasa; Kato, Chihiro; Suzuki, Kazuaki

    1984-01-01

    To establish a standard method for determing solid fat content, the NMR method was tested at six laboratories and the results were examined for collaboration. Two types of instruments, pulse NMR and wide-line NMR were used. Standard deviation in results at six laboratories was less than 1.5 for the step wise method, but more than 1.5 for the rapid method. The standard deviation in results at a single laboratory was much less than either of these cases. No significant difference could be observed in the values obtained using both instruments. Solid fat content values measured for a mixture of fully hydrogenated rapeseed and rapeseed oil agreed well with the percentage of solid by weight. (author)

  17. Flow NMR of polymers in external fields

    Energy Technology Data Exchange (ETDEWEB)

    Boehme, Ute; Bagusat, Frank; Scheler, Ulrich [Leibniz Institute of Polymer Research Dresden (Germany)

    2008-07-01

    Pulsed-field gradient NMR is applied to study the motion of polymers in an external electric field and under mechanical shear. The application of an electric field drives motion of charged species. In conjunction with the diffusion coefficient from the electrophoretic mobility the effective charge per molecule is derived. The electric field applicable in the aqueous system is too weak to deform the polymer or even abstract counterions. In a shear flow established in a Couette cell partial orientation of polymer chains is measured via residual dipolar couplings. The entire flow field in a non-symmetric flow cell is monitored by a combination of PFG NMR and NMR imaging exhibiting regions of high shear and locally low shear, where polymers relax.

  18. Muscular pathology: echographic and NMR imaging aspects

    International Nuclear Information System (INIS)

    Pascal-Suisse, P.; Beaurain, P.; Mougniot, C.

    1995-01-01

    A comparison of echographic techniques and NMR imaging has been done for the diagnosis of muscular trauma and tumor pathologies. In traumatic pathology, the echographic analysis allows to determine the complete assessment of recent muscular injuries. NMR imaging can be used in granuloma or fibrous callosity appreciation and for the analysis of deep injury (muscles and muscles-tendon junctions) and of muscular aponeurosis. Echography must be used together with color coding Doppler technique in the diagnosis of tumor pathology and for the study of slow fluxes. The recently available energy Doppler technique seems to be powerful in the study of vascularization of small expansive formations, but their extension to adjacent bone or tissue can only be appreciated using NMR imaging. (J.S.)

  19. Deuterium NMR, induced and intrinsic cholesteric lyomesophases

    International Nuclear Information System (INIS)

    Alcantara, M.R.

    1982-01-01

    Induced and intrinsic cholesteric lyotropic mesophases were studied. Induced cholesteric lyomesophases based on potassium laurate (KL) system, with small amounts of cholesterol added, were studied by deuterium NMR and by polarizing microscopy. Order profiles obtained from deuterium NMR of KL perdenderated chains in both induced cholesteric and normal mesophases were compared. The intrinsic cholesteric lyotropic mesophases were based on the amphiphile potassium N-lauroyl serinate (KLNS) in the resolved levo form. The study of the type I intrinsic cholesteric mesophase was made by optical microscopy under polarized light and the type II intrinsic cholesteric lyomesophase was characterized by deuterium NMR. The new texture was explained by the use of the theory of disclinations developed for thermotropic liquid crystals, specially for cholesteric type. (M.J.C.) [pt

  20. Spectral editing through laser-flash excitation in two-dimensional photo-CIDNP MAS NMR experiments

    Science.gov (United States)

    Sai Sankar Gupta, Karthick Babu; Daviso, Eugenio; Jeschke, Gunnar; Alia, A.; Ernst, Matthias; Matysik, Jörg

    2014-09-01

    In solid-state photochemically induced dynamic nuclear polarization (photo-CIDNP) MAS NMR experiments, strong signal enhancement is observed from molecules forming a spin-correlated radical pair in a rigid matrix. Two-dimensional 13C-13C dipolar-assisted rotational resonance (DARR) photo-CIDNP MAS NMR experiments have been applied to obtain exact chemical shift assignments from those cofactors. Under continuous illumination, the signals are enhanced via three-spin mixing (TSM) and differential decay (DD) and their intensity corresponds to the electron spin density in pz orbitals. In multiple-13C labelled samples, spin diffusion leads to propagation of signal enhancement to all 13C spins. Under steady-state conditions, direct signal assignment is possible due to the uniform signal intensity. The original intensities, however, are inaccessible and the information of the local electron spin density is lost. Upon laser-flash illumination, the signal is enhanced via the classical radical pair mechanism (RPM). The obtained intensities are related to isotropic hyperfine interactions aiso and both enhanced absorptive and emissive lines can be observed due to differences in the sign of the local isotropic hyperfine interaction. Exploiting the mechanism of the polarization, selectivity can be increased by the novel time-resolved two-dimensional dipolar-assisted rotational resonance (DARR) MAS NMR experiment which simplifies the signal assignment compared to complex spectra of the same RCs obtained by continuous illumination. Here we present two-dimensional time-resolved photo-CIDNP MAS NMR experiments providing both directly: signal assignment and spectral editing by sign and strength of aiso. Hence, this experiment provides a direct key to the electronic structure of the correlated radical pair.

  1. Structural determination of abutilins A and B, new flavonoids from Abutilon pakistanicum, by 1D and 2D NMR spectroscopy.

    Science.gov (United States)

    Ali, Bakhat; Imran, Muhammad; Hussain, Riaz; Ahmed, Zaheer; Malik, Abdul

    2010-02-01

    Two new flavonoids, abutilin A and B, were isolated from the chloroform soluble fraction of Abutilon pakistanicum and their structures assigned from (1)H and (13)C NMR spectra, DEPT and by 2D COSY, HMQC and HMBC experiments. Ferulic acid (3), (E)-cinnamic acid (4), 5-hydroxy-4',6,7,8-tetramethoxyflavone (5), kaempferol (6), luteolin (7) and luteolin 7-O-beta-D-glucopyranoside (8) have also been reported from this species. Copyright 2009 John Wiley & Sons, Ltd.

  2. Prediction of peak overlap in NMR spectra

    International Nuclear Information System (INIS)

    Hefke, Frederik; Schmucki, Roland; Güntert, Peter

    2013-01-01

    Peak overlap is one of the major factors complicating the analysis of biomolecular NMR spectra. We present a general method for predicting the extent of peak overlap in multidimensional NMR spectra and its validation using both, experimental data sets and Monte Carlo simulation. The method is based on knowledge of the magnetization transfer pathways of the NMR experiments and chemical shift statistics from the Biological Magnetic Resonance Data Bank. Assuming a normal distribution with characteristic mean value and standard deviation for the chemical shift of each observable atom, an analytic expression was derived for the expected overlap probability of the cross peaks. The analytical approach was verified to agree with the average peak overlap in a large number of individual peak lists simulated using the same chemical shift statistics. The method was applied to eight proteins, including an intrinsically disordered one, for which the prediction results could be compared with the actual overlap based on the experimentally measured chemical shifts. The extent of overlap predicted using only statistical chemical shift information was in good agreement with the overlap that was observed when the measured shifts were used in the virtual spectrum, except for the intrinsically disordered protein. Since the spectral complexity of a protein NMR spectrum is a crucial factor for protein structure determination, analytical overlap prediction can be used to identify potentially difficult proteins before conducting NMR experiments. Overlap predictions can be tailored to particular classes of proteins by preparing statistics from corresponding protein databases. The method is also suitable for optimizing recording parameters and labeling schemes for NMR experiments and improving the reliability of automated spectra analysis and protein structure determination.

  3. Cross comparison of the Collection 6 and Collection 6.1 Terra and Aqua MODIS Bands 1 and 2 using AVHRR N15 and N19

    Science.gov (United States)

    Chen, Xuexia; Wu, Aisheng; Xiong, Xiaoxiong J.; Chen, Na

    2017-09-01

    The Moderate Resolution Imaging Spectroradiometer (MODIS) is a key scientific instrument that was launched into Earth orbit by NASA in 1999 on board the Terra (EOS AM) satellite and in 2002 on board the Aqua (EOS PM) satellite. Terra and Aqua MODIS collect the entire Earth's images every 1 to 2 days in 36 spectral bands. MODIS band 1 (0.620- 0.670 μm) and band 2 (0.841-0.876 μm) have nadir spatial resolution of 250 m and their measurements are crucial to derive key land surface products. This study evaluates the performance of the Collection 6 (C6, and C6.1) L1B of both Terra and Aqua MODIS bands 1 and 2 using Simultaneous Nadir Overpass (SNO) data to compare with AVHRR/3 sensors. We examine the relative stability between Terra and Aqua MODIS in reference to NOAA N15 and N19 the Advanced Very High Resolution Radiometer (AVHRR/3). The comparisons for MODIS to AVHRR/3 are over a fifteenyear period from 2002 to 2017. Results from this study provide a quantitative assessment of Terra and Aqua MODIS band 1 and band 2 calibration stability and the relative differences through the NOAA N15 and N19 AVHRR/3 sensors.

  4. A multistage linear array assignment problem

    Science.gov (United States)

    Nicol, David M.; Shier, D. R.; Kincaid, R. K.; Richards, D. S.

    1988-01-01

    The implementation of certain algorithms on parallel processing computing architectures can involve partitioning contiguous elements into a fixed number of groups, each of which is to be handled by a single processor. It is desired to find an assignment of elements to processors that minimizes the sum of the maximum workloads experienced at each stage. This problem can be viewed as a multi-objective network optimization problem. Polynomially-bounded algorithms are developed for the case of two stages, whereas the associated decision problem (for an arbitrary number of stages) is shown to be NP-complete. Heuristic procedures are therefore proposed and analyzed for the general problem. Computational experience with one of the exact problems, incorporating certain pruning rules, is presented with one of the exact problems. Empirical results also demonstrate that one of the heuristic procedures is especially effective in practice.

  5. Rationalization of some genetic anticodonic assignments

    Science.gov (United States)

    Lacey, J. C., Jr.; Hall, L. M.; Mullins, D. W., Jr.

    1985-01-01

    The hydrophobicity of most amino acids correlates well with that of their anticodon nucleotides, with Trp, Tyr, Ile, and Ser being the exceptions to this rule. Using previous data on hydrophobicity and binding constants, and new data on rates of esterification of polyadenylic acid with several N-acetylaminoacyl imidazolides, several of the anticodon assignments are rationalized. Chemical reasons are shown supporting the idea of the inclusion of the Ile in the catalog of biological amino acids late in the evolution, through a mutation of the existing tRNA and its aminoacyl-tRNA-synthetase. It was found that an addition of hexane increases the incorporation of hydrophobic Ac-Phe into poly-A, in support of the Fox (1965) and Oparin (1965) emphasis on the biogenetic importance of phase-separated systems.

  6. 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

  7. Applications of NMR in biological metabolic research

    International Nuclear Information System (INIS)

    Nie Jiarui; Li Xiuqin; He Chunjian

    1989-01-01

    The nuclear magnetic resonance has become a powerful means of studying biological metabolism in non-invasive and non-destructive way. Being used to study the metabolic processes of living system in normal physiological conditions as well as in molecular level, the method is better than other conventional approaches. Using important parameters such as NMR-chemical shifts, longitudinal relaxation time and transverse relaxation time, it is possible to probe the metabolic processes as well as conformation, concentration, transportation and distribution of reacting and resulting substances. The NMR spectroscopy of 1 H, 31 P and 13 C nuclei has already been widely used in metabolic researches

  8. Programmable pulse series generator for NMR relaxometer

    International Nuclear Information System (INIS)

    Stolbunov, R.N.; Chichikov, S.A.; Lundin, A.G.

    2005-01-01

    Paper describes a pulse series generator for NMR relaxometer. The operation mode is set on the basis of the PC program by the PCI bus in the internal memory. The design is based on two Altera Company MAX7000S and Cyclone family microcircuits using the Qartus II 4.0 software. The basic parameters are as follows: pulse minimum length - 50 ns, time resolution - 10 ns, pulse maximum number - 1024, number of controlled output channels - 8. The designed device as a part of the NMR hardware-software system enables to record, to process and to store the experiment results in the form of electronic document [ru

  9. NMR studies of single crystal chromium diboride

    Energy Technology Data Exchange (ETDEWEB)

    Michioka, C. [Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan)]. E-mail: michioka@kuchem.kyoto-u.ac.jp; Itoh, Y. [Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan); Yoshimura, K. [Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan); Watabe, Y. [Department of Physics and Mathematics, Aoyama Gakuin University, Sagamihara, Kanagawa 229-8558 (Japan); Kousaka, Y. [Department of Physics and Mathematics, Aoyama Gakuin University, Sagamihara, Kanagawa 229-8558 (Japan); Ichikawa, H. [Department of Physics and Mathematics, Aoyama Gakuin University, Sagamihara, Kanagawa 229-8558 (Japan); Akimitsu, J. [Department of Physics and Mathematics, Aoyama Gakuin University, Sagamihara, Kanagawa 229-8558 (Japan)

    2007-03-15

    We report {sup 11}B NMR studies of a single crystal CrB{sub 2}. From the temperature dependence of the Fourier-transformed NMR spectra in the paramagnetic state, the hyperfine coupling constants are estimated to be A{sub Cr-B} = -0.64,-0.74 and -0.71kOe/{mu}{sub B} for H parallel c, H parallel a and H parallel [210], respectively. In the magnetically ordered state, the spectra in H parallel a and H parallel [210] consist of superposition of a broad hump and five peaks, which correspond to the incommensurate and commensurate spin structures.

  10. Diagnosis code assignment: models and evaluation metrics.

    Science.gov (United States)

    Perotte, Adler; Pivovarov, Rimma; Natarajan, Karthik; Weiskopf, Nicole; Wood, Frank; Elhadad, Noémie

    2014-01-01

    The volume of healthcare data is growing rapidly with the adoption of health information technology. We focus on automated ICD9 code assignment from discharge summary content and methods for evaluating such assignments. We study ICD9 diagnosis codes and discharge summaries from the publicly available Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC II) repository. We experiment with two coding approaches: one that treats each ICD9 code independently of each other (flat classifier), and one that leverages the hierarchical nature of ICD9 codes into its modeling (hierarchy-based classifier). We propose novel evaluation metrics, which reflect the distances among gold-standard and predicted codes and their locations in the ICD9 tree. Experimental setup, code for modeling, and evaluation scripts are made available to the research community. The hierarchy-based classifier outperforms the flat classifier with F-measures of 39.5% and 27.6%, respectively, when trained on 20,533 documents and tested on 2282 documents. While recall is improved at the expense of precision, our novel evaluation metrics show a more refined assessment: for instance, the hierarchy-based classifier identifies the correct sub-tree of gold-standard codes more often than the flat classifier. Error analysis reveals that gold-standard codes are not perfect, and as such the recall and precision are likely underestimated. Hierarchy-based classification yields better ICD9 coding than flat classification for MIMIC patients. Automated ICD9 coding is an example of a task for which data and tools can be shared and for which the research community can work together to build on shared models and advance the state of the art.

  11. Automatic NMR-based identification of chemical reaction types in mixtures of co-occurring reactions.

    Directory of Open Access Journals (Sweden)

    Diogo A R S Latino

    Full Text Available The combination of chemoinformatics approaches with NMR techniques and the increasing availability of data allow the resolution of problems far beyond the original application of NMR in structure elucidation/verification. The diversity of applications can range from process monitoring, metabolic profiling, authentication of products, to quality control. An application related to the automatic analysis of complex mixtures concerns mixtures of chemical reactions. We encoded mixtures of chemical reactions with the difference between the (1H NMR spectra of the products and the reactants. All the signals arising from all the reactants of the co-occurring reactions were taken together (a simulated spectrum of the mixture of reactants and the same was done for products. The difference spectrum is taken as the representation of the mixture of chemical reactions. A data set of 181 chemical reactions was used, each reaction manually assigned to one of 6 types. From this dataset, we simulated mixtures where two reactions of different types would occur simultaneously. Automatic learning methods were trained to classify the reactions occurring in a mixture from the (1H NMR-based descriptor of the mixture. Unsupervised learning methods (self-organizing maps produced a reasonable clustering of the mixtures by reaction type, and allowed the correct classification of 80% and 63% of the mixtures in two independent test sets of different similarity to the training set. With random forests (RF, the percentage of correct classifications was increased to 99% and 80% for the same test sets. The RF probability associated to the predictions yielded a robust indication of their reliability. This study demonstrates the possibility of applying machine learning methods to automatically identify types of co-occurring chemical reactions from NMR data. Using no explicit structural information about the reactions participants, reaction elucidation is performed without structure

  12. Automatic NMR-based identification of chemical reaction types in mixtures of co-occurring reactions.

    Science.gov (United States)

    Latino, Diogo A R S; Aires-de-Sousa, João

    2014-01-01

    The combination of chemoinformatics approaches with NMR techniques and the increasing availability of data allow the resolution of problems far beyond the original application of NMR in structure elucidation/verification. The diversity of applications can range from process monitoring, metabolic profiling, authentication of products, to quality control. An application related to the automatic analysis of complex mixtures concerns mixtures of chemical reactions. We encoded mixtures of chemical reactions with the difference between the (1)H NMR spectra of the products and the reactants. All the signals arising from all the reactants of the co-occurring reactions were taken together (a simulated spectrum of the mixture of reactants) and the same was done for products. The difference spectrum is taken as the representation of the mixture of chemical reactions. A data set of 181 chemical reactions was used, each reaction manually assigned to one of 6 types. From this dataset, we simulated mixtures where two reactions of different types would occur simultaneously. Automatic learning methods were trained to classify the reactions occurring in a mixture from the (1)H NMR-based descriptor of the mixture. Unsupervised learning methods (self-organizing maps) produced a reasonable clustering of the mixtures by reaction type, and allowed the correct classification of 80% and 63% of the mixtures in two independent test sets of different similarity to the training set. With random forests (RF), the percentage of correct classifications was increased to 99% and 80% for the same test sets. The RF probability associated to the predictions yielded a robust indication of their reliability. This study demonstrates the possibility of applying machine learning methods to automatically identify types of co-occurring chemical reactions from NMR data. Using no explicit structural information about the reactions participants, reaction elucidation is performed without structure elucidation of

  13. Direct Comparison of 19F qNMR and 1H qNMR by Characterizing Atorvastatin Calcium Content

    OpenAIRE

    Liu, Yang; Liu, Zhaoxia; Yang, Huaxin; He, Lan

    2016-01-01

    Quantitative nuclear magnetic resonance (qNMR) is a powerful tool in measuring drug content because of its high speed, sensitivity, and precision. Most of the reports were based on proton qNMR (1H qNMR) and only a few fluorine qNMR (19F qNMR) were reported. No research has been conducted to directly compare the advantage and disadvantage between these two methods. In the present study, both 19F and 1H qNMR were performed to characterize the content of atorvastatin calcium with the same intern...

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

    Directory of Open Access Journals (Sweden)

    James D Zook

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

  15. 1H NMR spectra dataset and solid-state NMR data of cowpea (Vigna unguiculata).

    Science.gov (United States)

    Alves Filho, Elenilson G; Silva, Lorena M A; Teofilo, Elizita M; Larsen, Flemming H; de Brito, Edy S

    2017-04-01

    In this article the NMR data from chemical shifts, coupling constants, and structures of all the characterized compounds were provided, beyond a complementary PCA evaluation for the corresponding manuscript (E.G. Alves Filho, L.M.A. Silva, E.M. Teofilo, F.H. Larsen, E.S. de Brito, 2017) [3]. In addition, a complementary assessment from solid-state NMR data was provided. For further chemometric analysis, numerical matrices from the raw 1 H NMR data were made available in Microsoft Excel workbook format (.xls).

  16. Resonance assignments of a VapC family toxin from Clostridium thermocellum.

    Science.gov (United States)

    Wang, Chen; Xuan, Jinsong; Cui, Qiu; Feng, Yingang

    2016-10-01

    Toxin-antitoxin (TA) systems widely exist in bacterial plasmids, phages, and chromosomes and play important roles in growth persistence and host-pathogen interaction. Virulence associated protein BC (VapBC) family TAs are the most abundant TAs in bacteria and many pathogens contain a large number of vapBC loci in the genome which have been extensively studied. Clostridium thermocellum, a cellulolytic anaerobic gram-positive bacterium with promising applications in biofuel production, also contains a VapBC TA in the genome. Despite the structures of several VapBC family TAs have been determined, the toxin and anti-toxin components of C. thermocellum VapBC have very low sequence identity to the proteins in PDB. Therefore, the structure and functional mechanism of this TA is largely unknown. Here we reported the NMR resonance assignments of the VapC toxin from C. thermocellum as a basis for further structural and functional studies.

  17. Resonance assignments of cohesin and dockerin domains from Clostridium acetobutylicum ATCC824.

    Science.gov (United States)

    Cui, Zhenling; Li, Yifei; Xiao, Yan; Feng, Yingang; Cui, Qiu; Cui, Qui

    2013-04-01

    Cohesin and dockerin domains are critical assembling components of cellulosome, a large extracellular multienzyme complex which is used by anaerobic cellulolytic bacteria to efficiently degrade lignocellulose. According to sequence homology, cohesins can be divided into three major groups, whereas cohesins from Clostridium acetobutylicum are beyond these groups and emanate from a branching point between the type I and type III cohesins. Cohesins and dockerins from C. acetobutylicum show low sequence homology to those from other cellulolytic bacteria, and their interactions are specific in corresponding species. Therefore the interactions between cohesins and dockerins from C. acetobutylicum are meaningful to the studies of both cellulosome assembling mechanism and the construction of designer cellulosome. Here we report the NMR resonance assignments of one cohesin from cellulosome scaffoldin cipA and one dockerin from a cellulosomal glycoside hydrolase (family 9) of C. acetobutylicum for further structural determination and functional studies.

  18. NMR imaging of the head-neck region. Topography of function - clinical findings - imaging and spectroscopy

    International Nuclear Information System (INIS)

    Vogl, T.J.

    1991-01-01

    The book on nmr imaging in the head-neck region offers, on a total of 221 pages, 344 detailed representations with 141 figures and 44 tables. It provides information as to the relevant topography of function, presents clinical findings, explains imaging characteristics and also takes account of spectroscopic procedures. The multifarious methods of investigation are described and discussed in connection with the differential diagnoses. A score of suitable diagnostic measures is assigned to each region of examination. The method's value is assessed against that of other imaging techniques. (orig.) [de

  19. 1H NMR study of fermented cocoa (Theobroma cacao L.) beans.

    Science.gov (United States)

    Caligiani, Augusta; Acquotti, Domenico; Cirlini, Martina; Palla, Gerardo

    2010-12-08

    This study reports for the first time the metabolic profile of cocoa (Theobroma cacao L.) beans using the (1)H NMR technique applied to polar extracts of fermented cocoa beans. The simultaneous detection and quantification of amino acids, polyalcohols, organic acids, sugars, methylxanthines, catechins, and phenols were obtained by assigning the major signals of the spectra for different varieties of cocoa beans (Forastero, Criollo, and Trinitario) from different countries (Ecuador, Ghana, Grenada, and Trinidad). The data set obtained, representative of all classes of soluble compounds of cocoa, was useful to characterize the fermented cocoa beans as a function of the variety and geographic origin.

  20. (1)H, (15)N and (13)C resonance assignments of translationally-controlled tumor protein from photosynthetic microalga Nannochloropsis oceanica.

    Science.gov (United States)

    Yao, Xingzhe; Xiao, Yan; Cui, Qiu; Feng, Yingang

    2015-10-01

    Translationally-controlled tumor protein (TCTP) is a eukaryote-conserved protein with crucial roles in cellular growth. It has also been proposed that plant TCTP has functions specific to plant, while no structure of TCTP from photosynthetic organism has been reported. Nannochloropsis is a photosynthetic microalga with high yield of lipid and high-value polyunsaturated fatty acid, which is promising for biodiesel production. Study of growth-related proteins may provide new clue for improving the yield of lipid. TCTP from Nannochloropsis oceanica shares low sequence identity with structure-known TCTPs. Here we reported the NMR resonance assignments of TCTP from N. oceanica for further structural and functional studies.

  1. 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

  2. Recommendations of the wwPDB NMR Validation Task Force

    Science.gov (United States)

    Montelione, Gaetano T.; Nilges, Michael; Bax, Ad; Güntert, Peter; Herrmann, Torsten; Richardson, Jane S.; Schwieters, Charles; Vranken, Wim F.; Vuister, Geerten W.; Wishart, David S.; Berman, Helen M.; Kleywegt, Gerard J.; Markley, John L.

    2013-01-01

    As methods for analysis of biomolecular structure and dynamics using nuclear magnetic resonance spectroscopy (NMR) continue to advance, the resulting 3D structures, chemical shifts, and other NMR data are broadly impacting biology, chemistry, and medicine. Structure model assessment is a critical area of NMR methods development, and is an essential component of the process of making these structures accessible and useful to the wider scientific community. For these reasons, the Worldwide Protein Data Bank (wwPDB) has convened an NMR Validation Task Force (NMR-VTF) to work with the wwPDB partners in developing metrics and policies for biomolecular NMR data harvesting, structure representation, and structure quality assessment. This paper summarizes the recommendations of the NMR-VTF, and lays the groundwork for future work in developing standards and metrics for biomolecular NMR structure quality assessment. PMID:24010715

  3. Current NMR Techniques for Structure-Based Drug Discovery.

    Science.gov (United States)

    Sugiki, Toshihiko; Furuita, Kyoko; Fujiwara, Toshimichi; Kojima, Chojiro

    2018-01-12

    A variety of nuclear magnetic resonance (NMR) applications have been developed for structure-based drug discovery (SBDD). NMR provides many advantages over other methods, such as the ability to directly observe chemical compounds and target biomolecules, and to be used for ligand-based and protein-based approaches. NMR can also provide important information about the interactions in a protein-ligand complex, such as structure, dynamics, and affinity, even when the interaction is too weak to be detected by ELISA or fluorescence resonance energy transfer (FRET)-based high-throughput screening (HTS) or to be crystalized. In this study, we reviewed current NMR techniques. We focused on recent progress in NMR measurement and sample preparation techniques that have expanded the potential of NMR-based SBDD, such as fluorine NMR ( 19 F-NMR) screening, structure modeling of weak complexes, and site-specific isotope labeling of challenging targets.

  4. Pentacyclic triterpenoids of Mentha villosa: structural identification and {sup 1}H and {sup 13}C resonance assignments; Triterpenoides pentaciclicos de Mentha villosa: identificacao estrutural e atribuicao dos deslocamentos quimicos dos atomos de hidrogenio e carbono

    Energy Technology Data Exchange (ETDEWEB)

    Monte, Francisco J. Queiroz; Oliveira, Eliete F. de [Ceara Univ., Fortaleza, CE (Brazil). Dept. de Quimica Organica e Inorganica; Braz Filho, Raimundo [Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, RJ (Brazil). Setor de Quimica de Produtos Naturais

    2001-08-01

    The structures of seven oleanene and ursene triterpenoids (1-7) isolated from aerial parts of Mentha villosa were identified. In addition, the complete {sup 1} H and {sup 13} C resonance assignments of these triterpenoids were accomplished using 1D and 2D NMR spectroscopic experiments. (author)

  5. Mathematical Modeling and Optimizing ofin VitroHormonal Combination for G × N15 Vegetative Rootstock Proliferation Using Artificial Neural Network-Genetic Algorithm (ANN-GA).

    Science.gov (United States)

    Arab, Mohammad M; Yadollahi, Abbas; Ahmadi, Hamed; Eftekhari, Maliheh; Maleki, Masoud

    2017-01-01

    The efficiency of a hybrid systems method which combined artificial neural networks (ANNs) as a modeling tool and genetic algorithms (GAs) as an optimizing method for input variables used in ANN modeling was assessed. Hence, as a new technique, it was applied for the prediction and optimization of the plant hormones concentrations and combinations for in vitro proliferation of Garnem (G × N15) rootstock as a case study. Optimizing hormones combination was surveyed by modeling the effects of various concentrations of cytokinin-auxin, i.e., BAP, KIN, TDZ, IBA, and NAA combinations (inputs) on four growth parameters (outputs), i.e., micro-shoots number per explant, length of micro-shoots, developed callus weight (CW) and the quality index (QI) of plantlets. Calculation of statistical values such as R 2 (coefficient of determination) related to the accuracy of ANN-GA models showed a considerably higher prediction accuracy for ANN models, i.e., micro-shoots number: R 2 = 0.81, length of micro-shoots: R 2 = 0.87, CW: R 2 = 0.88, QI: R 2 = 0.87. According to the results, among the input variables, BAP (19.3), KIN (9.64), and IBA (2.63) showed the highest values of variable sensitivity ratio for proliferation rate. The GA showed that media containing 1.02 mg/l BAP in combination with 0.098 mg/l IBA could lead to the optimal proliferation rate (10.53) for G × N15 rootstock. Another objective of the present study was to compare the performance of predicted and optimized cytokinin-auxin combination with the best optimized obtained concentrations of our other experiments. Considering three growth parameters (length of micro-shoots, micro-shoots number, and proliferation rate), the last treatment was found to be superior to the rest of treatments for G × N15 rootstock in vitro multiplication. Very little difference between the ANN predicted and experimental data confirmed high capability of ANN-GA method in predicting new optimized protocols for plant in vitro propagation.

  6. Unique opportunities for NMR methods in structural genomics.

    Science.gov (United States)

    Montelione, Gaetano T; Arrowsmith, Cheryl; Girvin, Mark E; Kennedy, Michael A; Markley, John L; Powers, Robert; Prestegard, James H; Szyperski, Thomas

    2009-04-01

    This Perspective, arising from a workshop held in July 2008 in Buffalo NY, provides an overview of the role NMR has played in the United States Protein Structure Initiative (PSI), and a vision of how NMR will contribute to the forthcoming PSI-Biology program. NMR has contributed in key ways to structure production by the PSI, and new methods have been developed which are impacting the broader protein NMR community.

  7. Some exercises in quantitative NMR imaging

    International Nuclear Information System (INIS)

    Bakker, C.J.G.

    1985-01-01

    The articles represented in this thesis result from a series of investigations that evaluate the potential of NMR imaging as a quantitative research tool. In the first article the possible use of proton spin-lattice relaxation time T 1 in tissue characterization, tumor recognition and monitoring tissue response to radiotherapy is explored. The next article addresses the question whether water proton spin-lattice relaxation curves of biological tissues are adequately described by a single time constant T 1 , and analyzes the implications of multi-exponentiality for quantitative NMR imaging. In the third article the use of NMR imaging as a quantitative research tool is discussed on the basis of phantom experiments. The fourth article describes a method which enables unambiguous retrieval of sign information in a set of magnetic resonance images of the inversion recovery type. The next article shows how this method can be adapted to allow accurate calculation of T 1 pictures on a pixel-by-pixel basis. The sixth article, finally, describes a simulation procedure which enables a straightforward determination of NMR imaging pulse sequence parameters for optimal tissue contrast. (orig.)

  8. Quantitative evaluation of experimental NMR restraints.

    NARCIS (Netherlands)

    Nabuurs, S.B.; Spronk, C.A.E.M.; Krieger, E.; Maassen, Hans; Vriend, G.; Vuister, G.W.

    2003-01-01

    Nuclear Overhauser effect (NOE) data are an indispensable source of structural information in biomolecular structure determination by NMR spectroscopy. The number and type of experimental restraints used in the structure calculation and the RMS deviation of the restraints are usually reported. We

  9. Quantification of complex mixtures by NMR

    NARCIS (Netherlands)

    Duynhoven, van J.P.M.; Velzen, van E.; Jacobs, D.M.

    2013-01-01

    NMR has firmly established itself as an analytical tool that can quantify analyte concentrations in complex mixtures in a rapid, cost-effective, accurate and precise manner. Here, the technological advances with respect to instrumentation, sample preparation, data acquisition and data processing

  10. NMR characterization of polymers: Review and update

    Science.gov (United States)

    NMR spectroscopy is a major technique for the characterization and analysis of polymers. A large number of methodologies have been developed in both the liquid and the solid state, and the literature has grown considerably (1-5). The field now covers a broad spectrum of activities, including polym...

  11. Structures of Biomolecules by NMR Spectroscopy

    Indian Academy of Sciences (India)

    IAS Admin

    GENERAL | ARTICLE integral part of NMR-based structural biology research. A num- ber of computational tools are being developed which utilize such information from BMRB and PDB at various stages of the structure determination process. 2. An Overview of the Structure Determination Process. A flowchart of the different ...

  12. Hyperpolarized NMR Probes for Biological Assays

    Directory of Open Access Journals (Sweden)

    Sebastian Meier

    2014-01-01

    Full Text Available During the last decade, the development of nuclear spin polarization enhanced (hyperpolarized molecular probes has opened up new opportunities for studying the inner workings of living cells in real time. The hyperpolarized probes are produced ex situ, introduced into biological systems and detected with high sensitivity and contrast against background signals using high resolution NMR spectroscopy. A variety of natural, derivatized and designed hyperpolarized probes has emerged for diverse biological studies including assays of intracellular reaction progression, pathway kinetics, probe uptake and export, pH, redox state, reactive oxygen species, ion concentrations, drug efficacy or oncogenic signaling. These probes are readily used directly under natural conditions in biofluids and are often directly developed and optimized for cellular assays, thus leaving little doubt about their specificity and utility under biologically relevant conditions. Hyperpolarized molecular probes for biological NMR spectroscopy enable the unbiased detection of complex processes by virtue of the high spectral resolution, structural specificity and quantifiability of NMR signals. Here, we provide a survey of strategies used for the selection, design and use of hyperpolarized NMR probes in biological assays, and describe current limitations and developments.

  13. Structural Studies of Biological Solids Using NMR

    Science.gov (United States)

    Ramamoorthy, Ayyalusamy

    2011-03-01

    High-resolution structure and dynamics of biological molecules are important in understanding their function. While studies have been successful in solving the structures of water-soluble biomolecules, it has been proven difficult to determine the structures of membrane proteins and fibril systems. Recent studies have shown that solid-state NMR is a promising technique and could be highly valuable in studying such non-crystalline and non-soluble biosystems. I will present strategies to study the structures of such challenging systems and also about the applications of solid-state NMR to study the modes of membrane-peptide interactions for a better assessment of the prospects of antimicrobial peptides as substitutes to antibiotics in the control of human disease. Our studies on the mechanism of membrane disruption by LL-37 (a human antimicrobial peptide), analogs of the naturally occurring antimicrobial peptide magainin2 extracted from the skin of the African frog Xenopus Laevis, and pardaxin will be presented. Solid-state NMR experiments were used to determine the secondary structure, dynamics and topology of these peptides in lipid bilayers. Similarities and difference in the cell-lysing mechanism, and their dependence on the membrane composition, of these peptides will be discussed. Atomic-level resolution NMR structures of amyloidogenic proteins revealing the misfolding pathway and early intermediates that play key roles in amyloid toxicity will also be presented.

  14. Hydrate Shell Growth Measured Using NMR.

    Science.gov (United States)

    Haber, Agnes; Akhfash, Masoumeh; Loh, Charles K; Aman, Zachary M; Fridjonsson, Einar O; May, Eric F; Johns, Michael L

    2015-08-18

    Benchtop nuclear magnetic resonance (NMR) pulsed field gradient (PFG) and relaxation measurements were used to monitor the clathrate hydrate shell growth occurring in water droplets dispersed in a continuous cyclopentane phase. These techniques allowed the growth of hydrate inside the opaque exterior shell to be monitored and, hence, information about the evolution of the shell's morphology to be deduced. NMR relaxation measurements were primarily used to monitor the hydrate shell growth kinetics, while PFG NMR diffusion experiments were used to determine the nominal droplet size distribution (DSD) of the unconverted water inside the shell core. A comparison of mean droplet sizes obtained directly via PFG NMR and independently deduced from relaxation measurements showed that the assumption of the shell model-a perfect spherical core of unconverted water-for these hydrate droplet systems is correct, but only after approximately 24 h of shell growth. Initially, hydrate growth is faster and heat-transfer-limited, leading to porous shells with surface areas larger than that of spheres with equivalent volumes. Subsequently, the hydrate growth rate becomes mass-transfer-limited, and the shells become thicker, spherical, and less porous.

  15. Advanced Laboratory NMR Spectrometer with Applications.

    Science.gov (United States)

    Biscegli, Clovis; And Others

    1982-01-01

    A description is given of an inexpensive nuclear magnetic resonance (NMR) spectrometer suitable for use in advanced laboratory courses. Applications to the nondestructive analysis of the oil content in corn seeds and in monitoring the crystallization of polymers are presented. (SK)

  16. NMR imaging of the cardiovascular system

    International Nuclear Information System (INIS)

    Canby, R.C.; Evanochko, W.T.; Pohost, G.M.

    1986-01-01

    Proton nuclear magnetic resonance (NMR) imaging permits high-resolution tomographic and three-dimensional images of the human body to be obtained without exposure to ionizing radiation. Such imaging not only yields anatomic resolution comparable to X-ray examinations but also provides a potential means to discriminate between healthy tissue and diseased tissue. This potential is based on certain NMR properties known as relaxation times, which determine, in part, the signal intensity in an image. These properties are related to such factors as the sizes and concentrations of proteins and mobile lipids and the compartmentalization of the protons of water. Although NMR imaging (also called magnetic resonance imaging, MRI) is becoming widely available for clinical use, application to the cardiovascular system, though promising, remains primarily a research tool. Gated proton NMR imaging can generate cardiac images with excellent morphologic detail and contrast; however, its ultimate importance as a cardiovascular diagnostic modality will depend on the development of several unique applications. These applications are discussed in this paper

  17. The bar coil for NMR tomograph

    International Nuclear Information System (INIS)

    Bogorodzki, P.; Piatkowski, A.; Wasielewski, J.

    1995-01-01

    The bar coil (bi-planar) for the NMR tomograph, designed for medical diagnostics, has been described. The tests of coil shown that it generates good homogenous magnetic field in a big volume what results in improving of the signal-to-noise ratio

  18. NMR blood vessel imaging method and apparatus

    International Nuclear Information System (INIS)

    Riederer, S.J.

    1988-01-01

    A high speed method of forming computed images of blood vessels based on measurements of characteristics of a body is described comprising the steps of: subjecting a predetermined body area containing blood vessels of interest to, successively, applications of a short repetition time (TR) NMR pulse sequence during the period of high blood velocity and then to corresponding applications during the period of low blood velocity for successive heart beat cycles; weighting the collected imaging data from each application of the NMR pulse sequence according to whether the data was acquired during the period of high blood velocity or a period of low blood velocity of the corresponding heart beat cycle; accumulating weighted imaging data from a plurality of NMR pulse sequences corresponding to high blood velocity periods and from a plurality of NMR pulse sequences corresponding to low blood velocity periods; subtracting the weighted imaging data corresponding to each specific phase encoding acquired during the high blood velocity periods from the weighted imaging data for the same phase encoding corresponding to low blood velocity periods in order to compute blood vessel imaging data; and forming an image of the blood vessels of interest from the blood vessel imaging data

  19. Theoretical molecular structure, vibrational frequencies and NMR ...

    African Journals Online (AJOL)

    Theoretical results have been successfully compared with available experimental data in the literature. Regarding the calculations, 2mpe-4bb prefers enol-imine form and DFT method is superior to HF approach except for predicting bond lengths. KEY WORDS: Schiff bases, Normal mode frequencies, HF, DFT, NMR. Bull.

  20. Recent Advances in Targeted and Untargeted Metabolomics by NMR and MS/NMR Methods

    Energy Technology Data Exchange (ETDEWEB)

    Bingol, Ahmet K.

    2018-04-18

    Metabolomics has made significant progress in multiple fronts in the last 18 months. This minireview aimed to give an overview of these advancements in the light of their contribution to targeted and untargeted metabolomics. New computational approaches have emerged to overcome manual absolute quantitation step of metabolites in 1D 1H NMR spectra. This provides more consistency between inter-laboratory comparisons. Integration of 2D NMR metabolomics databases under a unified web server allowed very accurate identification of the metabolites that have been catalogued in these databases. For the remaining uncatalogued and unknown metabolites, new cheminformatics approaches have been developed by combining NMR and mass spectrometry. These hybrid NMR/MS approaches accelerated the identification of unknowns in untargeted studies, and now they are allowing to profile ever larger number of metabolites in application studies.