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714 results on '"Schwalbe H"'

101. FXR with DM175 and NCoA-2 peptide

Author

Kudlinzki, D., primary, Merk, D., additional, Linhard, V.L., additional, Saxena, K., additional, Sreeramulu, S., additional, Nilsson, E., additional, Dekker, N., additional, Wissler, L., additional, Bamberg, K., additional, Schubert-Zsilavecz, M., additional, and Schwalbe, H., additional

Published
2015
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105. e-NMR gLite grid enabled infrastructure

Author

Ferreira, N.L., Wassenaar, T.A., de Vries, S.J., van Dijk, M., van der Schot, G., van der Zwan, J., Boelens, R., Bonvin, A.M.J.J., Giachetti, A., Carotenuto, D., Rosato, A., Bertini, I., Herrmann, T., Bagaria, A., Zharavin, V., Jonker, H.R.A., Güntert, P., Schwalbe, H., Vranken, W.F., Proença, A., Pina, A., García Tobío, J., Ribeiro, L., NMR Spectroscopy, Sub NMR Spectroscopy, and Dep Scheikunde

Abstract

The e-NMR project is an European e-infrastructure that aims at providing the bio-NMR community with a software platform integrating and streamlining computational approaches necessary for NMR data analysis. The infrastructure is grid enabled with fteen gLite based partners sharing computational resources. A main focus of the consortium is to provide protocoled services through easy-to-use web interfaces, while retaining su cient exibility to handle speci c requests by expert users. Various programs relevant for structural biology scientists are grid ported and already available through the e-NMR web portal, including HADDOCK, XPLORNIH, CYANA and CS-ROSETTA among others. A general overview of the project current status toward EGEE/EGI integration, as well as brief guidelines on how to become an e-NMR site/user will be considered. With more than 170 registered users, enmr.eu is currently the second largest virtual organization in the life sciences. The state of the project can be found on the web page http://www.enmr.eu.

Published
2010

106. The state of the art of chemical biology

Author

Altmann, K.H., Buchner J., Kessler H., Diederich F., Krautler B., Lippard S., Liskamp R., Müller K., Nolan E.M., Samorì B., Schneider G., Schreiber S.L., Schwalbe H., Toniolo C., van Boecker C.A.A., Waldmann H., and Walsch C.T.

Published
2009

107. Inhibition of HIV-1 by a peptid ligand of the genomic RNA packaging signal Psi

Author

Dietz, J., Koch, J., Kaur, A., Raja, C., Stein, S., Grez, M., Pustowka, A., Mensch, S., Ferner, J., Möller, L., Bannert, N., Tampe, R., Divita, G., Mely, Y., Schwalbe, H., Dietrich, U., Institut Gilbert-Laustriat : Biomolécules, Biotechnologie, Innovation Thérapeutique, Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), and Barthel, Ingrid

Published
2008

109. NMR in the SPINE Structural Proteomics project

Author

AB, E., Atkinson, A.R., Banci, L., Bertini, I., Ciofi-Baffoni, S., Brunner, K., Diercks, T., Doetsch, V, Engelke, F., Folkers, G.E., Griesinger, C., Gronwald, W., Gunther, U., Habeck, M., de Jong, R.N., Kalbitzer, H.R., Kieffer, B., Leeflang, B.R., Loss, S., Luchinat, C., Marquardsen, T., Moskau, D., Neidig, K.P., Nilges, M., Piccioli, M., Pierattelli, R., Rieping, W., Schippmann, T., Schwalbe, H., Travé, G., Trenner, J., Wöhnert, J., Zweckstetter, M., Kaptein, R., Chemie van glyco-conjugaten, NMR-spectroscopie, and Dep Scheikunde

Published
2006

110. Glutamic acid-rich proteins of rod photoreceptors are natively unfolded

Author

Batra-Safferling, R., Abarca-Heidemann, K., Körschen, H. G., Tziatzios, C., Stoldt, M., Budyak, I., Willbold, D., Schwalbe, H., Klein-Seetharaman, J., and Kaupp, U. B.

Subjects
carbohydrates (lipids), ddc:570
Abstract

Broadly neutralizing HIV antibodies (bNAbs) can recognize carbohydrate-dependent epitopes on gp120. In contrast to previously characterized glycan-dependent bNAbs that recognize high-mannose N-glycans, PGT121 binds complex-type N-glycans in glycan microarrays. We isolated the B-cell clone encoding PGT121, which segregates into PGT121-like and 10-1074-like groups distinguished by sequence, binding affinity, carbohydrate recognition, and neutralizing activity. Group 10-1074 exhibits remarkable potency and breadth but no detectable binding to protein-free glycans. Crystal structures of unliganded PGT121, 10-1074, and their likely germ-line precursor reveal that differential carbohydrate recognition maps to a cleft between complementarity determining region (CDR)H2 and CDRH3. This cleft was occupied by a complex-type N-glycan in a "liganded" PGT121 structure. Swapping glycan contact residues between PGT121 and 10-1074 confirmed their importance for neutralization. Although PGT121 binds complex-type N-glycans, PGT121 recognized high-mannose-only HIV envelopes in isolation and on virions. As HIV envelopes exhibit varying proportions of high-mannose- and complex-type N-glycans, these results suggest promiscuous carbohydrate interactions, an advantageous adaptation ensuring neutralization of all viruses within a given strain.

Published
2006

113. Tracing the tail of ubiquinone in mitochondrial complex I

Author

Angerer, H., Nasiri, H.R., Niedergesass, V., Kerscher, S., Schwalbe, H., Brandt, U., Angerer, H., Nasiri, H.R., Niedergesass, V., Kerscher, S., Schwalbe, H., and Brandt, U.

Abstract

Item does not contain fulltext, Mitochondrial complex I (proton pumping NADH:ubiquinone oxidoreductase) is the largest and most complicated component of the respiratory electron transfer chain. Despite its central role in biological energy conversion the structure and function of this membrane integral multiprotein complex is still poorly understood. Recent insights into the structure of complex I by X-ray crystallography have shown that iron-sulfur cluster N2, the immediate electron donor for ubiquinone, resides about 30A above the membrane domain and mutagenesis studies suggested that the active site for the hydrophobic substrate is located next to this redox-center. To trace the path for the hydrophobic tail of ubiquinone when it enters the peripheral arm of complex I, we performed an extensive structure/function analysis of complex I from Yarrowia lipolytica monitoring the interaction of site-directed mutants with five ubiquinone derivatives carrying different tails. The catalytic activity of a subset of mutants was strictly dependent on the presence of intact isoprenoid moieties in the tail. Overall a consistent picture emerged suggesting that the tail of ubiquinone enters through a narrow path at the interface between the 49-kDa and PSST subunits. Most notably we identified a set of methionines that seems to form a hydrophobic gate to the active site reminiscent to the M-domains involved in the interaction with hydrophobic targeting sequences with the signal recognition particle of the endoplasmic reticulum. Interestingly, two of the amino acids critical for the interaction with the ubiquinone tail are different in bovine complex I and we could show that one of these exchanges is responsible for the lower sensitivity of Y. lipolytica complex I towards the inhibitor rotenone. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).

Published
2012

114. Blind testing of routine, fully automated determination of protein structures from NMR data.

Author

Rosato, A., Aramini, J.M., Arrowsmith, C., Bagaria, A., Baker, D., Cavalli, A., Doreleijers, J., Eletsky, A., Giachetti, A., Guerry, P., Gutmanas, A., Guntert, P., He, Y., Herrmann, T., Huang, Y.J., Jaravine, V., Jonker, H.R., Kennedy, M.A., Lange, O.F., Liu, G., Malliavin, T.E., Mani, R., Mao, B., Montelione, G.T., Nilges, M., Rossi, P., Schot, G. van der, Schwalbe, H., Szyperski, T.A., Vendruscolo, M., Vernon, R., Vranken, W.F., Vries, S.D. de, Vuister, G.W., Wu, B., Yang, Y., Bonvin, A.M., Rosato, A., Aramini, J.M., Arrowsmith, C., Bagaria, A., Baker, D., Cavalli, A., Doreleijers, J., Eletsky, A., Giachetti, A., Guerry, P., Gutmanas, A., Guntert, P., He, Y., Herrmann, T., Huang, Y.J., Jaravine, V., Jonker, H.R., Kennedy, M.A., Lange, O.F., Liu, G., Malliavin, T.E., Mani, R., Mao, B., Montelione, G.T., Nilges, M., Rossi, P., Schot, G. van der, Schwalbe, H., Szyperski, T.A., Vendruscolo, M., Vernon, R., Vranken, W.F., Vries, S.D. de, Vuister, G.W., Wu, B., Yang, Y., and Bonvin, A.M.

Abstract

Item does not contain fulltext, The protocols currently used for protein structure determination by nuclear magnetic resonance (NMR) depend on the determination of a large number of upper distance limits for proton-proton pairs. Typically, this task is performed manually by an experienced researcher rather than automatically by using a specific computer program. To assess whether it is indeed possible to generate in a fully automated manner NMR structures adequate for deposition in the Protein Data Bank, we gathered 10 experimental data sets with unassigned nuclear Overhauser effect spectroscopy (NOESY) peak lists for various proteins of unknown structure, computed structures for each of them using different, fully automatic programs, and compared the results to each other and to the manually solved reference structures that were not available at the time the data were provided. This constitutes a stringent "blind" assessment similar to the CASP and CAPRI initiatives. This study demonstrates the feasibility of routine, fully automated protein structure determination by NMR.

Published
2012

116. Side-chain conformations in an unfolded protein: chi1 distributions in denatured hen lysozyme determined by heteronuclear 13C, 15N NMR spectroscopy

Author

Hennig, M, Bermel, W, Spencer, A, Dobson, C, Smith, L, and Schwalbe, H

Abstract

Using a 13C and 15N-labelled sample, multi-dimensional heteronuclear NMR techniques have been carried out to characterise hen lysozyme denatured in 8 M urea at pH 2.0. The measurement of 3J(C',Cgamma) and 3J(N,Cgamma) coupling constants has enabled side-chain chi1 torsion angle populations to be probed in the denatured polypeptide chain. Analysis of the coupling constant data has allowed the relative populations of the three staggered rotamers about chi1 to be defined for 51 residues. The amino acids can broadly be divided into five classes that show differing side-chain conformational preferences in the denatured state. These range from a strong preference for the -60 degrees chi1 rotamer for methionine and leucine (74-79 % population) to a favouring of the +60 degrees chi1 rotamer for threonine (67 % population). The differences in behaviour reflect the steric and electrostatic characteristics of the side-chains concerned. A close agreement is seen between the chi1 populations calculated from the experimental coupling constant data and predictions from the statistical model for a random coil that uses the chi1 torsion angle distributions in a data base of native protein structures. Short-range interactions therefore dominate in determining the local conformational properties of side-chains in a denatured protein. Deviations are, however, observed for many of the aromatic residues involved in hydrophobic clusters within the denatured protein. For these residues the effects of additional non-local interactions in the clusters presumably play a major role in determining the chi1 preferences.

Published
1999

117. e-NMR gLite grid enabled infrastructure

Author

NMR Spectroscopy, Sub NMR Spectroscopy, Dep Scheikunde, Ferreira, N.L., Wassenaar, T.A., de Vries, S.J., van Dijk, M., van der Schot, G., van der Zwan, J., Boelens, R., Bonvin, A.M.J.J., Giachetti, A., Carotenuto, D., Rosato, A., Bertini, I., Herrmann, T., Bagaria, A., Zharavin, V., Jonker, H.R.A., Güntert, P., Schwalbe, H., Vranken, W.F., Proença, A., Pina, A., García Tobío, J., Ribeiro, L., NMR Spectroscopy, Sub NMR Spectroscopy, Dep Scheikunde, Ferreira, N.L., Wassenaar, T.A., de Vries, S.J., van Dijk, M., van der Schot, G., van der Zwan, J., Boelens, R., Bonvin, A.M.J.J., Giachetti, A., Carotenuto, D., Rosato, A., Bertini, I., Herrmann, T., Bagaria, A., Zharavin, V., Jonker, H.R.A., Güntert, P., Schwalbe, H., Vranken, W.F., Proença, A., Pina, A., García Tobío, J., and Ribeiro, L.

Published
2010

118. New principle for the determination of coupling constants that largely suppresses differential relaxation effects

Author

Rexroth, A., Schmidt, P., Geppert, T., Schwalbe, H., Griesinger, C., and Szalma, S.

Subjects
Macromolecules -- Research, Relaxation phenomena -- Analysis, Chemistry
Abstract

The three-spin system ABC used to measure a large J(A,C) (coupling constant) and a small coupling J(B,C) constant in large isotopically labeled biomacromolecules decreases the differential relaxation by about a factor of 10. The double quantum (DQC) and zero quantum coherences (ZQC) are used to obtain the sums and differences of the coupling constants. The new method is expected to yield coupling constant values Jeff for molecules up to three times as large as the analyzed molecules.

Published
1995

119. F-labeling of the adenine H2-site to study large RNAs by NMR spectroscopy.

Author

Sochor, F., Silvers, R., Müller, D., Richter, C., Fürtig, B., and Schwalbe, H.

Abstract

In comparison to proteins and protein complexes, the size of RNA amenable to NMR studies is limited despite the development of new isotopic labeling strategies including deuteration and ligation of differentially labeled RNAs. Due to the restricted chemical shift dispersion in only four different nucleotides spectral resolution remains limited in larger RNAs. Labeling RNAs with the NMR-active nucleus F has previously been introduced for small RNAs up to 40 nucleotides (nt). In the presented work, we study the natural occurring RNA aptamer domain of the guanine-sensing riboswitch comprising 73 nucleotides from Bacillus subtilis. The work includes protocols for improved in vitro transcription of 2-fluoroadenosine-5′-triphosphat (2F-ATP) using the mutant P266L of the T7 RNA polymerase. Our NMR analysis shows that the secondary and tertiary structure of the riboswitch is fully maintained and that the specific binding of the cognate ligand hypoxanthine is not impaired by the introduction of the F isotope. The thermal stability of the F-labeled riboswitch is not altered compared to the unmodified sequence, but local base pair stabilities, as measured by hydrogen exchange experiments, are modulated. The characteristic change in the chemical shift of the imino resonances detected in a H,N-HSQC allow the identification of Watson-Crick base paired uridine signals and the F resonances can be used as reporters for tertiary and secondary structure transitions, confirming the potential of F-labeling even for sizeable RNAs in the range of 70 nucleotides. [ABSTRACT FROM AUTHOR]

Published
2016
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120. NMR in the SPINE Structural Proteomics project

Author

Chemie van glyco-conjugaten, NMR-spectroscopie, Dep Scheikunde, AB, E., Atkinson, A.R., Banci, L., Bertini, I., Ciofi-Baffoni, S., Brunner, K., Diercks, T., Doetsch, V, Engelke, F., Folkers, G.E., Griesinger, C., Gronwald, W., Gunther, U., Habeck, M., de Jong, R.N., Kalbitzer, H.R., Kieffer, B., Leeflang, B.R., Loss, S., Luchinat, C., Marquardsen, T., Moskau, D., Neidig, K.P., Nilges, M., Piccioli, M., Pierattelli, R., Rieping, W., Schippmann, T., Schwalbe, H., Travé, G., Trenner, J., Wöhnert, J., Zweckstetter, M., Kaptein, R., Chemie van glyco-conjugaten, NMR-spectroscopie, Dep Scheikunde, AB, E., Atkinson, A.R., Banci, L., Bertini, I., Ciofi-Baffoni, S., Brunner, K., Diercks, T., Doetsch, V, Engelke, F., Folkers, G.E., Griesinger, C., Gronwald, W., Gunther, U., Habeck, M., de Jong, R.N., Kalbitzer, H.R., Kieffer, B., Leeflang, B.R., Loss, S., Luchinat, C., Marquardsen, T., Moskau, D., Neidig, K.P., Nilges, M., Piccioli, M., Pierattelli, R., Rieping, W., Schippmann, T., Schwalbe, H., Travé, G., Trenner, J., Wöhnert, J., Zweckstetter, M., and Kaptein, R.

Published
2006

121. Measurement of C',C coupling constants in 13C-labeled proteins: a new method for the stereospecific assignment of gamma-methyl groups in valine residues

Author

Schwalbe, H., Rexroth, A., Eggenberger, U., Geppert, T., and Griesinger, C.

Subjects
Proteins -- Affinity labeling, Amino acids -- Analysis, Chemistry
Abstract

Proteins were uniformly labeled for the stereospecific assignments of valine methyl groups, and a new technique was developed to estimate 3J(C', C-gamma) couplings. The methodology is based on the E. Cosy3,4 technique to estimate small coupling constants, which has been effectively utilized in homo and heteronuclear spin systems. It is also based on the fairly massive J(C', C-alpha) coupling of around 55 Hz between the C' and C-alpha carbons in amino acids.

Published
1993

122. NMR solution structure of apo-MptpA

Author

Stehle, T., primary, Sreeramulu, S., additional, Loehr, F., additional, Richter, C., additional, Saxena, K., additional, Jonker, H.R.A., additional, and Schwalbe, H., additional

Published
2012
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126. Stereospecific assignment of leucine methyl groups with 13C in natural abundance or with random 13C labeling

Author

Sattler, M., Schwalbe, H., and Griesinger, C.

Subjects
Leucine -- Research, Methyl groups -- Research, Peptides -- Research, Chemistry
Abstract

The stereospecific assignment of leucine methyl groups is undertaken using a heteronuclear NMR procedure. The procedure may be used for both polypeptides with carbon in natural abundance and randomly labeled polypeptides possessing 13C at least in the delta positions. Moreover, the stereochemical assignment of the H(sub beta) protons and the resolution in either the carbon or proton domain of the signals of the two methyl groups are necessary. There are no constraints on the method and is applied with leucine in cyclolinopeptide A.

Published
1992

128. Thiostrepton, epimer form of residue 9

Author

Jonker, H.R.A., primary, Baumann, S., additional, Wolf, A., additional, Schoof, S., additional, Hiller, F., additional, Schulte, K.W., additional, Kirschner, K.N., additional, Schwalbe, H., additional, and Arndt, H.-D., additional

Published
2011
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129. Thiostrepton, oxidized at CA-CB bond of residue 9

Author

Jonker, H.R.A., primary, Baumann, S., additional, Wolf, A., additional, Schoof, S., additional, Hiller, F., additional, Schulte, K.W., additional, Kirschner, K.N., additional, Schwalbe, H., additional, and Arndt, H.-D., additional

Published
2011
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130. Thiostrepton, reduced at N-CA bond of residue 14

Author

Jonker, H.R.A., primary, Baumann, S., additional, Wolf, A., additional, Schoof, S., additional, Hiller, F., additional, Schulte, K.W., additional, Kirschner, K.N., additional, Schwalbe, H., additional, and Arndt, H.-D., additional

Published
2011
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131. Thiostrepton

Author

Jonker, H.R.A., primary, Baumann, S., additional, Wolf, A., additional, Schoof, S., additional, Hiller, F., additional, Schulte, K.W., additional, Kirschner, K.N., additional, Schwalbe, H., additional, and Arndt, H.-D., additional

Published
2011
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132. Interleukin-1-beta LBT L3 Mutant

Author

Barthelmes, K., primary, Reynolds, A.M., additional, Peisach, E., additional, Jonker, H.R.A., additional, DeNunzio, N.J., additional, Allen, K.N., additional, Imperiali, B., additional, and Schwalbe, H., additional

Published
2011
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137. Measurement of 2J(H,C)- and 3J(H,C)-coupling constants by alpha/beta selective HC(C)H-TOCSY.

Author

Duchardt, E., Richter, C., Reif, B., Glaser, S.J., Engels, J.A., Griesinger, C., Schwalbe, H., Duchardt, E., Richter, C., Reif, B., Glaser, S.J., Engels, J.A., Griesinger, C., and Schwalbe, H.

Abstract

Item does not contain fulltext, A new heteronuclear NMR pulse sequence for the measurement of nJ(C,H) coupling constants, the alpha/beta selective HC(C)H-TOCSY, is described. It is shown that the S3E element (Meissner et al., 1997a,b) can be used to obtain spin state selective coherence transfer in molecules, in which adjacent CH moieties are labeled with 13C. Application of the alpha/beta selective HC(C)H-TOCSY to a 10 nt RNA tetraloop 5'-CGCUUUUGCG-3', in which the four uridine residues are 13C labeled in the sugar moiety, allowed measurement of two bond and three bond J(C,H) coupling constants, which provide additional restraints to characterize the sugar ring conformation of RNA in cases of conformational averaging.

Published
2001

147. Synthesis of Cylindramide

Author

Laschat, S., primary, Cramer, N., additional, Buchweitz, M., additional, Frey, W., additional, Baro, A., additional, Mathieu, D., additional, Richter, C., additional, and Schwalbe, H., additional

Published
2006
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