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Journal of Biomolecular NMR

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https://www.readbyqxmd.com/read/29143948/label-free-nmr-based-dissociation-kinetics-determination
#1
Pablo Trigo-Mouriño, Christian Griesinger, Donghan Lee
Understanding the dissociation of molecules is the basis to modulate interactions of biomedical interest. Optimizing drugs for dissociation rates is found to be important for their efficacy, selectivity, and safety. Here, we show an application of the high-power relaxation dispersion (RD) method to the determination of the dissociation rates of weak binding ligands from receptors. The experiment probes proton RD on the ligand and, therefore, avoids the need for any isotopic labeling. The large ligand excess eases the detection significantly...
November 16, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29143165/structure-of-monomeric-interleukin-8-and-its-interactions-with-the-n-terminal-binding-site-i-of-cxcr1-by-solution-nmr-spectroscopy
#2
Sabrina Berkamp, Sang Ho Park, Anna A De Angelis, Francesca M Marassi, Stanley J Opella
The structure of monomeric human chemokine IL-8 (residues 1-66) was determined in aqueous solution by NMR spectroscopy. The structure of the monomer is similar to that of each subunit in the dimeric full-length protein (residues 1-72), with the main differences being the location of the N-loop (residues 10-22) relative to the C-terminal α-helix and the position of the side chain of phenylalanine 65 near the truncated dimerization interface (residues 67-72). NMR was used to analyze the interactions of monomeric IL-8 (1-66) with ND-CXCR1 (residues 1-38), a soluble polypeptide corresponding to the N-terminal portion of the ligand binding site (Binding Site-I) of the chemokine receptor CXCR1 in aqueous solution, and with 1TM-CXCR1 (residues 1-72), a membrane-associated polypeptide that includes the same N-terminal portion of the binding site, the first trans-membrane helix, and the first intracellular loop of the receptor in nanodiscs...
November 15, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29134388/nicolaas-bloembergen-a-pioneer-in-magnetic-resonance-and%C3%A2-in-maser-and-laser-physics
#3
Rob Kaptein, Rolf Boelens, Claudio Luchinat
No abstract text is available yet for this article.
November 13, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29127559/a-13-c-detected-15-n-double-quantum-nmr-experiment-to-probe-arginine-side-chain-guanidinium-15-n-%C3%AE-chemical-shifts
#4
Harold W Mackenzie, D Flemming Hansen
Arginine side-chains are often key for enzyme catalysis, protein-ligand and protein-protein interactions. The importance of arginine stems from the ability of the terminal guanidinium group to form many key interactions, such as hydrogen bonds and salt bridges, as well as its perpetual positive charge. We present here an arginine (13)C(ζ)-detected NMR experiment in which a double-quantum coherence involving the two (15)N(η) nuclei is evolved during the indirect chemical shift evolution period. As the precession frequency of the double-quantum coherence is insensitive to exchange of the two (15)N(η); this new approach is shown to eliminate the previously deleterious line broadenings of (15)N(η) resonances caused by the partially restricted rotation about the C(ζ)-N(ε) bond...
November 10, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29119516/protein-nucleotide-contacts-in-motor-proteins-detected-by-dnp-enhanced-solid-state-nmr
#5
Thomas Wiegand, Wei-Chih Liao, Ta Chung Ong, Alexander Däpp, Riccardo Cadalbert, Christophe Copéret, Anja Böckmann, Beat H Meier
DNP (dynamic nuclear polarization)-enhanced solid-state NMR is employed to directly detect protein-DNA and protein-ATP interactions and identify the residue type establishing the intermolecular contacts. While conventional solid-state NMR can detect protein-DNA interactions in large oligomeric protein assemblies in favorable cases, it typically suffers from low signal-to-noise ratios. We show here, for the oligomeric DnaB helicase from Helicobacter pylori complexed with ADP and single-stranded DNA, that this limitation can be overcome by using DNP-enhanced spectroscopy...
November 8, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29119515/the-prosecco-server-for-chemical-shift-predictions-in-ordered-and-disordered-proteins
#6
Máximo Sanz-Hernández, Alfonso De Simone
The chemical shifts measured in solution-state and solid-state nuclear magnetic resonance (NMR) are powerful probes of the structure and dynamics of protein molecules. The exploitation of chemical shifts requires methods to correlate these data with the protein structures and sequences. We present here an approach to calculate accurate chemical shifts in both ordered and disordered proteins using exclusively the information contained in their sequences. Our sequence-based approach, protein sequences and chemical shift correlations (PROSECCO), achieves the accuracy of the most advanced structure-based methods in the characterization of chemical shifts of folded proteins and improves the state of the art in the study of disordered proteins...
November 8, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29116557/bidirectional-band-selective-magnetization-transfer-along-the-protein-backbone-doubles-the-information-content-of-solid-state-nmr-correlation-experiments
#7
M M Jolly, J A Jarvis, M Carravetta, M H Levitt, P T F Williamson
Resonance assignment is the first stage towards solving the structure of a protein. This is normally achieved by the employment of separate inter and intra residue experiments. By utilising the mixed rotation and rotary recoupling (MIRROR) condition it is possible to double the information content through the efficient bidirectional transfer of magnetization from the CO to its adjacent Cα and the Cα of the subsequent amino acid. We have incorporated this into a 3D experiment, a 3D-MIRROR-NCOCA, where correlations present in the 3D spectrum permit the sequential assignment of the protein backbone from a single experiment as we have demonstrated on a microcrystalline preparation of GB3...
November 8, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29098507/automatic-methyl-assignment-in-large-proteins-by-the-magic-algorithm
#8
Yoan R Monneau, Paolo Rossi, Anusarka Bhaumik, Chengdong Huang, Yajun Jiang, Tamjeed Saleh, Tao Xie, Qiong Xing, Charalampos G Kalodimos
Selective methyl labeling is an extremely powerful approach to study the structure, dynamics and function of biomolecules by NMR. Despite spectacular progress in the field, such studies remain rather limited in number. One of the main obstacles remains the assignment of the methyl resonances, which is labor intensive and error prone. Typically, NOESY crosspeak patterns are manually correlated to the available crystal structure or an in silico template model of the protein. Here, we propose methyl assignment by graphing inference construct, an exhaustive search algorithm with no peak network definition requirement...
November 2, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29094285/the-conformation-of-the-congo-red-ligand-bound-to-amyloid-fibrils-het-s-218-289-a-solid-state-nmr-study
#9
Chandrakala Gowda, Giorgia Zandomeneghi, Herbert Zimmermann, Anne K Schütz, Anja Böckmann, Matthias Ernst, Beat H Meier
We have previously shown that Congo red (CR) binds site specifically to amyloid fibrils formed by HET-s(218-289) with the long axis of the CR molecule almost parallel to the fibril axis. HADDOCK docking studies indicated that CR adopts a roughly planar conformation with the torsion angle ϕ characterizing the relative orientation of the two phenyl rings being a few degrees. In this study, we experimentally determine the torsion angle ϕ at the center of the CR molecule when bound to HET-s(218-289) amyloid fibrils using solid-state NMR tensor-correlation experiments...
November 1, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29071460/triple-resonance-formula-see-text-nmr-relaxation-experiments-for-studies-of-intrinsically-disordered-proteins
#10
Pavel Srb, Jiří Nováček, Pavel Kadeřávek, Alžbeta Rabatinová, Libor Krásný, Jitka Žídková, Janette Bobálová, Vladimír Sklenář, Lukáš Žídek
Description of protein dynamics is known to be essential in understanding their function. Studies based on a well established [Formula: see text] NMR relaxation methodology have been applied to a large number of systems. However, the low dispersion of [Formula: see text] chemical shifts very often observed within intrinsically disordered proteins complicates utilization of standard 2D HN correlated spectra because a limited number of amino acids can be characterized. Here we present a suite of triple resonance HNCO-type NMR experiments for measurements of five [Formula: see text] relaxation parameters ([Formula: see text], [Formula: see text], NOE, cross-correlated relaxation rates [Formula: see text] and [Formula: see text]) in doubly [Formula: see text],[Formula: see text]-labeled proteins...
October 25, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29063258/nmr-relaxation-parameters-of-methyl-groups-as-a-tool-to-map-the-interfaces-of-helix-helix-interactions-in-membrane-proteins
#11
D M Lesovoy, K S Mineev, P E Bragin, O V Bocharova, E V Bocharov, A S Arseniev
In the case of soluble proteins, chemical shift mapping is used to identify the intermolecular interfaces when the NOE-based calculations of spatial structure of the molecular assembly are impossible or impracticable. However, the reliability of the membrane protein interface mapping based on chemical shifts or other relevant parameters was never assessed. In the present work, we investigate the predictive power of various NMR parameters that can be used for mapping of helix-helix interfaces in dimeric TM domains...
October 23, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29043470/comprehensive-analysis-of-nmr-data-using-advanced-line-shape-fitting
#12
Markus Niklasson, Renee Otten, Alexandra Ahlner, Cecilia Andresen, Judith Schlagnitweit, Katja Petzold, Patrik Lundström
NMR spectroscopy is uniquely suited for atomic resolution studies of biomolecules such as proteins, nucleic acids and metabolites, since detailed information on structure and dynamics are encoded in positions and line shapes of peaks in NMR spectra. Unfortunately, accurate determination of these parameters is often complicated and time consuming, in part due to the need for different software at the various analysis steps and for validating the results. Here, we present an integrated, cross-platform and open-source software that is significantly more versatile than the typical line shape fitting application...
October 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29032520/mollib-a-molecular-and-nmr-data-analysis-software
#13
Justin L Lorieau
Mollib is a software framework for the analysis of molecular structures, properties and data with an emphasis on data collected by NMR. It uses an open source model and a plugin framework to promote community-driven development of new and enhanced features. Mollib includes tools for the automatic retrieval and caching of protein databank (PDB) structures, the hydrogenation of biomolecules, the analysis of backbone dihedral angles and hydrogen bonds, and the fitting of residual dipolar coupling (RDC) and residual anisotropic chemical shift (RACS) data...
October 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29032519/nmr-experiments-for-the-rapid-identification-of-p-o%C3%A2-%C3%A2-%C3%A2-h-x-type-hydrogen-bonds-in-nucleic-acids
#14
Elke Duchardt-Ferner, Jens Wöhnert
Hydrogen bonds involving the backbone phosphate groups occur with high frequency in functional RNA molecules. They are often found in well-characterized tertiary structural motifs presenting powerful probes for the rapid identification of these motifs for structure elucidation purposes. We have shown recently that stable hydrogen bonds to the phosphate backbone can in principle be detected by relatively simple NMR-experiments, providing the identity of both the donor hydrogen and the acceptor phosphorous within the same experiment (Duchardt-Ferner et al...
October 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28913741/pressure-dependence-of-side-chain-13-c-chemical-shifts-in-model-peptides-ac-gly-gly-xxx-ala-nh2
#15
Markus Beck Erlach, Joerg Koehler, Edson Crusca, Claudia E Munte, Masatsune Kainosho, Werner Kremer, Hans Robert Kalbitzer
For evaluating the pressure responses of folded as well as intrinsically unfolded proteins detectable by NMR spectroscopy the availability of data from well-defined model systems is indispensable. In this work we report the pressure dependence of (13)C chemical shifts of the side chain atoms in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx, one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of a number of nuclei have a nonlinear dependence on pressure in the range from 0...
October 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28900789/gradient-reconstitution-of-membrane-proteins-for-solid-state-nmr-studies
#16
Denis Lacabanne, Alons Lends, Clément Danis, Britta Kunert, Marie-Laure Fogeron, Vlastimil Jirasko, Claire Chuilon, Lauriane Lecoq, Cédric Orelle, Vincent Chaptal, Pierre Falson, Jean-Michel Jault, Beat H Meier, Anja Böckmann
We here adapted the GRecon method used in electron microscopy studies for membrane protein reconstitution to the needs of solid-state NMR sample preparation. We followed in detail the reconstitution of the ABC transporter BmrA by dialysis as a reference, and established optimal reconstitution conditions using the combined sucrose/cyclodextrin/lipid gradient characterizing GRecon. We established conditions under which quantitative reconstitution of active protein at low lipid-to-protein ratios can be obtained, and also how to upscale these conditions in order to produce adequate amounts for NMR...
October 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28887770/optimization-of-1-h-decoupling-eliminates-sideband-artifacts-in-3d-trosy-based-triple-resonance-experiments
#17
Youlin Xia, Paolo Rossi, Marco Tonelli, Chengdong Huang, Charalampos G Kalodimos, Gianluigi Veglia
TROSY-based triple resonance experiments are essential for protein backbone assignment of large biomolecular systems by solution NMR spectroscopy. In a survey of the current Bruker pulse sequence library for TROSY-based experiments we found that several sequences were plagued by artifacts that affect spectral quality and hamper data analysis. Specifically, these experiments produce sidebands in the (13)C(t 1) dimension with inverted phase corresponding to (1)HN resonance frequencies, with approximately 5% intensity of the parent (13)C crosspeaks...
September 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28879611/evaluation-of-15-n-detected-h-n-correlation-experiments-on-increasingly-large-rnas
#18
Robbin Schnieders, Christian Richter, Sven Warhaut, Vanessa de Jesus, Sara Keyhani, Elke Duchardt-Ferner, Heiko Keller, Jens Wöhnert, Lars T Kuhn, Alexander L Breeze, Wolfgang Bermel, Harald Schwalbe, Boris Fürtig
Recently, (15)N-detected multidimensional NMR experiments have been introduced for the investigation of proteins. Utilization of the slow transverse relaxation of nitrogen nuclei in a (15)N-TROSY experiment allowed recording of high quality spectra for high molecular weight proteins, even in the absence of deuteration. Here, we demonstrate the applicability of three (15)N-detected H-N correlation experiments (TROSY, BEST-TROSY and HSQC) to RNA. With the newly established (15)N-detected BEST-TROSY experiment, which proves to be the most sensitive (15)N-detected H-N correlation experiment, spectra for five RNA molecules ranging in size from 5 to 100 kDa were recorded...
September 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28864905/measurement-of-protein-backbone-13-co-and-15-n-relaxation-dispersion-at-high-resolution
#19
Maxim Mayzel, Alexandra Ahlner, Patrik Lundström, Vladislav Y Orekhov
Peak overlap in crowded regions of two-dimensional spectra prevents characterization of dynamics for many sites of interest in globular and intrinsically disordered proteins. We present new three-dimensional pulse sequences for measurement of Carr-Purcell-Meiboom-Gill relaxation dispersions at backbone nitrogen and carbonyl positions. To alleviate increase in the measurement time associated with the additional spectral dimension, we use non-uniform sampling in combination with two distinct methods of spectrum reconstruction: compressed sensing and co-processing with multi-dimensional decomposition...
September 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28861670/anthranilic-acid-the-new-player-in-the-ensemble-of-aromatic-residue-labeling-precursor-compounds
#20
Julia Schörghuber, Leonhard Geist, Marilena Bisaccia, Frederik Weber, Robert Konrat, Roman J Lichtenecker
The application of metabolic precursors for selective stable isotope labeling of aromatic residues in cell-based protein overexpression has already resulted in numerous NMR probes to study the structural and dynamic characteristics of proteins. With anthranilic acid, we present the structurally simplest precursor for exclusive tryptophan side chain labeling. A synthetic route to (13)C, (2)H isotopologues allows the installation of isolated (13)C-(1)H spin systems in the indole ring of tryptophan, representing a versatile tool to investigate side chain motion using relaxation-based experiments without the loss of magnetization due to strong (1)JCC and weaker (2)JCH scalar couplings, as well as dipolar interactions with remote hydrogens...
September 2017: Journal of Biomolecular NMR
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