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Journal of Biomolecular NMR

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https://www.readbyqxmd.com/read/30414042/a-con-based-nmr-assignment-strategy-for-pro-rich-intrinsically-disordered-proteins-with-low-signal-dispersion-the-c-terminal-domain-of-histone-h1-0-as-a-case-study
#1
Belén Chaves-Arquero, David Pantoja-Uceda, Alicia Roque, Inmaculada Ponte, Pedro Suau, M Angeles Jiménez
The C-terminal domain of histone H1.0 (C-H1.0) is involved in DNA binding and is a main determinant of the chromatin condensing properties of histone H1.0. Phosphorylation at the (S/T)-P-X-(K/R) motifs affects DNA binding and is crucial for regulation of C-H1.0 function. Since C-H1.0 is an intrinsically disordered domain, solution NMR is an excellent approach to characterize the effect of phosphorylation on the structural and dynamic properties of C-H1.0. However, its very repetitive, low-amino acid-diverse and Pro-rich sequence, together with the low signal dispersion observed at the 1 H-15 N HSQC spectra of both non- and tri-phosphorylated C-H1...
November 9, 2018: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/30311122/joint-x-ray-nmr-structure-refinement-of-multidomain-multisubunit-systems
#2
Azzurra Carlon, Enrico Ravera, Giacomo Parigi, Garib N Murshudov, Claudio Luchinat
Data integration in structural biology has become a paradigm for the characterization of biomolecular systems, and it is now accepted that combining different techniques can fill the gaps in each other's blind spots. In this frame, one of the combinations, which we have implemented in REFMAC-NMR, is residual dipolar couplings from NMR together with experimental data from X-ray diffraction. The first are exquisitely sensitive to the local details but does not give any information about overall shape, whereas the latter encodes more the information about the overall shape but at the same time tends to miss the local details even at the highest resolutions...
October 11, 2018: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/30306288/-15-n-transverse-relaxation-measurements-for-the-characterization-of-%C3%A2%C2%B5s-ms-dynamics-are-deteriorated-by-the-deuterium-isotope-effect-on-15-n-resulting-from-solvent-exchange
#3
Pratibha Kumari, Lukas Frey, Alexander Sobol, Nils-Alexander Lakomek, Roland Riek
15 N R2 relaxation measurements are key for the elucidation of the dynamics of both folded and intrinsically disordered proteins (IDPs). Here we show, on the example of the intrinsically disordered protein α-synuclein and the folded domain PDZ2, that at physiological pH and near physiological temperatures amide-water exchange can severely skew Hahn-echo based 15 N R2 relaxation measurements as well as low frequency data points in CPMG relaxation dispersion experiments. The nature thereof is the solvent exchange with deuterium in the sample buffer, which modulates the 15 N chemical shift tensor via the deuterium isotope effect, adding to the apparent relaxation decay which leads to systematic errors in the relaxation data...
October 10, 2018: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/30206780/direct-amide-15-n-to-13-c-transfers-for-solid-state-assignment-experiments-in-deuterated-proteins
#4
Alons Lends, Francesco Ravotti, Giorgia Zandomeneghi, Anja Böckmann, Matthias Ernst, Beat H Meier
The assignment of protein backbone and side-chain NMR chemical shifts is the first step towards the characterization of protein structure. The recent introduction of proton detection in combination with fast MAS has opened up novel opportunities for assignment experiments. However, typical 3D sequential-assignment experiments using proton detection under fast MAS lead to signal intensities much smaller than the theoretically expected ones due to the low transfer efficiency of some of the steps. Here, we present a selective 3D experiment for deuterated and (amide) proton back-exchanged proteins where polarization is directly transferred from backbone nitrogen to selected backbone or sidechain carbons...
September 11, 2018: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/30276607/a-methyl-1-h-double-quantum-cpmg-experiment-to-study-protein-conformational-exchange
#5
Anusha B Gopalan, Tairan Yuwen, Lewis E Kay, Pramodh Vallurupalli
Protein conformational changes play crucial roles in enabling function. The Carr-Purcell-Meiboom-Gill (CPMG) experiment forms the basis for studying such dynamics when they involve the interconversion between highly populated and sparsely formed states, the latter having lifetimes ranging from ~ 0.5 to ~ 5 ms. Among the suite of experiments that have been developed are those that exploit methyl group probes by recording methyl 1 H single quantum (Tugarinov and Kay in J Am Chem Soc 129:9514-9521, 2007) and triple quantum (Yuwen et al...
October 2018: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/30229369/conformational-exchange-of-aromatic-side-chains-by-1-h-cpmg-relaxation-dispersion
#6
Heiner N Raum, Matthias Dreydoppel, Ulrich Weininger
Aromatic side chains are attractive probes of protein dynamics on the millisecond time scale, because they are often key residues in enzyme active sites and protein binding sites. Further they allow to study specific processes, like histidine tautomerization and ring flips. Till now such processes have been studied by aromatic 13 C CPMG relaxation dispersion experiments. Here we investigate the possibility of aromatic 1 H CPMG relaxation dispersion experiments as a complementary method. Artifact-free dispersions are possible on uniformly 1 H and 13 C labeled samples for histidine δ2 and ε1, as well as for tryptophan δ1...
October 2018: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/30203383/3-o-methyl-d-glucose-mutarotation-and-proton-exchange-rates-assessed-by-13-c-1-h-nmr-and-by-chemical-exchange-saturation-transfer-and-spin-lock-measurements
#7
Michal Rivlin, Gil Navon
3-O-Methyl-D-glucose (3OMG) was recently suggested as an agent to image tumors using chemical exchange saturation transfer (CEST) MRI. To characterize the properties of 3OMG in solution, the anomeric equilibrium and the mutarotation rates of 3OMG were studied by 1 H and 13 C NMR. This information is essential in designing the in vivo CEST experiments. At room temperature, the ratio of α and β 3OMG anomers at equilibrium was 1:1.4, and the time to reach 95% equilibrium was 6 h. The chemical exchange rates between the hydroxyl protons of 3OMG and water, measured by CEST and spin lock at pH 6...
October 2018: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/30141148/rapid-automated-determination-of-chemical-shift-anisotropy-values-in-the-carbonyl-and-carboxyl-groups-of-fd-y21m-bacteriophage-using-solid-state-nmr
#8
Tom Aharoni, Amir Goldbourt
Determination of chemical shift anisotropy (CSA) in immobilized proteins and protein assemblies is one of several tools to determine protein dynamics on the timescales of microseconds and faster. The large CSA values of C=O groups in the rigid limit makes them in particular attractive for measurements of large amplitude motions, or their absence. In this study, we implement a 3D R-symmetry-based sequence that recouples the second spatial component of the 13 C CSA with the corresponding isotropic 13 C'-13 C cross-peaks in order to probe backbone and sidechain dynamics in an intact fd-y21m filamentous phage viral capsid...
October 2018: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/30121872/correlated-motions-of-c-n-and-c-%C3%AE-c-%C3%AE-pairs-in-protonated-and-per-deuterated-gb3
#9
Liliya Vugmeyster, Aaron Griffin, Dmitry Ostrovsky, Shibani Bhattacharya, Parker J Nichols, C James McKnight, Beat Vögeli
We investigated correlated µs-ms time scale motions of neighboring 13 C'-15 N and 13 Cα -13 Cβ nuclei in both protonated and perdeuterated samples of GB3. The techniques employed, NMR relaxation due to cross-correlated chemical shift modulations, specifically target concerted changes in the isotropic chemical shifts of the two nuclei associated with spatial fluctuations. Field-dependence of the relaxation rates permits identification of the parameters defining the chemical exchange rate constant under the assumption of a two-site exchange...
October 2018: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/30117038/conformationally-locked-lanthanide-chelating-tags-for-convenient-pseudocontact-shift-protein-nuclear-magnetic-resonance-spectroscopy
#10
Daniel Joss, Roché M Walliser, Kaspar Zimmermann, Daniel Häussinger
Pseudocontact shifts (PCS) generated by lanthanide chelating tags yield valuable restraints for investigating protein structures, dynamics and interactions in solution. In this work, dysprosium-, thulium- and terbium-complexes of eight-fold methylated 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid tags [DOTA-M8-(4R4S)-SSPy] are presented that induce large pseudocontact shifts up to 5.5 ppm and adopt exclusively the square antiprismatic conformation. This is in contrast to our earlier findings on complexes of the stereoisomeric DOTA-M8-(8S)-SSPy, where significant amounts of the twisted square antiprismatic conformer for the Dy tag were observed...
October 2018: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/30097912/automatic-13-c-chemical-shift-reference-correction-for-unassigned-protein-nmr-spectra
#11
Xi Chen, Andrey Smelter, Hunter N B Moseley
Poor chemical shift referencing, especially for 13 C in protein Nuclear Magnetic Resonance (NMR) experiments, fundamentally limits and even prevents effective study of biomacromolecules via NMR, including protein structure determination and analysis of protein dynamics. To solve this problem, we constructed a Bayesian probabilistic framework that circumvents the limitations of previous reference correction methods that required protein resonance assignment and/or three-dimensional protein structure. Our algorithm named Bayesian Model Optimized Reference Correction (BaMORC) can detect and correct 13 C chemical shift referencing errors before the protein resonance assignment step of analysis and without three-dimensional structure...
October 2018: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/30066206/structural-investigation-of-glycan-recognition-by-the-erad-quality-control-lectin-yos9
#12
Andreas Kniss, Sina Kazemi, Frank Löhr, Maren Berger, Vladimir V Rogov, Peter Güntert, Thomas Sommer, Ernst Jarosch, Volker Dötsch
Yos9 is an essential component of the endoplasmic reticulum associated protein degradation (ERAD) system that is responsible for removing terminally misfolded proteins from the ER lumen and mediating proteasomal degradation in the cytosol. Glycoproteins that fail to attain their native conformation in the ER expose a distinct oligosaccharide structure, a terminal α1,6-linked mannose residue, that is specifically recognized by the mannose 6-phoshate receptor homology (MRH) domain of Yos9. We have determined the structure of the MRH domain of Yos9 in its free form and complexed with 3α, 6α-mannopentaose...
October 2018: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/30121871/on-the-use-of-pichia-pastoris-for-isotopic-labeling-of-human-gpcrs-for-nmr-studies
#13
Lindsay Clark, Igor Dikiy, Daniel M Rosenbaum, Kevin H Gardner
NMR studies of human integral membrane proteins provide unique opportunities to probe structure and dynamics at specific locations and on multiple timescales, often with significant implications for disease mechanism and drug development. Since membrane proteins such as G protein-coupled receptors (GPCRs) are highly dynamic and regulated by ligands or other perturbations, NMR methods are potentially well suited to answer basic functional questions (such as addressing the biophysical basis of ligand efficacy) as well as guiding applications (such as novel ligand design)...
August 2018: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/30073492/improving-yields-of-deuterated-methyl-labeled-protein-by-growing-in-h-2-o
#14
Evan S O'Brien, Danny W Lin, Brian Fuglestad, Matthew A Stetz, Travis Gosse, Cecilia Tommos, A Joshua Wand
Solution NMR continues to make strides in addressing protein systems of significant size and complexity. A fundamental requirement to fully exploit the 15 N-1 H TROSY and 13 C-1 H3 methyl TROSY effects is highly deuterated protein. Unfortunately, traditional overexpression in Escherichia coli (E. coli) during growth on media prepared in D2 O leads to many difficulties and limitations, such as cell toxicity, decreased yield, and the need to unfold or destabilize proteins for back exchange of amide protons. These issues are exacerbated for non-ideal systems such as membrane proteins...
August 2018: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29948439/segmental-isotope-labelling-and-solid-state-nmr-of-a-12-%C3%A3-59-kda-motor-protein-identification-of-structural-variability
#15
Thomas Wiegand, Riccardo Cadalbert, Christine von Schroetter, Frédéric H-T Allain, Beat H Meier
Segmental isotope labelling enables the NMR study of an individual domain within a multidomain protein, but still in the context of the entire full-length protein. Compared to the fully labelled protein, spectral overlap can be greatly reduced. We here describe segmental labelling of the (double-) hexameric DnaB helicase from Helicobacter pylori using a ligation approach. Solid-state spectra demonstrate that the ligated protein has the same structure and structural order as the directly expressed full-length protein...
August 2018: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29869771/methyl-selective-isotope-labeling-using-%C3%AE-ketoisovalerate-for-the-yeast-pichia-pastoris-recombinant-protein-expression-system
#16
Rika Suzuki, Masayoshi Sakakura, Masaki Mori, Moe Fujii, Satoko Akashi, Hideo Takahashi
Methyl-detected NMR spectroscopy is a useful tool for investigating the structures and interactions of large macromolecules such as membrane proteins. The procedures for preparation of methyl-specific isotopically-labeled proteins were established for the Escherichia coli (E. coli) expression system, but typically it is not feasible to express eukaryotic proteins using E. coli. The Pichia pastoris (P. pastoris) expression system is the most common yeast expression system, and is known to be superior to the E...
August 2018: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29860649/methyl-group-reorientation-under-ligand-binding-probed-by-pseudocontact-shifts
#17
Mathilde Lescanne, Puneet Ahuja, Anneloes Blok, Monika Timmer, Tomas Akerud, Marcellus Ubbink
Liquid-state NMR spectroscopy is a powerful technique to elucidate binding properties of ligands on proteins. Ligands binding in hydrophobic pockets are often in close proximity to methyl groups and binding can lead to subtle displacements of methyl containing side chains to accommodate the ligand. To establish whether pseudocontact shifts can be used to characterize ligand binding and the effects on methyl groups, the N-terminal domain of HSP90 was tagged with caged lanthanoid NMR probe 5 at three positions and titrated with a ligand...
August 2018: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29779067/cost-effective-large-scale-expression-of-proteins-for-nmr-studies
#18
Julia Klopp, Aurélie Winterhalter, Rémy Gébleux, Daniela Scherer-Becker, Christian Ostermeier, Alvar D Gossert
We present protocols for high-level expression of isotope-labelled proteins in E. coli in cost-effective ways. This includes production of large amounts of unlabeled proteins and 13 C-methyl methionine labeling in rich media, where yields of up to a gram of soluble protein per liter of culture are reached. Procedures for uniform isotope labeling of 2 H, 13 C and 15 N using auto-induction or isopropyl-β-D-1-thiogalactopyranoside-induction are described, with primary focus on minimal isotope consumption and high reproducibility of protein expression...
August 2018: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29536230/segmental-isotopic-labeling-by-asparaginyl-endopeptidase-mediated-protein-ligation
#19
Kornelia M Mikula, Luisa Krumwiede, Andreas Plückthun, Hideo Iwaï
Segmental isotopic labeling can facilitate NMR studies of large proteins, multi-domain proteins, and proteins with repetitive sequences by alleviating NMR signal overlaps. Segmental isotopic labeling also allows us to investigate an individual domain in the context of a full-length protein by NMR. Several established methods are available for segmental isotopic labeling such as intein-mediated ligation, but each has specific requirements and limitations. Here, we report an enzymatic approach using bacterially produced asparagine endopeptidase from Oldenlandia affinis for segmental isotopic labeling of a protein with repetitive sequences, a designed armadillo repeat protein, by overcoming some of the shortcomings of enzymatic ligation for segmental isotopic labeling...
August 2018: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29197976/genetically-encoded-amino-acids-with-tert-butyl-and-trimethylsilyl-groups-for-site-selective-studies-of-proteins-by-nmr-spectroscopy
#20
Choy Theng Loh, Luke A Adams, Bim Graham, Gottfried Otting
The amino acids 4-(tert-butyl)phenylalanine (Tbf) and 4-(trimethylsilyl)phenylalanine (TMSf), as well as a partially deuterated version of Tbf (dTbf), were chemically synthesized and site-specifically incorporated into different proteins, using an amber stop codon, suppressor tRNA and the broadband aminoacyl-tRNA synthetase originally evolved for the incorporation of p-cyano-phenylalanine. The 1 H-NMR signals of the tert-butyl and TMS groups were compared to the 1 H-NMR signal of tert-butyltyrosine (Tby) in protein systems with molecular weights ranging from 8 to 54 kDa...
August 2018: Journal of Biomolecular NMR
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