2,988 results match your criteria Journal of biomolecular NMR[Journal]


CONFINE-MAS: a magic-angle spinning NMR probe that confines the sample in case of a rotor explosion.

J Biomol NMR 2018 Dec 10;72(3-4):171-177. Epub 2018 Dec 10.

Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland.

Magic-angle spinning (MAS) is mandatory in solid-state NMR experiments to achieve resolved spectra. In rare cases, instabilities in the rotation or damage of either the rotor or the rotor cap can lead to a so called "rotor crash" involving a disintegration of the sample container and possibly the release of an aerosol or of dust. We present a modified design of a 3. Read More

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http://dx.doi.org/10.1007/s10858-018-0218-xDOI Listing
December 2018
1 Read

Oligomeric transition and dynamics of RNA binding by the HuR RRM1 domain in solution.

J Biomol NMR 2018 Dec 8;72(3-4):179-192. Epub 2018 Dec 8.

Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil.

Human antigen R (HuR) functions as a major post-transcriptional regulator of gene expression through its RNA-binding activity. HuR is composed by three RNA recognition motifs, namely RRM1, RRM2, and RRM3. The two N-terminal RRM domains are disposed in tandem and contribute mostly to HuR interaction with adenine and uracil-rich elements (ARE) in mRNA. Read More

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http://link.springer.com/10.1007/s10858-018-0217-y
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http://dx.doi.org/10.1007/s10858-018-0217-yDOI Listing
December 2018
2 Reads

Selective suppression of excipient signals in 2D H-C methyl spectra of biopharmaceutical products.

J Biomol NMR 2018 Dec 27;72(3-4):149-161. Epub 2018 Nov 27.

Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, 9600 Gudelsky Dr., Rockville, MD, 20850, USA.

While the use of H-C methyl correlated NMR spectroscopy at natural isotopic abundance has been demonstrated as feasible on protein therapeutics as large as monoclonal antibodies, spectral interference from aliphatic excipients remains a significant obstacle to its widespread application. These signals can cause large baseline artifacts, obscure protein resonances, and cause dynamic range suppression of weak peaks in non-uniform sampling applications, thus hampering both traditional peak-based spectral analyses as well as emerging chemometric methods of analysis. Here we detail modifications to the 2D H-C gradient-selected HSQC experiment that make use of selective pulsing techniques for targeted removal of interfering excipient signals in spectra of the NISTmAb prepared in several different formulations. Read More

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http://dx.doi.org/10.1007/s10858-018-0214-1DOI Listing
December 2018

BEST and SOFAST experiments for resonance assignment of histidine and tyrosine side chains in C/N labeled proteins.

J Biomol NMR 2018 Dec 21;72(3-4):115-124. Epub 2018 Nov 21.

Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000, Grenoble, France.

Aromatic amino-acid side chains are essential components for the structure and function of proteins. We present herein a set of NMR experiments for time-efficient resonance assignment of histidine and tyrosine side chains in uniformly C/N-labeled proteins. The use of band-selective C pulses allows to deal with linear chains of coupled spins, thus avoiding signal loss that occurs in branched spin systems during coherence transfer. Read More

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http://dx.doi.org/10.1007/s10858-018-0216-zDOI Listing
December 2018
10 Reads

Automated projection spectroscopy in solid-state NMR.

J Biomol NMR 2018 Dec 14;72(3-4):163-170. Epub 2018 Nov 14.

Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany.

Given that solid-state NMR is being used for protein samples of increasing molecular weight and complexity, higher-dimensionality methods are likely to be more and more indispensable for unambiguous chemical shift assignments in the near future. In addition, solid-state NMR spectral properties are increasingly comparable with solution NMR, allowing adaptation of more sophisticated solution NMR strategies for the solid state in addition to the conventional methodology. Assessing first principles, here we demonstrate the application of automated projection spectroscopy for a micro-crystalline protein in the solid state. Read More

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http://dx.doi.org/10.1007/s10858-018-0215-0DOI Listing
December 2018

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.

J Biomol NMR 2018 Dec 9;72(3-4):139-148. Epub 2018 Nov 9.

Departamento de Química-Física Biológica, Instituto de Química Física Rocasolano (IQFR-CSIC), Serrano 119, 28006, Madrid, Spain.

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. Read More

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http://link.springer.com/10.1007/s10858-018-0213-2
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http://dx.doi.org/10.1007/s10858-018-0213-2DOI Listing
December 2018
2 Reads

Joint X-ray/NMR structure refinement of multidomain/multisubunit systems.

J Biomol NMR 2018 Oct 11. Epub 2018 Oct 11.

Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.

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. Read More

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http://dx.doi.org/10.1007/s10858-018-0212-3DOI Listing
October 2018

N transverse relaxation measurements for the characterization of µs-ms dynamics are deteriorated by the deuterium isotope effect on N resulting from solvent exchange.

J Biomol NMR 2018 Dec 10;72(3-4):125-137. Epub 2018 Oct 10.

Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.

N R 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 N R 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 N chemical shift tensor via the deuterium isotope effect, adding to the apparent relaxation decay which leads to systematic errors in the relaxation data. Read More

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http://dx.doi.org/10.1007/s10858-018-0211-4DOI Listing
December 2018

A methyl H double quantum CPMG experiment to study protein conformational exchange.

J Biomol NMR 2018 Oct 1;72(1-2):79-91. Epub 2018 Oct 1.

TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad, Telangana, 500107, India.

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. Read More

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http://link.springer.com/10.1007/s10858-018-0208-z
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http://dx.doi.org/10.1007/s10858-018-0208-zDOI Listing
October 2018
3 Reads

Conformational exchange of aromatic side chains by H CPMG relaxation dispersion.

J Biomol NMR 2018 Oct 18;72(1-2):105-114. Epub 2018 Sep 18.

Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany.

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 C CPMG relaxation dispersion experiments. Read More

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http://dx.doi.org/10.1007/s10858-018-0210-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6209042PMC
October 2018

Direct amide N to C transfers for solid-state assignment experiments in deuterated proteins.

J Biomol NMR 2018 Sep 11. Epub 2018 Sep 11.

Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.

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. Read More

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http://dx.doi.org/10.1007/s10858-018-0207-0DOI Listing
September 2018

3-O-Methyl-D-glucose mutarotation and proton exchange rates assessed by C, H NMR and by chemical exchange saturation transfer and spin lock measurements.

J Biomol NMR 2018 Oct 10;72(1-2):93-103. Epub 2018 Sep 10.

School of Chemistry, Tel Aviv University, Tel Aviv, Israel.

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 H and C NMR. This information is essential in designing the in vivo CEST experiments. Read More

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http://dx.doi.org/10.1007/s10858-018-0209-yDOI Listing
October 2018

Rapid automated determination of chemical shift anisotropy values in the carbonyl and carboxyl groups of fd-y21m bacteriophage using solid state NMR.

J Biomol NMR 2018 Oct 23;72(1-2):55-67. Epub 2018 Aug 23.

School of Chemistry, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel.

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 C CSA with the corresponding isotropic C'-C cross-peaks in order to probe backbone and sidechain dynamics in an intact fd-y21m filamentous phage viral capsid. Read More

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http://dx.doi.org/10.1007/s10858-018-0206-1DOI Listing
October 2018

Correlated motions of C'-N and C-C pairs in protonated and per-deuterated GB3.

J Biomol NMR 2018 Oct 18;72(1-2):39-54. Epub 2018 Aug 18.

Department of Biochemistry and Molecular Genetics, University of Colorado, School of Medicine, Anschutz Medical Campus, Aurora, CO, 80045, USA.

We investigated correlated µs-ms time scale motions of neighboring C'-N and C-C 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. Read More

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http://dx.doi.org/10.1007/s10858-018-0205-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6218248PMC
October 2018
10 Reads

On the use of Pichia pastoris for isotopic labeling of human GPCRs for NMR studies.

J Biomol NMR 2018 Aug 18;71(4):203-211. Epub 2018 Aug 18.

Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA.

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). However, such studies on eukaryotic membrane proteins have often been limited by the inability to incorporate optimal isotopic labels for NMR methods developed for large protein/lipid complexes, including methyl TROSY. Read More

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http://dx.doi.org/10.1007/s10858-018-0204-3DOI Listing
August 2018
1 Read

Conformationally locked lanthanide chelating tags for convenient pseudocontact shift protein nuclear magnetic resonance spectroscopy.

J Biomol NMR 2018 Oct 16;72(1-2):29-38. Epub 2018 Aug 16.

Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland.

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. Read More

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http://dx.doi.org/10.1007/s10858-018-0203-4DOI Listing
October 2018
11 Reads

Automatic C chemical shift reference correction for unassigned protein NMR spectra.

J Biomol NMR 2018 Oct 10;72(1-2):11-28. Epub 2018 Aug 10.

Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40356, USA.

Poor chemical shift referencing, especially for 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 C chemical shift referencing errors before the protein resonance assignment step of analysis and without three-dimensional structure. Read More

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http://dx.doi.org/10.1007/s10858-018-0202-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6209040PMC
October 2018
6 Reads

Improving yields of deuterated, methyl labeled protein by growing in HO.

J Biomol NMR 2018 Aug 2;71(4):263-273. Epub 2018 Aug 2.

Johnson Research Foundation and Department of Biochemistry & Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104-6059, USA.

Solution NMR continues to make strides in addressing protein systems of significant size and complexity. A fundamental requirement to fully exploit the N-H TROSY and C-H methyl TROSY effects is highly deuterated protein. Unfortunately, traditional overexpression in Escherichia coli (E. Read More

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http://dx.doi.org/10.1007/s10858-018-0200-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6165672PMC
August 2018
12 Reads

Structural investigation of glycan recognition by the ERAD quality control lectin Yos9.

J Biomol NMR 2018 Oct 31;72(1-2):1-10. Epub 2018 Jul 31.

Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany.

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. Read More

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http://dx.doi.org/10.1007/s10858-018-0201-6DOI Listing
October 2018
1 Read

Advanced isotopic labeling for the NMR investigation of challenging proteins and nucleic acids.

J Biomol NMR 2018 07;71(3):115-117

Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.

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http://link.springer.com/10.1007/s10858-018-0199-9
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http://dx.doi.org/10.1007/s10858-018-0199-9DOI Listing
July 2018
8 Reads

Insight into human insulin aggregation revisited using NMR derived translational diffusion parameters.

J Biomol NMR 2018 06 12;71(2):101-114. Epub 2018 Jun 12.

National Medicines Institute, Chełmska 30, 00-725, Warsaw, Poland.

The NMR derived translational diffusion coefficients were performed on unlabeled and uniformly labeled C,N human insulin in water, both in neat, with zinc ions only, and in pharmaceutical formulation, containing only m-cresol as phenolic ligand, glycerol and zinc ions. The results show the dominant role of the pH parameter and the concentration on aggregation. The diffusion coefficient Dav was used for monitoring the overall average state of oligomeric ensemble in solution. Read More

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http://dx.doi.org/10.1007/s10858-018-0197-yDOI Listing
June 2018
1 Read

Segmental isotope labelling and solid-state NMR of a 12 × 59 kDa motor protein: identification of structural variability.

J Biomol NMR 2018 Aug 12;71(4):237-245. Epub 2018 Jun 12.

Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland.

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. Read More

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http://dx.doi.org/10.1007/s10858-018-0196-zDOI Listing

Perspective: next generation isotope-aided methods for protein NMR spectroscopy.

J Biomol NMR 2018 Jun 22. Epub 2018 Jun 22.

Department of Structural BioImaging, Faculty of Life Sciences, Kumamoto University, 5-1, Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan.

In this perspective, we describe our efforts to innovate the current isotope-aided NMR methodology to investigate biologically important large proteins and protein complexes, for which only limited structural information could be obtained by conventional NMR approaches. At the present time, it is widely believed that only backbone amide and methyl signals are amenable for investigating such difficult targets. Therefore, our primary mission is to disseminate our novel knowledge within the biological NMR community; specifically, that any type of NMR signals other than methyl and amide groups can be obtained, even for quite large proteins, by optimizing the transverse relaxation properties by isotope labeling methods. Read More

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http://dx.doi.org/10.1007/s10858-018-0198-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6096516PMC
June 2018
2 Reads

Binding of a small molecule water channel inhibitor to aquaporin Z examined by solid-state MAS NMR.

J Biomol NMR 2018 Jun 18. Epub 2018 Jun 18.

School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.

Aquaporins are integral membrane proteins that facilitate water flow across biological membranes. Their involvement in multiple physiological functions and disease states has prompted intense research to discover water channel activity modulators. However, inhibitors found so far are weak and/or lack specificity. Read More

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http://dx.doi.org/10.1007/s10858-018-0195-0DOI Listing
June 2018
1 Read

Concentration-dependent changes to diffusion and chemical shift of internal standard molecules in aqueous and micellar solutions.

J Biomol NMR 2018 Jun 6. Epub 2018 Jun 6.

Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada.

Sodium 4,4-dimethyl-4-silapentane-1-sulfonate (DSS) is the most widely accepted internal standard for protein NMR studies in aqueous conditions. Since its introduction as a reference standard, however, concerns have been raised surrounding its propensity to interact with biological molecules through electrostatic and hydrophobic interactions. While DSS has been shown to interact with certain proteins, membrane protein studies by solution-state NMR require use of membrane mimetics such as detergent micelles and, to date, no study has explicitly examined the potential for interaction between membrane mimetics and DSS. Read More

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http://dx.doi.org/10.1007/s10858-018-0194-1DOI Listing

Methyl-selective isotope labeling using α-ketoisovalerate for the yeast Pichia pastoris recombinant protein expression system.

J Biomol NMR 2018 Aug 5;71(4):213-223. Epub 2018 Jun 5.

Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.

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. Read More

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http://dx.doi.org/10.1007/s10858-018-0192-3DOI Listing
August 2018
7 Reads

Removal of slow-pulsing artifacts in in-phase N relaxation dispersion experiments using broadband H decoupling.

J Biomol NMR 2018 06 2;71(2):69-77. Epub 2018 Jun 2.

Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O Box 9502, 2300 RA, Leiden, The Netherlands.

Understanding of the molecular mechanisms of protein function requires detailed insight into the conformational landscape accessible to the protein. Conformational changes can be crucial for biological processes, such as ligand binding, protein folding, and catalysis. NMR spectroscopy is exquisitely sensitive to such dynamic changes in protein conformations. Read More

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http://dx.doi.org/10.1007/s10858-018-0193-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6061081PMC
June 2018
2 Reads

Methyl group reorientation under ligand binding probed by pseudocontact shifts.

J Biomol NMR 2018 Aug 2;71(4):275-285. Epub 2018 Jun 2.

Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.

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. Read More

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http://dx.doi.org/10.1007/s10858-018-0190-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6132577PMC

NMR probing of invisible excited states using selectively labeled RNAs.

J Biomol NMR 2018 07 1;71(3):165-172. Epub 2018 Jun 1.

Department of Chemistry & Biochemistry, University of Maryland, College Park, 8314 Paint Branch Dr, College Park, MD, 20782, USA.

Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion NMR experiments are invaluable for probing sparsely and transiently populated biomolecular states that cannot be directly detected by traditional NMR experiments and that are invisible by other biophysical approaches. A notable gap for RNA is the absence of CPMG experiments for measurement of methine base H and methylene C5' chemical shifts of ribose moieties in the excited state, partly because of complications from homonuclear C-C scalar couplings. Here we present site-specific C labeling that makes possible the design of pulse sequences for recording accurate H-C MQ and SQ CPMG experiments for ribose methine H1'-C1' and H2'-C2', base and ribose H CPMG, as well as a new H-C TROSY-detected methylene (CH) C5' CPMG relaxation pulse schemes. Read More

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http://dx.doi.org/10.1007/s10858-018-0184-3DOI Listing
July 2018
3 Reads

Microsecond motions probed by near-rotary-resonance RN MAS NMR experiments: the model case of protein overall-rocking in crystals.

J Biomol NMR 2018 05 30;71(1):53-67. Epub 2018 May 30.

Martin-Luther-Universität Halle-Wittenberg, Halle, Germany.

Solid-state near-rotary-resonance measurements of the spin-lattice relaxation rate in the rotating frame (R) is a powerful NMR technique for studying molecular dynamics in the microsecond time scale. The small difference between the spin-lock (SL) and magic-angle-spinning (MAS) frequencies allows sampling very slow motions, at the same time it brings up some methodological challenges. In this work, several issues affecting correct measurements and analysis of N R data are considered in detail. Read More

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http://dx.doi.org/10.1007/s10858-018-0191-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5986846PMC

Impact of two-bond N-N scalar couplings on N transverse relaxation measurements for arginine side chains of proteins.

J Biomol NMR 2018 05 29;71(1):45-51. Epub 2018 May 29.

Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, 77555-1068, USA.

NMR relaxation of arginine (Arg) N nuclei is useful for studying side-chain dynamics of proteins. In this work, we studied the impact of two geminal N-N scalar couplings on measurements of transverse relaxation rates (R ) for Arg side-chain N nuclei. For 12 Arg side chains of the DNA-binding domain of the Antp protein, we measured the geminal N-N couplings ( J ) of the N nuclei and found that the magnitudes of the J coupling constants were virtually uniform with an average of 1. Read More

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http://dx.doi.org/10.1007/s10858-018-0189-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6020141PMC
May 2018
4 Reads

Late metabolic precursors for selective aromatic residue labeling.

J Biomol NMR 2018 07 28;71(3):129-140. Epub 2018 May 28.

Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria.

In recent years, we developed a toolbox of heavy isotope containing compounds, which serve as metabolic amino acid precursors in the E. coli-based overexpression of aromatic residue labeled proteins. Our labeling techniques show excellent results both in terms of selectivity and isotope incorporation levels. Read More

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http://dx.doi.org/10.1007/s10858-018-0188-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6096522PMC
July 2018
13 Reads

Multiple frequency saturation pulses reduce CEST acquisition time for quantifying conformational exchange in biomolecules.

J Biomol NMR 2018 05 23;71(1):19-30. Epub 2018 May 23.

Department of Chemistry, New York University, 100 Washington Square East, New York, NY, 10003, USA.

Exchange between conformational states is required for biomolecular catalysis, allostery, and folding. A variety of NMR experiments have been developed to quantify motional regimes ranging from nanoseconds to seconds. In this work, we describe an approach to speed up the acquisition of chemical exchange saturation transfer (CEST) experiments that are commonly used to probe millisecond to second conformational exchange in proteins and nucleic acids. Read More

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http://dx.doi.org/10.1007/s10858-018-0186-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5989009PMC
May 2018
1 Read

Rapid measurement of long-range distances in proteins by multidimensional C-F REDOR NMR under fast magic-angle spinning.

J Biomol NMR 2018 05 21;71(1):31-43. Epub 2018 May 21.

Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA.

The ability to simultaneously measure many long-range distances is critical to efficient and accurate determination of protein structures by solid-state NMR (SSNMR). So far, the most common distance constraints for proteins are C-N distances, which are usually measured using the rotational-echo double-resonance (REDOR) technique. However, these measurements are restricted to distances of up to ~ 5 Å due to the low gyromagnetic ratios of N and C. Read More

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http://link.springer.com/10.1007/s10858-018-0187-0
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http://dx.doi.org/10.1007/s10858-018-0187-0DOI Listing
May 2018
1 Read
3.140 Impact Factor

Cost-effective large-scale expression of proteins for NMR studies.

J Biomol NMR 2018 Aug 19;71(4):247-262. Epub 2018 May 19.

Institute for Molecular Biology and Biophysics, ETH Zürich, HPP L25.1, Hönggerbergring 24, 8093, Zurich, Switzerland.

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 C-methyl methionine labeling in rich media, where yields of up to a gram of soluble protein per liter of culture are reached. Read More

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http://dx.doi.org/10.1007/s10858-018-0179-0DOI Listing
August 2018
2 Reads

Application of Dirichlet process mixture model to the identification of spin systems in protein NMR spectra.

J Biomol NMR 2018 05 18;71(1):11-18. Epub 2018 May 18.

Captor Therapeutics Ltd., ul. Duńska 11, 54-427, Wrocław, Poland.

Analysis of structure, function and interactions of proteins by NMR spectroscopy usually requires the assignment of resonances to the corresponding nuclei in protein. This task, although automated by methods such as FLYA or PINE, is still frequently performed manually. To facilitate the manual sequence-specific chemical shift assignment of complex proteins, we propose a method based on Dirichlet process mixture model (DPMM) that performs automated matching of groups of signals observed in NMR spectra to corresponding nuclei in protein sequence. Read More

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http://dx.doi.org/10.1007/s10858-018-0185-2DOI Listing
May 2018
2 Reads

Farseer-NMR: automatic treatment, analysis and plotting of large, multi-variable NMR data.

J Biomol NMR 2018 May 11. Epub 2018 May 11.

BioNMR Group, Inorganic and Organic Chemistry Department, University of Barcelona, Barcelona, Spain.

We present Farseer-NMR ( https://git.io/vAueU ), a software package to treat, evaluate and combine NMR spectroscopic data from sets of protein-derived peaklists covering a range of experimental conditions. The combined advances in NMR and molecular biology enable the study of complex biomolecular systems such as flexible proteins or large multibody complexes, which display a strong and functionally relevant response to their environmental conditions, e. Read More

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http://dx.doi.org/10.1007/s10858-018-0182-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5986830PMC

Complete assignment of Ala, Ile, Leu, Met and Val methyl groups of human blood group A and B glycosyltransferases using lanthanide-induced pseudocontact shifts and methyl-methyl NOESY.

J Biomol NMR 2018 04 26;70(4):245-259. Epub 2018 Apr 26.

Institute for Chemistry and Metabolomics, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.

Human blood group A and B glycosyltransferases (GTA, GTB) are highly homologous glycosyltransferases. A number of high-resolution crystal structures is available showing that these enzymes convert from an open conformation into a catalytically active closed conformation upon substrate binding. However, the mechanism of glycosyltransfer is still under debate, and the precise nature as well as the time scales of conformational transitions are unknown. Read More

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http://dx.doi.org/10.1007/s10858-018-0183-4DOI Listing
April 2018
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Production of isotope-labeled proteins in insect cells for NMR.

J Biomol NMR 2018 07 23;71(3):173-184. Epub 2018 Apr 23.

Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland.

Baculovirus-infected insect cells have become a powerful tool to express recombinant proteins for structural and functional studies by NMR spectroscopy. This article provides an introduction into the insect cell/baculovirus expression system and its use for the production of recombinant isotope-labeled proteins. We discuss recent advances in inexpensive isotope-labeling methods using labeled algal or yeast extracts as the amino acid source and give examples of advanced NMR applications for proteins, which have become accessible by this eukaryotic expression host. Read More

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http://dx.doi.org/10.1007/s10858-018-0172-7DOI Listing
July 2018
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Atomic structures of excited state A-T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations.

J Biomol NMR 2018 04 19;70(4):229-244. Epub 2018 Apr 19.

Department of Chemistry, Duke University, Durham, NC, 27710, USA.

NMR relaxation dispersion studies indicate that in canonical duplex DNA, Watson-Crick base pairs (bps) exist in dynamic equilibrium with short-lived low abundance excited state Hoogsteen bps. N1-methylated adenine (mA) and guanine (mG) are naturally occurring forms of damage that stabilize Hoogsteen bps in duplex DNA. NMR dynamic ensembles of DNA duplexes with mA-T Hoogsteen bps reveal significant changes in sugar pucker and backbone angles in and around the Hoogsteen bp, as well as kinking of the duplex towards the major groove. Read More

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http://dx.doi.org/10.1007/s10858-018-0177-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6048961PMC
April 2018
5 Reads

TROSY pulse sequence for simultaneous measurement of the N R and {H}-N NOE in deuterated proteins.

J Biomol NMR 2018 04 16;70(4):205-209. Epub 2018 Apr 16.

Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY, 10032, USA.

A TROSY-based NMR experiment is described for simultaneous measurement of the N longitudinal relaxation rate constant R and the {H}-N nuclear Overhauser enhancement. The experiment is based on the observation that the TROSY mixing pulse sequence element symmetrically exchanges H and N magnetizations. The accuracy of the proposed technique is validated by comparison to independent measurements of both relaxation parameters for the protein ubiquitin. Read More

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http://dx.doi.org/10.1007/s10858-018-0181-6DOI Listing
April 2018
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Isotope labeling for studying RNA by solid-state NMR spectroscopy.

J Biomol NMR 2018 07 12;71(3):151-164. Epub 2018 Apr 12.

Centre for Biomolecular Drug Research (BMWZ) and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hanover, Germany.

Nucleic acids play key roles in most biological processes, either in isolation or in complex with proteins. Often they are difficult targets for structural studies, due to their dynamic behavior and high molecular weight. Solid-state nuclear magnetic resonance spectroscopy (ssNMR) provides a unique opportunity to study large biomolecules in a non-crystalline state at atomic resolution. Read More

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http://dx.doi.org/10.1007/s10858-018-0180-7DOI Listing
July 2018
2 Reads

Fast evaluation of protein dynamics from deficient N relaxation data.

J Biomol NMR 2018 04 28;70(4):219-228. Epub 2018 Mar 28.

Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warszawa, Poland.

Simple and convenient method of protein dynamics evaluation from the insufficient experimental N relaxation data is presented basing on the ratios, products, and differences of longitudinal and transverse N relaxation rates obtained at a single magnetic field. Firstly, the proposed approach allows evaluating overall tumbling correlation time (nanosecond time scale). Next, local parameters of the model-free approach characterizing local mobility of backbone amide N-H vectors on two different time scales, S and R , can be elucidated. Read More

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http://dx.doi.org/10.1007/s10858-018-0176-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5953972PMC
April 2018
2 Reads

Trimethylsilyl tag for probing protein-ligand interactions by NMR.

J Biomol NMR 2018 04 21;70(4):211-218. Epub 2018 Mar 21.

Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.

Protein-ligand titrations can readily be monitored with a trimethylsilyl (TMS) tag. Owing to the intensity, narrow line shape and unique chemical shift of a TMS group, dissociation constants can be determined from straightforward 1D H-NMR spectra not only in the fast but also in the slow exchange limit. The tag is easily attached to cysteine residues and a sensitive reporter of ligand binding also at sites where it does not interfere with ligand binding or catalytic efficiency of the target protein. Read More

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http://dx.doi.org/10.1007/s10858-018-0173-6DOI Listing
April 2018
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Measuring the signs of the methyl H chemical shift differences between major and 'invisible' minor protein conformational states using methyl H multi-quantum spectroscopy.

J Biomol NMR 2018 03 21;70(3):187-202. Epub 2018 Mar 21.

TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal Ranga Reddy District, Hyderabad, Telangana, 500107, India.

Carr-Purcell-Meiboom-Gill (CPMG) type relaxation dispersion experiments are now routinely used to characterise protein conformational dynamics that occurs on the μs to millisecond (ms) timescale between a visible major state and 'invisible' minor states. The exchange rate(s) ([Formula: see text]), population(s) of the minor state(s) and the absolute value of the chemical shift difference [Formula: see text] (ppm) between different exchanging states can be extracted from the CPMG data. However the sign of [Formula: see text] that is required to reconstruct the spectrum of the 'invisible' minor state(s) cannot be obtained from CPMG data alone. Read More

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http://dx.doi.org/10.1007/s10858-018-0171-8DOI Listing
March 2018
6 Reads

Segmental isotopic labeling by asparaginyl endopeptidase-mediated protein ligation.

J Biomol NMR 2018 Aug 13;71(4):225-235. Epub 2018 Mar 13.

Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, 00014, Helsinki, Finland.

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. Read More

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http://dx.doi.org/10.1007/s10858-018-0175-4DOI Listing
August 2018
2 Reads

Correction to: Characterization of fibril dynamics on three timescales by solid-state NMR.

J Biomol NMR 2018 03;70(3):203

Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.

In our recent publication (Smith et al., J Biomol NMR 65:171-191, 2016) on the dynamics of HET-s(218-289), we reported on page 176, that calculation of solid-state NMR R rate constants using analytical equations based on Redfield theory (Kurbanov et al., J Chem Phys 135:184104:184101-184109, 2011) failed when the correlation time of motion becomes too long. Read More

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http://dx.doi.org/10.1007/s10858-018-0170-9DOI Listing
March 2018
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Deuteration and selective labeling of alanine methyl groups of β-adrenergic receptor expressed in a baculovirus-insect cell expression system.

J Biomol NMR 2018 07 8;71(3):185-192. Epub 2018 Mar 8.

Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan.

G protein-coupled receptors (GPCRs) exist in equilibrium between multiple conformations, and their populations and exchange rates determine their functions. However, analyses of the conformational dynamics of GPCRs in lipid bilayers are still challenging, because methods for observations of NMR signals of large proteins expressed in a baculovirus-insect cell expression system (BVES) are limited. Here, we report a method to incorporate methyl-CH-labeled alanine with > 45% efficiency in highly deuterated proteins expressed in BVES. Read More

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http://dx.doi.org/10.1007/s10858-018-0174-5DOI Listing
July 2018
8 Reads

Detection of side-chain proton resonances of fully protonated biosolids in nano-litre volumes by magic angle spinning solid-state NMR.

J Biomol NMR 2018 03 3;70(3):177-185. Epub 2018 Mar 3.

Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600, Pessac, France.

We present a new solid-state NMR proton-detected three-dimensional experiment dedicated to the observation of protein proton side chain resonances in nano-liter volumes. The experiment takes advantage of very fast magic angle spinning and double quantum 13C-13C transfer to establish efficient (H)CCH correlations detected on side chain protons. Our approach is demonstrated on the HET-s prion domain in its functional amyloid fibrillar form, fully protonated, with a sample amount of less than 500 µg using a MAS frequency of 70 kHz. Read More

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http://link.springer.com/10.1007/s10858-018-0168-3
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http://dx.doi.org/10.1007/s10858-018-0168-3DOI Listing
March 2018
7 Reads

C APSY-NMR for sequential assignment of intrinsically disordered proteins.

J Biomol NMR 2018 03 28;70(3):167-175. Epub 2018 Feb 28.

CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy.

The increasingly recognized biological relevance of intrinsically disordered proteins requires a continuous expansion of the tools for their characterization via NMR spectroscopy, the only technique so far able to provide atomic-resolution information on these highly mobile macromolecules. Here we present the implementation of projection spectroscopy in C-direct detected NMR experiments to achieve the sequence specific assignment of IDPs. The approach was used to obtain the complete backbone assignment at high temperature of α-synuclein, a paradigmatic intrinsically disordered protein. Read More

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http://dx.doi.org/10.1007/s10858-018-0167-4DOI Listing
March 2018
2 Reads