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Journal of Biomolecular NMR

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https://www.readbyqxmd.com/read/28074361/partially-deuterated-samples-of-het-s-218-289-fibrils-assignment-and-deuterium-isotope-effect
#1
Albert A Smith, Francesco Ravotti, Emilie Testori, Riccardo Cadalbert, Matthias Ernst, Anja Böckmann, Beat H Meier
Fast magic-angle spinning and partial sample deuteration allows direct detection of (1)H in solid-state NMR, yielding significant gains in mass sensitivity. In order to further analyze the spectra, (1)H detection requires assignment of the (1)H resonances. In this work, resonance assignments of backbone H(N) and Hα are presented for HET-s(218-289) fibrils, based on the existing assignment of Cα, Cβ, C', and N resonances. The samples used are partially deuterated for higher spectral resolution, and the shifts in resonance frequencies of Cα and Cβ due to the deuterium isotope effect are investigated...
January 10, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28035651/high-quality-nmr-structures-a-new-force-field-with-implicit-water-and-membrane-solvation-for-xplor-nih
#2
Ye Tian, Charles D Schwieters, Stanley J Opella, Francesca M Marassi
Structure determination of proteins by NMR is unique in its ability to measure restraints, very accurately, in environments and under conditions that closely mimic those encountered in vivo. For example, advances in solid-state NMR methods enable structure determination of membrane proteins in detergent-free lipid bilayers, and of large soluble proteins prepared by sedimentation, while parallel advances in solution NMR methods and optimization of detergent-free lipid nanodiscs are rapidly pushing the envelope of the size limit for both soluble and membrane proteins...
December 29, 2016: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28028745/hexagonal-ice-in-pure-water-and-biological-nmr-samples
#3
Thomas Bauer, Julia Gath, Andreas Hunkeler, Matthias Ernst, Anja Böckmann, Beat H Meier
Ice, in addition to "liquid" water and protein, is an important component of protein samples for NMR spectroscopy at subfreezing temperatures but it has rarely been observed spectroscopically in this context. We characterize its spectroscopic behavior in the temperature range from 100 to 273 K, and find that it behaves like pure water ice. The interference of magic-angle spinning (MAS) as well as rf multiple-pulse sequences with Bjerrum-defect motion greatly influences the ice spectra.
December 27, 2016: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28028744/bacterial-production-of-site-specific-13-c-labeled-phenylalanine-and-methodology-for-high-level-incorporation-into-bacterially-expressed-recombinant-proteins
#4
Bhargavi Ramaraju, Hana McFeeters, Bernhard Vogler, Robert L McFeeters
Nuclear magnetic resonance spectroscopy studies of ever larger systems have benefited from many different forms of isotope labeling, in particular, site specific isotopic labeling. Site specific (13)C labeling of methyl groups has become an established means of probing systems not amenable to traditional methodology. However useful, methyl reporter sites can be limited in number and/or location. Therefore, new complementary site specific isotope labeling strategies are valuable. Aromatic amino acids make excellent probes since they are often found at important interaction interfaces and play significant structural roles...
December 27, 2016: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28012125/high-pressure-31-p-nmr-spectroscopy-on-guanine-nucleotides
#5
Michael Spoerner, Matthias Karl, Pedro Lopes, Marcus Hoering, Karoline Loeffel, Andrea Nuehs, Joseph Adelsberger, Werner Kremer, Hans Robert Kalbitzer
The (31)P NMR pressure response of guanine nucleotides bound to proteins has been studied in the past for characterizing the pressure perturbation of conformational equilibria. The pressure response of the (31)P NMR chemical shifts of the phosphate groups of GMP, GDP, and GTP as well as the commonly used GTP analogs GppNHp, GppCH2p and GTPγS was measured in the absence and presence of Mg(2+)-ions within a pressure range up to 200 MPa. The pressure dependence of chemical shifts is clearly non-linear. For all nucleotides a negative first order pressure coefficient B 1 was determined indicating an upfield shift of the resonances with pressure...
December 23, 2016: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/27885546/target-specific-nmr-detection-of-protein-ligand-interactions-with-antibody-relayed-15-n-group-selective-std
#6
Anasztázia Hetényi, Zsófia Hegedűs, Roberta Fajka-Boja, Éva Monostori, Katalin E Kövér, Tamás A Martinek
Fragment-based drug design has been successfully applied to challenging targets where the detection of the weak protein-ligand interactions is a key element. (1)H saturation transfer difference (STD) NMR spectroscopy is a powerful technique for this work but it requires pure homogeneous proteins as targets. Monoclonal antibody (mAb)-relayed (15)N-GS STD spectroscopy has been developed to resolve the problem of protein mixtures and impure proteins. A (15)N-labelled target-specific mAb is selectively irradiated and the saturation is relayed through the target to the ligand...
November 24, 2016: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/27866371/sparse-multidimensional-iterative-lineshape-enhanced-smile-reconstruction-of-both-non-uniformly-sampled-and-conventional-nmr-data
#7
Jinfa Ying, Frank Delaglio, Dennis A Torchia, Ad Bax
Implementation of a new algorithm, SMILE, is described for reconstruction of non-uniformly sampled two-, three- and four-dimensional NMR data, which takes advantage of the known phases of the NMR spectrum and the exponential decay of underlying time domain signals. The method is very robust with respect to the chosen sampling protocol and, in its default mode, also extends the truncated time domain signals by a modest amount of non-sampled zeros. SMILE can likewise be used to extend conventional uniformly sampled data, as an effective multidimensional alternative to linear prediction...
November 19, 2016: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/27844185/a-j-modulated-protonless-nmr-experiment-characterizes-the-conformational-ensemble-of-the-intrinsically-disordered-protein-wip
#8
Eva Rozentur-Shkop, Gil Goobes, Jordan H Chill
Intrinsically disordered proteins (IDPs) are multi-conformational polypeptides that lack a single stable three-dimensional structure. It has become increasingly clear that the versatile IDPs play key roles in a multitude of biological processes, and, given their flexible nature, NMR is a leading method to investigate IDP behavior on the molecular level. Here we present an IDP-tailored J-modulated experiment designed to monitor changes in the conformational ensemble characteristic of IDPs by accurately measuring backbone one- and two-bond J((15)N,(13)Cα) couplings...
November 14, 2016: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/27837295/pitfalls-in-compressed-sensing-reconstruction-and-how-to-avoid-them
#9
Alexandra Shchukina, Paweł Kasprzak, Rupashree Dass, Michał Nowakowski, Krzysztof Kazimierczuk
Multidimensional NMR can provide unmatched spectral resolution, which is crucial when dealing with samples of biological macromolecules. The resolution, however, comes at the high price of long experimental time. Non-uniform sampling (NUS) of the evolution time domain allows to suppress this limitation by sampling only a small fraction of the data, but requires sophisticated algorithms to reconstruct omitted data points. A significant group of such algorithms known as compressed sensing (CS) is based on the assumption of sparsity of a reconstructed spectrum...
November 11, 2016: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/27803998/accelerating-proton-spin-diffusion-in-perdeuterated-proteins-at-100%C3%A2-khz-mas
#10
Johannes J Wittmann, Vipin Agarwal, Johannes Hellwagner, Alons Lends, Riccardo Cadalbert, Beat H Meier, Matthias Ernst
Fast magic-angle spinning (>60 kHz) has many advantages but makes spin-diffusion-type proton-proton long-range polarization transfer inefficient and highly dependent on chemical-shift offset. Using 100%-HN-[(2)H,(13)C,(15)N]-ubiquitin as a model substance, we quantify the influence of the chemical-shift difference on the spin diffusion between proton spins and compare two experiments which lead to an improved chemical-shift compensation of the transfer: rotating-frame spin diffusion and a new experiment, reverse amplitude-modulated MIRROR...
November 1, 2016: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/27988858/sequence-specific-assignment-of-methyl-groups-from-the-neuronal-snare-complex-using-lanthanide-induced-pseudocontact-shifts
#11
Yun-Zu Pan, Bradley Quade, Kyle D Brewer, Monika Szabo, James D Swarbrick, Bim Graham, Josep Rizo
Neurotransmitter release depends critically on the neuronal SNARE complex formed by syntaxin-1, SNAP-25 and synaptobrevin, as well as on other proteins such as Munc18-1, Munc13-1 and synaptotagmin-1. Although three-dimensional structures are available for these components, it is still unclear how they are assembled between the synaptic vesicle and plasma membranes to trigger fast, Ca(2+)-dependent membrane fusion. Methyl TROSY NMR experiments provide a powerful tool to study complexes between these proteins, but assignment of the methyl groups of the SNARE complex is hindered by its limited solubility...
December 2016: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/27878649/-15-n-and-13-c-sofast-hmqc-editing-enhances-3d-noesy-sensitivity-in-highly-deuterated-selectively-1-h-13-c-labeled-proteins
#12
Paolo Rossi, Youlin Xia, Nandish Khanra, Gianluigi Veglia, Charalampos G Kalodimos
The ongoing NMR method development effort strives for high quality multidimensional data with reduced collection time. Here, we apply 'SOFAST-HMQC' to frequency editing in 3D NOESY experiments and demonstrate the sensitivity benefits using highly deuterated and (15)N, methyl labeled samples in H2O. The experiments benefit from a combination of selective T 1 relaxation (or L-optimized effect), from Ernst angle optimization and, in certain types of experiments, from using the mixing time for both NOE buildup and magnetization recovery...
December 2016: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/27866370/perspective-revisiting-the-field-dependence-of-trosy-sensitivity
#13
Koh Takeuchi, Haribabu Arthanari, Gerhard Wagner
The discovery of the TROSY effect (Pervushin et al. in Proc Natl Acad Sci USA 94:12366-12371, 1997) for reducing transverse relaxation and line sharpening through selecting pathways in which dipole-dipole and CSA Hamiltonians partially cancel each other had a tremendous impact on solution NMR studies of macromolecules. Together with the methyl TROSY (Tugarinov and Kay in J Biomol NMR 28:165-172, 2004) it enabled structural and functional studies of significantly larger systems. The optimal field strengths for TROSY have been estimated to be on spectrometers operating around 900 MHz (21...
December 2016: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/27858311/nmr-structure-of-the-hiv-1-reverse-transcriptase-thumb-subdomain
#14
Naima G Sharaf, Andrew E Brereton, In-Ja L Byeon, P Andrew Karplus, Angela M Gronenborn
The solution NMR structure of the isolated thumb subdomain of HIV-1 reverse transcriptase (RT) has been determined. A detailed comparison of the current structure with dozens of the highest resolution crystal structures of this domain in the context of the full-length enzyme reveals that the overall structures are very similar, with only two regions exhibiting local conformational differences. The C-terminal capping pattern of the αH helix is subtly different, and the loop connecting the αI and αJ helices in the p51 chain of the full-length p51/p66 heterodimeric RT differs from our NMR structure due to unique packing interactions in mature RT...
December 2016: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/27766502/dynamic-domains-of-amyloid-fibrils-can-be-site-specifically-assigned-with-proton-detected-3d-nmr-spectroscopy
#15
Alexander S Falk, Ansgar B Siemer
Several amyloid fibrils have cores framed by highly dynamic, intrinsically disordered, domains that can play important roles for function and toxicity. To study these domains in detail using solid-state NMR spectroscopy, site-specific resonance assignments are required. Although the rapid dynamics of these domains lead to considerable averaging of orientation-dependent NMR interactions and thereby line-narrowing, the proton linewidths observed in these samples is far larger than what is regularly observed in solution...
November 2016: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/27778134/determination-of-ligand-binding-modes-in-weak-protein-ligand-complexes-using-sparse-nmr-data
#16
Biswaranjan Mohanty, Martin L Williams, Bradley C Doak, Mansha Vazirani, Olga Ilyichova, Geqing Wang, Wolfgang Bermel, Jamie S Simpson, David K Chalmers, Glenn F King, Mehdi Mobli, Martin J Scanlon
We describe a general approach to determine the binding pose of small molecules in weakly bound protein-ligand complexes by deriving distance constraints between the ligand and methyl groups from all methyl-containing residues of the protein. We demonstrate that using a single sample, which can be prepared without the use of expensive precursors, it is possible to generate high-resolution data rapidly and obtain the resonance assignments of Ile, Leu, Val, Ala and Thr methyl groups using triple resonance scalar correlation data...
October 24, 2016: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/27771863/solution-nmr-structure-of-the-hltf-hiran-domain-a-conserved-module-in-swi2-snf2-dna-damage-tolerance-proteins
#17
Dmitry M Korzhnev, Dante Neculai, Sirano Dhe-Paganon, Cheryl H Arrowsmith, Irina Bezsonova
HLTF is a SWI2/SNF2-family ATP-dependent chromatin remodeling enzyme that acts in the error-free branch of DNA damage tolerance (DDT), a cellular mechanism that enables replication of damaged DNA while leaving damage repair for a later time. Human HLTF and a closely related protein SHPRH, as well as their yeast homologue Rad5, are multi-functional enzymes that share E3 ubiquitin-ligase activity required for activation of the error-free DDT. HLTF and Rad5 also function as ATP-dependent dsDNA translocases and possess replication fork reversal activities...
October 22, 2016: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/27771862/a-protocol-for-the-refinement-of-nmr-structures-using-simultaneously-pseudocontact-shift-restraints-from-multiple-lanthanide-ions
#18
Davide Sala, Andrea Giachetti, Claudio Luchinat, Antonio Rosato
The binding of paramagnetic metal ions to proteins produces a number of different effects on the NMR spectra of the system. In particular, when the magnetic susceptibility of the metal ion is anisotropic, pseudocontact shifts (PCSs) arise and can be easily measured. They constitute very useful restraints for the solution structure determination of metal-binding proteins. In this context, there has been great interest in the use of lanthanide(III) ions to induce PCSs in diamagnetic proteins, e.g. through the replacement native calcium(II) ions...
October 22, 2016: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/27744623/high-sensitivity-high-resolution-full-range-relaxometry-using-a-fast-mechanical-sample-shuttling-device-and-a-cryo-probe
#19
Ching-Yu Chou, Minglee Chu, Chi-Fon Chang, Tsunai Yu, Tai-Huang Huang, Dimitris Sakellariou
Field-dependent NMR studies of bio-molecular systems using a sample shuttling hardware operating on a high-field NMR apparatus have provided valuable structural and dynamic information. We have recently published a design of a compact sample transportation device, called "field-cycler", which was installed in a commercial spectrometer and which provided highly precise positioning and stability during high speed shuttling. In this communication, we demonstrate the first use of a sample shuttling device on a commercial high field standard bore NMR spectrometer, equipped with a commercial triple resonance cryogenically cooled NMR probe...
October 15, 2016: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/27734179/quantifying-protein-dynamics-in-the-ps-ns-time-regime-by-nmr-relaxation
#20
Griselda Hernández, David M LeMaster
Both (15)N chemical shift anisotropy (CSA) and sufficiently rapid exchange linebroadening transitions exhibit relaxation contributions that are proportional to the square of the magnetic field. Deconvoluting these contributions is further complicated by residue-dependent variations in protein amide (15)N CSA values which have proven difficult to accurately measure. Exploiting recently reported improvements for the implementation of T1 and T1ρ experiments, field strength-dependent studies have been carried out on the B3 domain of protein G (GB3) as well as on the immunophilin FKBP12 and a H87V variant of that protein in which the major conformational exchange linebroadening transition is suppressed...
October 12, 2016: Journal of Biomolecular NMR
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