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Journal of Biomolecular NMR

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
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...
November 23, 2016: Journal of Biomolecular NMR
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
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...
November 19, 2016: Journal of Biomolecular NMR
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...
November 17, 2016: Journal of Biomolecular NMR
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
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
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
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
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
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
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
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
Mengli Cai, Ying Huang, Renbin Yang, Robert Craigie, G M Clore
We present a simple, convenient and robust protocol for expressing perdeuterated proteins in E. coli BL21(DE3) cells in shaker flasks that reduces D2O usage tenfold and d7-glucose usage by 30 %. Using a modified M9 medium and optimized growth conditions, we were able to grow cells in linear log phase to an OD600 of up to 10. Inducing the cells with isopropyl β-D-1-thiogalactopyranoside at an OD600 of 10, instead of less than 1, enabled us to increase the cell mass tenfold per unit volume of cell culture...
October 5, 2016: Journal of Biomolecular NMR
Amir Seginer, Gregory L Olsen, Lucio Frydman
Thanks to their special spatiotemporal encoding/decoding scheme, ultrafast (UF) NMR sequences can deliver arbitrary 2D spectra following a single excitation. Regardless of their nature, these sequences have in common their tracing of a path in the [Formula: see text]-[Formula: see text] plane, that will deliver the spectrum being sought after a 1D Fourier transformation versus [Formula: see text]. This need to simultaneously digitize two domains, tends to impose bandwidth limitations along all spectral axes...
September 28, 2016: Journal of Biomolecular NMR
Madeleine Strickland, Charles D Schwieters, Christoph Göbl, Ana C L Opina, Marie-Paule Strub, Rolf E Swenson, Olga Vasalatiy, Nico Tjandra
Lanthanide complexes based on the DOTA (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) cage are commonly used as phase contrast agents in magnetic resonance imaging, but can also be utilized in structural NMR applications due to their ability to induce either paramagnetic relaxation enhancement or a pseudocontact shift (PCS) depending on the choice of the lanthanide. The size and sign of the PCS for any given atom is determined by its coordinates relative to the metal center, and the characteristics of the lanthanide's magnetic susceptibility tensor...
September 22, 2016: Journal of Biomolecular NMR
M J Bostock, D J Holland, D Nietlispach
NMR spectroscopy is central to atomic resolution studies in biology and chemistry. Key to this approach are multidimensional experiments. Obtaining such experiments with sufficient resolution, however, is a slow process, in part since each time increment in every indirect dimension needs to be recorded twice, in quadrature. We introduce a modified compressed sensing (CS) algorithm enabling reconstruction of data acquired with random acquisition of quadrature components in gradient-selection NMR. We name this approach random quadrature detection (RQD)...
September 20, 2016: Journal of Biomolecular NMR
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
Wai Ching Veronica Wong, Aurimas Narkevicius, Wing Ying Chow, David G Reid, Rakesh Rajan, Roger A Brooks, Maggie Green, Melinda J Duer
We have prepared mouse fur extensively (13)C,(15)N-labelled in all amino acid types enabling application of 2D solid state NMR techniques which establish covalent and spatial proximities within, and in favorable cases between, residues. (13)C double quantum-single quantum correlation and proton driven spin diffusion techniques are particularly useful for resolving certain amino acid types. Unlike 1D experiments on isotopically normal material, the 2D methods allow the chemical shifts of entire spin systems of numerous residue types to be determined, particularly those with one or more distinctively shifted atoms such as Gly, Ser, Thr, Tyr, Phe, Val, Leu, Ile and Pro...
October 2016: Journal of Biomolecular NMR
Simon P Skinner, Rasmus H Fogh, Wayne Boucher, Timothy J Ragan, Luca G Mureddu, Geerten W Vuister
NMR spectroscopy is an indispensably powerful technique for the analysis of biomolecules under ambient conditions, both for structural- and functional studies. However, in practice the complexity of the technique has often frustrated its application by non-specialists. In this paper, we present CcpNmr version-3, the latest software release from the Collaborative Computational Project for NMR, for all aspects of NMR data analysis, including liquid- and solid-state NMR data. This software has been designed to be simple, functional and flexible, and aims to ensure that routine tasks can be performed in a straightforward manner...
October 2016: Journal of Biomolecular NMR
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