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Journal of Biomolecular NMR

Abhishek Mandal, Jennifer C Boatz, Travis B Wheeler, Patrick C A van der Wel
A number of recent advances in the field of magic-angle-spinning (MAS) solid-state NMR have enabled its application to a range of biological systems of ever increasing complexity. To retain biological relevance, these samples are increasingly studied in a hydrated state. At the same time, experimental feasibility requires the sample preparation process to attain a high sample concentration within the final MAS rotor. We discuss these considerations, and how they have led to a number of different approaches to MAS NMR sample preparation...
February 22, 2017: Journal of Biomolecular NMR
Elizabeth Dickinson, John R P Arnold, Julie Fisher
The cause of the pregnancy condition preeclampsia (PE) is thought to be endothelial dysfunction caused by oxidative stress. As abnormal glucose tolerance has also been associated with PE, we use a fluorinated-mimic of this metabolite to establish whether any oxidative damage to lipids and proteins in the erythrocyte membrane has increased cell membrane permeability. Data were acquired using (19)F Dynamic-NMR (DNMR) to measure exchange of 3-fluoro-3-deoxyglucose (3-FDG) across the membrane of erythrocytes from 10 pregnant women (5 healthy control women, and 5 from women suffering from PE)...
February 21, 2017: Journal of Biomolecular NMR
Tommaso Banelli, Marco Vuano, Federico Fogolari, Andrea Fusiello, Gennaro Esposito, Alessandra Corazza
We describe a new algorithmic approach able to automatically pick and track the NMR resonances of a large number of 2D NMR spectra acquired during a stepwise variation of a physical parameter. The method has been named Trace in Track (TINT), referring to the idea that a gaussian decomposition traces peaks within the tracks recognised through 3D mathematical morphology. It is capable of determining the evolution of the chemical shifts, intensity and linewidths of each tracked peak.The performances obtained in term of track reconstruction and correct assignment on realistic synthetic spectra were high above 90% when a noise level similar to that of experimental data were considered...
February 17, 2017: Journal of Biomolecular NMR
Sophie N Koroloff, Deanna M Tesch, Emmanuel O Awosanya, Alexander A Nevzorov
Multidimensional separated local-field and spin-exchange experiments employed by oriented-sample solid-state NMR are essential for structure determination and spectroscopic assignment of membrane proteins reconstituted in macroscopically aligned lipid bilayers. However, these experiments typically require a large number of scans in order to establish interspin correlations. Here we have shown that a combination of optimized repetitive cross polarization (REP-CP) and membrane-embedded free radicals allows one to enhance the signal-to-noise ratio by factors 2...
February 15, 2017: Journal of Biomolecular NMR
Tobias Harsch, Philipp Schneider, Bärbel Kieninger, Harald Donaubauer, Hans Robert Kalbitzer
Side chain amide protons of asparagine and glutamine residues in random-coil peptides are characterized by large chemical shift differences and can be stereospecifically assigned on the basis of their chemical shift values only. The bimodal chemical shift distributions stored in the biological magnetic resonance data bank (BMRB) do not allow such an assignment. However, an analysis of the BMRB shows, that a substantial part of all stored stereospecific assignments is not correct. We show here that in most cases stereospecific assignment can also be done for folded proteins using an unbiased artificial chemical shift data base (UACSB)...
February 15, 2017: Journal of Biomolecular NMR
Tomas Miljenović, Xinying Jia, Peter Lavrencic, Bostjan Kobe, Mehdi Mobli
NMR spectroscopy is a powerful method in structural and functional analysis of macromolecules and has become particularly prevalent in studies of protein structure, function and dynamics. Unique to NMR spectroscopy is the relatively low constraints on sample preparation and the high level of control of sample conditions. Proteins can be studied in a wide range of buffer conditions, e.g. different pHs and variable temperatures, allowing studies of proteins under conditions that are closer to their native environment compared to other structural methods such as X-ray crystallography and electron microscopy...
February 10, 2017: Journal of Biomolecular NMR
Thomas Bauer, Claudio Dotta, Livia Balacescu, Julia Gath, Andreas Hunkeler, Anja Böckmann, Beat H Meier
The temperature-dependent resonance-line broadening of HET-s(218-289) in its amyloid form is investigated in the range between 110 K and 280 K. Significant differences are observed between residues in the structured hydrophobic triangular core, which are broadened the least and can be detected down to 100 K, and in the solvent-exposed parts, which are broadened the most and often disappear from the observed spectrum around 200 K. Below the freezing of the bulk water, around 273 K, the protein fibrils are still surrounded by a layer of mobile water whose thickness decreases with temperature, leading to drying out of the fibrils...
February 4, 2017: Journal of Biomolecular NMR
Albert A Smith
Software for fitting of NMR spectra in MATLAB is presented. Spectra are fitted in the frequency domain, using Fourier transformed lineshapes, which are derived using the experimental acquisition and processing parameters. This yields more accurate fits compared to common fitting methods that use Lorentzian or Gaussian functions. Furthermore, a very time-efficient algorithm for calculating and fitting spectra has been developed. The software also performs initial peak picking, followed by subsequent fitting and refinement of the peak list, by iteratively adding and removing peaks to improve the overall fit...
February 3, 2017: Journal of Biomolecular NMR
Julia M Würz, Peter Güntert
The automated identification of signals in multidimensional NMR spectra is a challenging task, complicated by signal overlap, noise, and spectral artifacts, for which no universally accepted method is available. Here, we present a new peak picking algorithm, CYPICK, that follows, as far as possible, the manual approach taken by a spectroscopist who analyzes peak patterns in contour plots of the spectrum, but is fully automated. Human visual inspection is replaced by the evaluation of geometric criteria applied to contour lines, such as local extremality, approximate circularity (after appropriate scaling of the spectrum axes), and convexity...
February 3, 2017: Journal of Biomolecular NMR
Changmiao Guo, Guangjin Hou, Xingyu Lu, Tatyana Polenova
REDOR-based experiments with simultaneous (1)H-(13)C and (1)H-(15)N dipolar dephasing are explored for investigating intermolecular protein-protein interfaces in complexes formed by a U-(13)C,(15)N-labeled protein and its natural abundance binding partner. The application of a double-REDOR filter (dREDOR) results in a complete dephasing of proton magnetization in the U-(13)C,(15)N-enriched molecule while the proton magnetization of the unlabeled binding partner is not dephased. This retained proton magnetization is then transferred across the intermolecular interface by (1)H-(13)C or (1)H-(15)N cross polarization, permitting to establish the residues of the U-(13)C,(15)N-labeled protein, which constitute the binding interface...
January 24, 2017: Journal of Biomolecular NMR
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
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
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
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
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...
January 2017: Journal of Biomolecular NMR
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
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
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
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
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
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