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Journal of Biomolecular NMR

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https://www.readbyqxmd.com/read/28434103/structure-restraints-from-heteronuclear-pseudocontact-shifts-generated-by-lanthanide-tags-at-two-different-sites
#1
Benjamin J G Pearce, Shereen Jabar, Choy-Theng Loh, Monika Szabo, Bim Graham, Gottfried Otting
Pseudocontact shifts (PCS) encode long-range information on 3D structures of protein backbones and side-chains. The level of structural detail that can be obtained increases with the number of different sites tagged with a paramagnetic metal ion to generate PCSs. Here we show that PCSs from two different sites can suffice to determine the structure of polypeptide chains and their location and orientation relative to the magnetic susceptibility tensor χ, provided that PCSs are available for (1)H as well as heteronuclear spins...
April 22, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28421403/erratum-to-ccpnmr-analysisassign-a-flexible-platform-for-integrated-nmr-analysis
#2
Simon P Skinner, Rasmus H Fogh, Wayne Boucher, Timothy J Ragan, Luca G Mureddu, Geerten W Vuister
No abstract text is available yet for this article.
April 18, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28393280/nmr-line-shape-analysis-of-a-multi-state-ligand-binding-mechanism-in-chitosanase
#3
Shoko Shinya, Mariana G Ghinet, Ryszard Brzezinski, Kyoko Furuita, Chojiro Kojima, Sneha Shah, Evgenii L Kovrigin, Tamo Fukamizo
Chitosan interaction with chitosanase was examined through analysis of spectral line shapes in the NMR HSQC titration experiments. We established that the substrate, chitosan hexamer, binds to the enzyme through the three-state induced-fit mechanism with fast formation of the encounter complex followed by slow isomerization of the bound-state into the final conformation. Mapping of the chemical shift perturbations in two sequential steps of the mechanism highlighted involvement of the substrate-binding subsites and the hinge region in the binding reaction...
April 9, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28393279/non-equilibrium-hydrogen-exchange-for-determination-of-h-bond-strength-and-water-accessibility-in-solid-proteins
#4
Kristof Grohe, Kumar Tekwani Movellan, Suresh Kumar Vasa, Karin Giller, Stefan Becker, Rasmus Linser
We demonstrate measurement of non-equilibrium backbone amide hydrogen-deuterium exchange rates (HDX) for solid proteins. The target of this study are the slowly exchanging residues in solid samples, which are associated with stable secondary-structural elements of proteins. These hydrogen exchange processes escape methods measuring equilibrium exchange rates of faster processes. The method was applied to a micro-crystalline preparation of the SH3 domain of chicken α-spectrin. Therefore, from a 100% back-exchanged micro-crystalline protein preparation, the supernatant buffer was exchanged by a partially deuterated buffer to reach a final protonation level of approximately 20% before packing the sample in a 1...
April 9, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28365903/lanthanoid-tagging-via-an-unnatural-amino-acid-for-protein-structure-characterization
#5
Wen-Xue Jiang, Xin-Hua Gu, Xu Dong, Chun Tang
Lanthanoid pseudo-contact shift (PCS) provides long-range structural information between a paramagnetic tag and protein nuclei. However, for proteins with native cysteines, site-specific attachment may only utilize functional groups orthogonal to sulfhydryl chemistry. Here we report two lanthanoid probes, DTTA-C3-yne and DTTA-C4-yne, which can be conjugated to an unnatural amino acid pAzF in the target protein via azide-alkyne cycloaddition. Demonstrated with ubiquitin and cysteine-containing enzyme EIIB, we show that large PCSs of distinct profiles can be generated for each tag/lanthanoid combination...
April 1, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28357518/longitudinal-relaxation-optimized-amide-1-h-cest-experiments-for-studying-slow-chemical-exchange-processes-in-fully-protonated-proteins
#6
Tairan Yuwen, Lewis E Kay
Chemical Exchange Saturation Transfer (CEST) experiments are increasingly used to study slow timescale exchange processes in biomolecules. Although (15)N- and (13)C-CEST have been the approaches of choice, the development of spin state selective (1)H-CEST pulse sequences that separate the effects of chemical and dipolar exchange [T. Yuwen, A. Sekhar and L. E. Kay, Angew Chem Int Ed Engl 2016 doi: 10.1002/anie.201610759 (Yuwen et al. 2017)] significantly increases the utility of (1)H-based experiments. Pulse schemes have been described previously for studies of highly deuterated proteins...
March 29, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28332026/interpolating-and-extrapolating-with-hmsist-%C3%A2-seeking-a-tmax-for-optimal-sensitivity-resolution-and-frequency-accuracy
#7
Sven G Hyberts, Scott A Robson, Gerhard Wagner
Non-Uniform Sampling has the potential to exploit the optimal resolution of high-field NMR instruments. This is not possible in 3D and 4D NMR experiments when using traditional uniform sampling due to the long overall measurement time. Nominally, uniformly sampled time domain data acquired to a maximum evolution time tmax can be extended to high resolution via a virtual maximum evolution time t*max while extrapolating with linear prediction or iterative soft thresholding (IST). At the high resolution obtainable with extrapolation of US data, however, the accuracy of peak positions is compromised as observed when comparing inter- and intra-residue peaks in a 3D HNCA experiment...
March 22, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28317074/probing-conformational-dynamics-in-biomolecules-via-chemical-exchange-saturation-transfer-a-primer
#8
Pramodh Valluruapalli, Ashok Sekhar, Tairan Yuwen, Lewis E Kay
Although Chemical Exchange Saturation Transfer (CEST) type NMR experiments have been used to study chemical exchange processes in molecules since the early 1960s, there has been renewed interest in the past several years in using this approach to study biomolecular conformational dynamics. The methodology is particularly powerful for the study of sparsely populated, transiently formed conformers that are recalcitrant to investigation using traditional biophysical tools, and it is complementary to relaxation dispersion and magnetization transfer experiments that have traditionally been used to study chemical exchange processes...
March 19, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28289927/nmr-assignments-of-sparsely-labeled-proteins-using-a-genetic-algorithm
#9
Qi Gao, Gordon R Chalmers, Kelley W Moremen, James H Prestegard
Sparse isotopic labeling of proteins for NMR studies using single types of amino acid ((15)N or (13)C enriched) has several advantages. Resolution is enhanced by reducing numbers of resonances for large proteins, and isotopic labeling becomes economically feasible for glycoproteins that must be expressed in mammalian cells. However, without access to the traditional triple resonance strategies that require uniform isotopic labeling, NMR assignment of crosspeaks in heteronuclear single quantum coherence (HSQC) spectra is challenging...
March 13, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28286915/cross-correlated-relaxation-rates-between-protein-backbone-h-x-dipolar-interactions
#10
Beat Vögeli
The relaxation interference between dipole-dipole interactions of two separate spin pairs carries structural and dynamics information. In particular, when compared to individual dynamic behavior of those spin pairs, such cross-correlated relaxation (CCR) rates report on the correlation between the spin pairs. We have recently mapped out correlated motion along the backbone of the protein GB3, using CCR rates among and between consecutive H(N)-N and H(α)-C(α) dipole-dipole interactions. Here, we provide a detailed account of the measurement of the four types of CCR rates...
March 12, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28271365/noesy-watercontrol-a-new-noesy-sequence-for-the-observation-of-under-water-protein-resonances
#11
Allan M Torres, Gang Zheng, William S Price
Highly selective and efficient water signal suppression is indispensable in biomolecular 2D nuclear Overhauser effect spectroscopy (NOESY) experiments. However, the application of conventional water suppression schemes can cause a significant or complete loss of the biomolecular resonances at and around the water chemical shift (ω2). In this study, a new sequence, NOESY-WaterControl, was developed to address this issue. The new sequence was tested on lysozyme and bovine pancreatic trypsin inhibitor (BPTI), demonstrating its efficiency in both water suppression and, more excitingly, preserving water-proximate biomolecular resonances in ω2...
March 7, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28247186/site-selective-13-c-labeling-of-proteins-using-erythrose
#12
Ulrich Weininger
NMR-spectroscopy enables unique experimental studies on protein dynamics at atomic resolution. In order to obtain a full atom view on protein dynamics, and to study specific local processes like ring-flips, proton-transfer, or tautomerization, one has to perform studies on amino-acid side chains. A key requirement for these studies is site-selective labeling with (13)C and/or (1)H, which is achieved in the most general way by using site-selectively (13)C-enriched glucose (1- and 2-(13)C) as the carbon source in bacterial expression systems...
February 28, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28243768/reconstruction-of-non-uniformly-sampled-five-dimensional-nmr-spectra-by-signal-separation-algorithm
#13
Krzysztof Kosiński, Jan Stanek, Michał J Górka, Szymon Żerko, Wiktor Koźmiński
A method for five-dimensional spectral reconstruction of non-uniformly sampled NMR data sets is proposed. It is derived from the previously published signal separation algorithm, with major alterations to avoid unfeasible processing of an entire five-dimensional spectrum. The proposed method allows credible reconstruction of spectra from as little as a few hundred data points and enables sensitive resonance detection in experiments with a high dynamic range of peak intensities. The efficiency of the method is demonstrated on two high-resolution spectra for rapid sequential assignment of intrinsically disordered proteins, namely 5D HN(CA)CONH and 5D (HACA)CON(CO)CONH...
February 28, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28243767/practical-considerations-for-investigation-of-protein-conformational-dynamics-by-15-n-r-1%C3%AF-relaxation-dispersion
#14
Erik Walinda, Daichi Morimoto, Masahiro Shirakawa, Kenji Sugase
It is becoming increasingly apparent that proteins are not static entities and that their function often critically depends on accurate sampling of multiple conformational states in aqueous solution. Accordingly, the development of methods to study conformational states in proteins beyond their ground-state structure ("excited states") has crucial biophysical importance. Here we investigate experimental schemes for optimally probing chemical exchange processes in proteins on the micro- to millisecond timescale by (15)N R 1ρ relaxation dispersion...
February 28, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28213793/automation-of-peak-tracking-analysis-of-stepwise-perturbed-nmr-spectra
#15
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
https://www.readbyqxmd.com/read/28205016/sensitivity-enhancement-for-membrane-proteins-reconstituted-in-parallel-and-perpendicular-oriented-bicelles-obtained-by-using-repetitive-cross-polarization-and-membrane-incorporated-free-radicals
#16
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
https://www.readbyqxmd.com/read/28197852/stereospecific-assignment-of-the-asparagine-and-glutamine-sidechain-amide-protons-in-proteins-from-chemical-shift-analysis
#17
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
https://www.readbyqxmd.com/read/28188517/a-non-uniform-sampling-approach-enables-studies-of-dilute-and-unstable-proteins
#18
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
https://www.readbyqxmd.com/read/28161758/line-broadening-in-low-temperature-solid-state-nmr-spectra-of-fibrils
#19
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
https://www.readbyqxmd.com/read/28160196/infos-spectrum-fitting-software-for-nmr-analysis
#20
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
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