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Journal of Biomolecular NMR

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https://www.readbyqxmd.com/read/28815397/detecting-and-accounting-for-multiple-sources-of-positional-variance-in-peak-list-registration-analysis-and-spin-system-grouping
#1
Andrey Smelter, Eric C Rouchka, Hunter N B Moseley
Peak lists derived from nuclear magnetic resonance (NMR) spectra are commonly used as input data for a variety of computer assisted and automated analyses. These include automated protein resonance assignment and protein structure calculation software tools. Prior to these analyses, peak lists must be aligned to each other and sets of related peaks must be grouped based on common chemical shift dimensions. Even when programs can perform peak grouping, they require the user to provide uniform match tolerances or use default values...
August 16, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28756478/protein-19-f-labeling-using-transglutaminase-for-the-nmr-study-of-intermolecular-interactions
#2
Yoshikazu Hattori, David Heidenreich, Yuki Ono, Toshihiko Sugiki, Kei-Ichi Yokoyama, Ei-Ichiro Suzuki, Toshimichi Fujiwara, Chojiro Kojima
The preparation of stable isotope-labeled proteins is important for NMR studies, however, it is often hampered in the case of eukaryotic proteins which are not readily expressed in Escherichia coli. Such proteins are often conveniently investigated following post-expression chemical isotope tagging. Enzymatic (15)N-labeling of glutamine side chains using transglutaminase (TGase) has been applied to several proteins for NMR studies. (19)F-labeling is useful for interaction studies due to its high NMR sensitivity and susceptibility...
July 29, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28717997/an-enhanced-sensitivity-methyl-1-h-triple-quantum-pulse-scheme-for-measuring-diffusion-constants-of-macromolecules
#3
Rui Huang, Jacob P Brady, Ashok Sekhar, Tairan Yuwen, Lewis E Kay
We present a pulse scheme that exploits methyl (1)H triple-quantum (TQ) coherences for the measurement of diffusion rates of slowly diffusing molecules in solution. It is based on the well-known stimulated echo experiment, with encoding and decoding of TQ coherences. The size of quantifiable diffusion coefficients is thus lowered by an order of magnitude with respect to single-quantum (SQ) approaches. Notably, the sensitivity of the scheme is high, approximately ¾ that of the corresponding single quantum experiment, neglecting relaxation losses, and on the order of a factor of 4 more sensitive than a previously published sequence for AX3 spin systems (Zheng et al...
July 17, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28711957/an-improved-protocol-for-amino-acid-type-selective-isotope-labeling-in-insect-cells
#4
Yaqun Zhang, Hui Wei, Dianlin Xie, Deepa Calambur, Andrew Douglas, Mian Gao, Frank Marsilio, William J Metzler, Nicolas Szapiel, Ping Zhang, Mark R Witmer, Luciano Mueller, David Hedin
An improved expression protocol is proposed for amino acid type-specific [(13)C], [(15)N]-isotope labeling of proteins in baculovirus-infected (BV) insect cell cultures. This new protocol modifies the methods published by Gossert et al. (J Biomol NMR 51(4):449-456, 2011) and provides efficient incorporation of isotopically labeled amino acids, with similar yields per L versus unlabeled expression in rich media. Gossert et al. identified the presence of unlabeled amino acids in the yeastolate of the growth medium as a major limitation in isotope labeling using BV-infected insect cells...
July 15, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28674916/-2-h-13-c-correlation-solid-state-nmr-for-investigating-dynamics-and-water-accessibilities-of-proteins-and-carbohydrates
#5
Martin D Gelenter, Tuo Wang, Shu-Yu Liao, Hugh O'Neill, Mei Hong
Site-specific determination of molecular motion and water accessibility by indirect detection of (2)H NMR spectra has advantages over dipolar-coupling based techniques due to the large quadrupolar couplings and the ensuing high angular resolution. Recently, a Rotor Echo Short Pulse IRrAdiaTION mediated cross polarization ((RESPIRATION)CP) technique was developed, which allowed efficient transfer of (2)H magnetization to (13)C at moderate (2)H radiofrequency field strengths available on most commercial MAS probes...
July 3, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28653216/nmr-characterization-of-htpg-the-e-coli-hsp90-using-sparse-labeling-with-13-c-methyl-alanine
#6
Kari Pederson, Gordon R Chalmers, Qi Gao, Daniel Elnatan, Theresa A Ramelot, Li-Chung Ma, Gaetano T Montelione, Michael A Kennedy, David A Agard, James H Prestegard
A strategy for acquiring structural information from sparsely isotopically labeled large proteins is illustrated with an application to the E. coli heat-shock protein, HtpG (high temperature protein G), a 145 kDa dimer. It uses (13)C-alanine methyl labeling in a perdeuterated background to take advantage of the sensitivity and resolution of Methyl-TROSY spectra, as well as the backbone-centered structural information from (1)H-(13)C residual dipolar couplings (RDCs) of alanine methyl groups. In all, 40 of the 47 expected crosspeaks were resolved and 36 gave RDC data...
July 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28647789/probing-slow-timescale-dynamics-in-proteins-using-methyl-1-h-cest
#7
Tairan Yuwen, Rui Huang, Lewis E Kay
Although (15)N- and (13)C-based chemical exchange saturation transfer (CEST) experiments have assumed an important role in studies of biomolecular conformational exchange, (1)H CEST experiments are only beginning to emerge. We present a methyl-TROSY (1)H CEST experiment that eliminates deleterious (1)H-(1)H NOE dips so that CEST profiles can be analyzed robustly to extract methyl proton chemical shifts of rare protein conformers. The utility of the experiment, along with a version that is optimized for (13)CHD2 labeled proteins, is established through studies of exchanging protein systems...
July 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28616711/integrating-noe-and-rdc-using-sum-of-squares-relaxation-for-protein-structure-determination
#8
Y Khoo, A Singer, D Cowburn
We revisit the problem of protein structure determination from geometrical restraints from NMR, using convex optimization. It is well-known that the NP-hard distance geometry problem of determining atomic positions from pairwise distance restraints can be relaxed into a convex semidefinite program (SDP). However, often the NOE distance restraints are too imprecise and sparse for accurate structure determination. Residual dipolar coupling (RDC) measurements provide additional geometric information on the angles between atom-pair directions and axes of the principal-axis-frame...
July 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28573376/maximal-clique-method-for-the-automated-analysis-of-nmr-tocsy-spectra-of-complex-mixtures
#9
Da-Wei Li, Cheng Wang, Rafael Brüschweiler
Characterization of the chemical components of complex mixtures in solution is important in many areas of biochemistry and chemical biology, including metabolomics. The use of 2D NMR total correlation spectroscopy (TOCSY) experiments has proven very useful for the identification of known metabolites as well as for the characterization of metabolites that are unknown by taking advantage of the good resolution and high sensitivity of this homonuclear experiment. Due to the complexity of the resulting spectra, automation is critical to facilitate and speed-up their analysis and enable high-throughput applications...
July 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28560567/gd-3-chelated-lipid-accelerates-solid-state-nmr-spectroscopy-of-seven-transmembrane-proteins
#10
Chang Liu, Jing Liu, Xiaojun Xu, ShengQi Xiang, Shenlin Wang
Solid-state NMR (SSNMR) is an attractive technique for studying large membrane proteins in membrane-mimetic environments. However, SSNMR experiments often suffer from low efficiency, due to the inherent low sensitivity and the long recycle delays needed to recover the magnetization. Here we demonstrate that the incorporation of a small amount of a Gd(3+)-chelated lipid, Gd(3+)-DMPE-DTPA, into proteoliposomes greatly shortens the spin-lattice relaxation time ((1)H-T 1) of lipid-reconstituted membrane proteins and accelerates the data collection...
July 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28534082/conformational-dynamics-and-alignment-properties-of-loop-lanthanide-binding-tags-lbts-studied-in-interleukin-1%C3%AE
#11
Dominic Barthelmes, Katja Barthelmes, Kai Schnorr, Hendrik R A Jonker, Bianca Bodmer, Karen N Allen, Barbara Imperiali, Harald Schwalbe
Encodable lanthanide binding tags (LBTs) have become an attractive tool in modern structural biology as they can be expressed as fusion proteins of targets of choice. Previously, we have demonstrated the feasibility of inserting encodable LBTs into loop positions of interleukin-1β (Barthelmes et al. in J Am Chem Soc 133:808-819, 2011). Here, we investigate the differences in fast dynamics of selected loop-LBT interleukin-1β constructs by measuring (15)N nuclear spin relaxation experiments. We show that the loop-LBT does not significantly alter the dynamic motions of the host protein in the sub-τc-timescale and that the loop-LBT adopts a rigid conformation with significantly reduced dynamics compared to the terminally attached encodable LBT leading to increased paramagnetic alignment strength...
July 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28643194/erratum-to-pitfalls-in-compressed-sensing-reconstruction-and-how-to-avoid-them
#12
Alexandra Shchukina, Paweł Kasprzak, Rupashree Dass, Michał Nowakowski, Krzysztof Kazimierczuk
No abstract text is available yet for this article.
June 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28620800/non-uniform-sampling-in-biomolecular-nmr
#13
EDITORIAL
Martin Billeter
No abstract text is available yet for this article.
June 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28508110/joint-non-uniform-sampling-of-all-incremented-time-delays-for-quicker-acquisition-in-protein-relaxation-studies
#14
Mateusz Urbańczyk, Michał Nowakowski, Wiktor Koźmiński, Krzysztof Kazimierczuk
NMR relaxometry plays crucial role in studies of protein dynamics. The measurement of longitudinal and transverse relaxation rates of [Formula: see text]N is the main source of information on backbone motions. However, even the most basic approach exploiting a series of [Formula: see text]N HSQC spectra can require several hours of measurement time. Standard non-uniform sampling (NUS), i.e. random under-sampling of indirect time domain, typically cannot reduce this by more than 2-4[Formula: see text] due to relatively low "compressibility" of these spectra...
June 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
#15
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...
June 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28243768/reconstruction-of-non-uniformly-sampled-five-dimensional-nmr-spectra-by-signal-separation-algorithm
#16
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...
June 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28188517/a-non-uniform-sampling-approach-enables-studies-of-dilute-and-unstable-proteins
#17
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...
June 2017: 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
#18
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...
June 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/27837295/pitfalls-in-compressed-sensing-reconstruction-and-how-to-avoid-them
#19
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...
June 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/27650957/improving-resolution-in-multidimensional-nmr-using-random-quadrature-detection-with-compressed-sensing-reconstruction
#20
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)...
June 2017: Journal of Biomolecular NMR
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