journal
MENU ▼
Read by QxMD icon Read
search

Journal of Biomolecular NMR

journal
https://www.readbyqxmd.com/read/28913741/pressure-dependence-of-side-chain-13-c-chemical-shifts-in-model-peptides-ac-gly-gly-xxx-ala-nh2
#1
Markus Beck Erlach, Joerg Koehler, Edson Crusca, Claudia E Munte, Masatsune Kainosho, Werner Kremer, Hans Robert Kalbitzer
For evaluating the pressure responses of folded as well as intrinsically unfolded proteins detectable by NMR spectroscopy the availability of data from well-defined model systems is indispensable. In this work we report the pressure dependence of (13)C chemical shifts of the side chain atoms in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx, one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of a number of nuclei have a nonlinear dependence on pressure in the range from 0...
September 14, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28900789/gradient-reconstitution-of-membrane-proteins-for-solid-state-nmr-studies
#2
Denis Lacabanne, Alons Lends, Clément Danis, Britta Kunert, Marie-Laure Fogeron, Vlastimil Jirasko, Claire Chuilon, Lauriane Lecoq, Cédric Orelle, Vincent Chaptal, Pierre Falson, Jean-Michel Jault, Beat H Meier, Anja Böckmann
We here adapted the GRecon method used in electron microscopy studies for membrane protein reconstitution to the needs of solid-state NMR sample preparation. We followed in detail the reconstitution of the ABC transporter BmrA by dialysis as a reference, and established optimal reconstitution conditions using the combined sucrose/cyclodextrin/lipid gradient characterizing GRecon. We established conditions under which quantitative reconstitution of active protein at low lipid-to-protein ratios can be obtained, and also how to upscale these conditions in order to produce adequate amounts for NMR...
September 12, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28887770/optimization-of-1-h-decoupling-eliminates-sideband-artifacts-in-3d-trosy-based-triple-resonance-experiments
#3
Youlin Xia, Paolo Rossi, Marco Tonelli, Chengdong Huang, Charalampos G Kalodimos, Gianluigi Veglia
TROSY-based triple resonance experiments are essential for protein backbone assignment of large biomolecular systems by solution NMR spectroscopy. In a survey of the current Bruker pulse sequence library for TROSY-based experiments we found that several sequences were plagued by artifacts that affect spectral quality and hamper data analysis. Specifically, these experiments produce sidebands in the (13)C(t 1) dimension with inverted phase corresponding to (1)HN resonance frequencies, with approximately 5% intensity of the parent (13)C crosspeaks...
September 8, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28879611/evaluation-of-15-n-detected-h-n-correlation-experiments-on-increasingly-large-rnas
#4
Robbin Schnieders, Christian Richter, Sven Warhaut, Vanessa de Jesus, Sara Keyhani, Elke Duchardt-Ferner, Heiko Keller, Jens Wöhnert, Lars T Kuhn, Alexander L Breeze, Wolfgang Bermel, Harald Schwalbe, Boris Fürtig
Recently, (15)N-detected multidimensional NMR experiments have been introduced for the investigation of proteins. Utilization of the slow transverse relaxation of nitrogen nuclei in a (15)N-TROSY experiment allowed recording of high quality spectra for high molecular weight proteins, even in the absence of deuteration. Here, we demonstrate the applicability of three (15)N-detected H-N correlation experiments (TROSY, BEST-TROSY and HSQC) to RNA. With the newly established (15)N-detected BEST-TROSY experiment, which proves to be the most sensitive (15)N-detected H-N correlation experiment, spectra for five RNA molecules ranging in size from 5 to 100 kDa were recorded...
September 6, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28864905/measurement-of-protein-backbone-13-co-and-15-n-relaxation-dispersion-at-high-resolution
#5
Maxim Mayzel, Alexandra Ahlner, Patrik Lundström, Vladislav Y Orekhov
Peak overlap in crowded regions of two-dimensional spectra prevents characterization of dynamics for many sites of interest in globular and intrinsically disordered proteins. We present new three-dimensional pulse sequences for measurement of Carr-Purcell-Meiboom-Gill relaxation dispersions at backbone nitrogen and carbonyl positions. To alleviate increase in the measurement time associated with the additional spectral dimension, we use non-uniform sampling in combination with two distinct methods of spectrum reconstruction: compressed sensing and co-processing with multi-dimensional decomposition...
September 1, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28861670/anthranilic-acid-the-new-player-in-the-ensemble-of-aromatic-residue-labeling-precursor-compounds
#6
Julia Schörghuber, Leonhard Geist, Marilena Bisaccia, Frederik Weber, Robert Konrat, Roman J Lichtenecker
The application of metabolic precursors for selective stable isotope labeling of aromatic residues in cell-based protein overexpression has already resulted in numerous NMR probes to study the structural and dynamic characteristics of proteins. With anthranilic acid, we present the structurally simplest precursor for exclusive tryptophan side chain labeling. A synthetic route to (13)C, (2)H isotopologues allows the installation of isolated (13)C-(1)H spin systems in the indole ring of tryptophan, representing a versatile tool to investigate side chain motion using relaxation-based experiments without the loss of magnetization due to strong (1)JCC and weaker (2)JCH scalar couplings, as well as dipolar interactions with remote hydrogens...
August 31, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28856561/site-selective-13-c-labeling-of-histidine-and-tryptophan-using-ribose
#7
Ulrich Weininger
Experimental studies on protein dynamics at atomic resolution by NMR-spectroscopy in solution require isolated (1)H-X spin pairs. This is the default scenario in standard (1)H-(15)N backbone experiments. Side chain dynamic experiments, which allow to study specific local processes like proton-transfer, or tautomerization, require isolated (1)H-(13)C sites which must be produced by site-selective (13)C labeling. In the most general way this is achieved by using site-selectively (13)C-enriched glucose as the carbon source in bacterial expression systems...
August 30, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28815397/detecting-and-accounting-for-multiple-sources-of-positional-variance-in-peak-list-registration-analysis-and-spin-system-grouping
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
EDITORIAL
Martin Billeter
No abstract text is available yet for this article.
June 2017: Journal of Biomolecular NMR
journal
journal
30799
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"