Practical considerations over spectral quality in solid state NMR spectroscopy of soluble proteins.

abstract：:A three-dimensional 1H, 13C, 31P triple resonance experiment, HCP-CCH-TOCSY, is presented which provides unambiguous through-bond correlation of all 1H ribose protons on the 5' and 3' sides of the intervening phosphorus along the backbone bonding network in 13C-labeled RNA oligonucleotides. The correlation of the comp...

journal_title：Journal of biomolecular NMR

authors： Marino JP,Schwalbe H,Anklin C,Bermel W,Crothers DM,Griesinger C

更新日期：1995-01-01 00:00:00

abstract：:Sensitivity and resolution together determine the quality of NMR spectra in biological solids. For high-resolution structure determination with solid-state NMR, proton-detection emerged as an attractive strategy in the last few years. Recent progress in probe technology has extended the range of available MAS frequenc...

journal_title：Journal of biomolecular NMR

authors： Xue K,Sarkar R,Tosner Z,Lalli D,Motz C,Koch B,Pintacuda G,Reif B

更新日期：2019-11-01 00:00:00

abstract：:S3EPY is a Python extension to the program Sparky written to facilitate the assessment of coupling constants from in-phase/antiphase and spin-state-selective excitation (S(3)E) experiments. It enables the routine use of small scalar couplings by automating the coupling evaluation procedure. S3EPY provides an integrate...

journal_title：Journal of biomolecular NMR

authors： Novák P,Zídek L,Motácková V,Padrta P,Svenková A,Nuzillard JM,Krásný L,Sklenár V

更新日期：2010-02-01 00:00:00

abstract：:Strong solvent signals lead to a disappearance of weak protein signals close to the solvent resonance frequency and to base plane variations all over the spectrum. AUREMOL-SSA provides an automated approach for solvent artifact removal from multidimensional NMR protein spectra. Its core algorithm is based on singular ...

journal_title：Journal of biomolecular NMR

authors： Malloni WM,De Sanctis S,Tomé AM,Lang EW,Munte CE,Neidig KP,Kalbitzer HR

更新日期：2010-06-01 00:00:00

abstract：:Simultaneous recording of different NMR parameters is an efficient way to reduce the overall experimental time and speed up structural studies of biological macromolecules. This can especially be beneficial in the case of fast NMR-based drug screening applications or for collecting NOE restraints, where prohibitively ...

journal_title：Journal of biomolecular NMR

authors： Würtz P,Aitio O,Hellman M,Permi P

更新日期：2007-10-01 00:00:00

abstract：:We describe a general computational approach to site-specific resonance assignments in multidimensional NMR studies of uniformly (15)N,(13)C-labeled biopolymers, based on a simple Monte Carlo/simulated annealing (MCSA) algorithm contained in the program MCASSIGN2. Input to MCASSIGN2 includes lists of multidimensional ...

journal_title：Journal of biomolecular NMR

authors： Hu KN,Qiang W,Tycko R

更新日期：2011-07-01 00:00:00

abstract：:1H alpha, 13C alpha, and 15N alpha secondary shifts, defined as the difference between the observed value and the random coil value, have been calculated for interleukin-1 receptor antagonist protein and interleukin-1 beta. Averaging of the secondary chemical shifts with those of adjacent residues was used to smooth o...

journal_title：Journal of biomolecular NMR

authors： Stockman BJ,Scahill TA,Strakalaitis NA,Brunner DP,Yem AW,Deibel MR Jr

更新日期：1992-11-01 00:00:00

abstract：:We present a computer algorithm for the automated assignment of polypeptide backbone and 13C beta resonances of a protein of known primary sequence. Input to the algorithm consists of cross peaks from several 3D NMR experiments: HNCA, HN(CA)CO, HN(CA)HA, HNCACB, COCAH, HCA(CO)N, HNCO, HN(CO)CA, HN(COCA)HA, and CBCA(CO...

journal_title：Journal of biomolecular NMR

authors： Lukin JA,Gove AP,Talukdar SN,Ho C

更新日期：1997-02-01 00:00:00

abstract：:The process of resonance assignment represents a time-consuming and potentially error-prone bottleneck in structural studies of proteins by solid-state NMR (ssNMR). Software for the automation of this process is therefore of high interest. Procedures developed through the last decades for solution-state NMR are not di...

journal_title：Journal of biomolecular NMR

authors： Nielsen JT,Kulminskaya N,Bjerring M,Nielsen NC

更新日期：2014-06-01 00:00:00

abstract：:New nuclear magnetic resonance (NMR) methods are described for the measurement of cross-correlation rates of zero- and double-quantum coherences involving two nitrogen nuclei belonging to successive amino acids in proteins and peptides. Rates due to the concerted fluctuations of two NH(N) dipole-dipole interactions an...

journal_title：Journal of biomolecular NMR

authors： Pelupessy P,Ravindranathan S,Bodenhausen G

更新日期：2003-04-01 00:00:00

abstract：:A large number of amino acids other than the canonical amino acids can now be easily incorporated in vivo into proteins at genetically encoded positions. The technology requires an orthogonal tRNA/aminoacyl-tRNA synthetase pair specific for the unnatural amino acid that is added to the media while a TAG amber or frame...

journal_title：Journal of biomolecular NMR

authors： Jones DH,Cellitti SE,Hao X,Zhang Q,Jahnz M,Summerer D,Schultz PG,Uno T,Geierstanger BH

更新日期：2010-01-01 00:00:00

abstract：: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 se...

journal_title：Journal of biomolecular NMR

authors： Urbańczyk M,Nowakowski M,Koźmiński W,Kazimierczuk K

更新日期：2017-06-01 00:00:00

abstract：:We present NMRlib, a suite of jython-based tools designed for Bruker spectrometers (TopSpin versions 3.2-4.0) that allow easy setup, management, and exchange of NMR experiments. A NMR experiment can be set up and executed in a few clicks by navigating through the NMRlib GUI tree structure, without any further paramete...

journal_title：Journal of biomolecular NMR

authors： Favier A,Brutscher B

更新日期：2019-05-01 00:00:00

abstract：:Characterization of the structure and dynamics of nucleic acids by NMR benefits significantly from position specifically labeled nucleotides. Here an E. coli strain deficient in the transketolase gene (tktA) and grown on glucose that is labeled at different carbon sites is shown to facilitate cost-effective and large ...

journal_title：Journal of biomolecular NMR

authors： Thakur CS,Luo Y,Chen B,Eldho NV,Dayie TK

更新日期：2012-02-01 00:00:00

abstract：:Segmental isotopic labeling can facilitate NMR studies of large proteins, multi-domain proteins, and proteins with repetitive sequences by alleviating NMR signal overlaps. Segmental isotopic labeling also allows us to investigate an individual domain in the context of a full-length protein by NMR. Several established ...

journal_title：Journal of biomolecular NMR

authors： Mikula KM,Krumwiede L,Plückthun A,Iwaï H

更新日期：2018-08-01 00:00:00

abstract：:A pulse sequence is described for recording single-quantum (13)C-methyl relaxation dispersion profiles of (13)C-selectively labeled methyl groups in proteins that offers significant improvements in sensitivity relative to existing approaches where initial magnetization derives from (13)C polarization. Sensitivity gain...

journal_title：Journal of biomolecular NMR

authors： Lundström P,Vallurupalli P,Religa TL,Dahlquist FW,Kay LE

更新日期：2007-05-01 00:00:00

abstract：:With the completion of genome sequencing projects, there are a large number of proteins for which we have little or no functional information. Since protein function is closely related to three-dimensional conformation, structural proteomics is one avenue where the role of proteins with unknown function can be investi...

journal_title：Journal of biomolecular NMR

authors： Julien O,Gignac I,Hutton A,Yee A,Arrowsmith CH,Gagné SM

更新日期：2006-06-01 00:00:00

abstract：:Model-membrane systems composed of liquid-crystalline bicellar phases can be uniaxially oriented with respect to a magnetic field, thereby facilitating structural and dynamics studies of membrane-associated proteins. Here we quantitatively characterize a method that allows the manipulation of the direction of this uni...

journal_title：Journal of biomolecular NMR

authors： Zandomeneghi G,Tomaselli M,Williamson PT,Meier BH

更新日期：2003-02-01 00:00:00

abstract：:Understanding of the molecular mechanisms of protein function requires detailed insight into the conformational landscape accessible to the protein. Conformational changes can be crucial for biological processes, such as ligand binding, protein folding, and catalysis. NMR spectroscopy is exquisitely sensitive to such ...

journal_title：Journal of biomolecular NMR

authors： Chatterjee SD,Ubbink M,van Ingen H

更新日期：2018-06-01 00:00:00

abstract：:Four-dimensional NMR spectroscopy can be speeded up by a large factor by a projection-reconstruction technique related to that used in X-ray tomography. The limited amount of information recorded in a few suitably-tilted projection planes suffices to recreate the entire four-dimensional spectrum. The method is demonst...

journal_title：Journal of biomolecular NMR

authors： Kupce E,Freeman R

更新日期：2004-04-01 00:00:00

abstract：:Due to practical limitations in available 15N rf field strength, imperfections in 15N 180 degrees pulses arising from off-resonance effects can result in significant sensitivity loss, even if the chemical shift offset is relatively small. Indeed, in multi-dimensional NMR experiments optimized for protein backbone amid...

journal_title：Journal of biomolecular NMR

authors： Iwahara J,Clore GM

更新日期：2006-12-01 00:00:00

abstract：:Fast multidimensional NMR with a time resolution of a few seconds provides a new tool for high throughput screening and site-resolved real-time studies of kinetic molecular processes by NMR. Recently we have demonstrated the feasibility to record protein 1H-15N correlation spectra in a few seconds of acquisition time ...

journal_title：Journal of biomolecular NMR

authors： Schanda P,Kupce E,Brutscher B

更新日期：2005-12-01 00:00:00

abstract：:To evaluate sequential nearest-neighbor effects on quantum-chemical calculations of (13)C(alpha) chemical shifts, we selected the structure of the nucleic acid binding (NAB) protein from the SARS coronavirus determined by NMR in solution (PDB id 2K87). NAB is a 116-residue alpha/beta protein, which contains 9 prolines...

journal_title：Journal of biomolecular NMR

authors： Vila JA,Serrano P,Wüthrich K,Scheraga HA

更新日期：2010-09-01 00:00:00

abstract：: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 ...

journal_title：Journal of biomolecular NMR

authors： Schörghuber J,Geist L,Bisaccia M,Weber F,Konrat R,Lichtenecker RJ

更新日期：2017-09-01 00:00:00

abstract：:We describe a novel method for the robust, rapid, and reliable determination of J couplings in multi-dimensional NMR coupling data, including small couplings from larger proteins. The method, "High-resolution Iterative Frequency Identification of Couplings" (HIFI-C) is an extension of the adaptive and intelligent data...

journal_title：Journal of biomolecular NMR

authors： Cornilescu G,Bahrami A,Tonelli M,Markley JL,Eghbalnia HR

更新日期：2007-08-01 00:00:00

abstract：:Pulsed field gradients were incorporated into the HCACO experiment for acquiring spectra on isotopically enriched protein samples dissolved in H2O. Excellent water suppression and spectral quality were achieved using the modified pulse sequence (gd-HCACO), as demonstrated for a 13C-/15N-labeled sample of the SH2 domai...

journal_title：Journal of biomolecular NMR

authors： Zhang W,Gmeiner WH

更新日期：1996-05-01 00:00:00

abstract：:In our previous work, we proposed a new way to represent protein native states, using ensembles of a small number of conformations with relative Populations, or ESP in short. Using Ubiquitin as an example, we showed that using a small number of conformations could greatly reduce the potential of overfitting and assign...

journal_title：Journal of biomolecular NMR

authors： Vammi V,Song G

更新日期：2015-12-01 00:00:00

abstract：:2D 15N-1H correlation spectra are ideal for measuring backbone amide populations to determine amide exchange protection factors in studies of protein folding or other structural features. Most protein NMR spectroscopists use HSQC, which has been shown to be generally superior to HMQC in both resolution and sensitivity...

journal_title：Journal of biomolecular NMR

authors： Davis JH

更新日期：1995-06-01 00:00:00

abstract：:It has been demonstrated that protein folds can be determined using appropriate computational protocols with NMR chemical shifts as the sole source of experimental restraints. While such approaches are very promising they still suffer from low convergence resulting in long computation times to achieve accurate results...

journal_title：Journal of biomolecular NMR

authors： Rasia RM,Lescop E,Palatnik JF,Boisbouvier J,Brutscher B

更新日期：2011-11-01 00:00:00

abstract：:The (1)H, (13)C and (15)N NMR resonances of the backbone of serine protease PB92 have been assigned. This 269-residue protein is one of the largest monomeric proteins assigned so far. The amount and quality of information available suggest that even larger proteins could be assigned with present methods. Measured chem...

journal_title：Journal of biomolecular NMR

authors： Fogh RH,Schipper D,Boelens R,Kaptein R

更新日期：1994-01-01 00:00:00