Database proton NMR chemical shifts for RNA signal assignment and validation.


:The Biological Magnetic Resonance Data Bank contains NMR chemical shift depositions for 132 RNAs and RNA-containing complexes. We have analyzed the (1)H NMR chemical shifts reported for non-exchangeable protons of residues that reside within A-form helical regions of these RNAs. The analysis focused on the central base pair within a stretch of three adjacent base pairs (BP triplets), and included both Watson-Crick (WC; G:C, A:U) and G:U wobble pairs. Chemical shift values were included for all 4(3) possible WC-BP triplets, as well as 137 additional triplets that contain one or more G:U wobbles. Sequence-dependent chemical shift correlations were identified, including correlations involving terminating base pairs within the triplets and canonical and non-canonical structures adjacent to the BP triplets (i.e. bulges, loops, WC and non-WC BPs), despite the fact that the NMR data were obtained under different conditions of pH, buffer, ionic strength, and temperature. A computer program (RNAShifts) was developed that enables convenient comparison of RNA (1)H NMR assignments with database predictions, which should facilitate future signal assignment/validation efforts and enable rapid identification of non-canonical RNA structures and RNA-ligand/protein interaction sites.


J Biomol NMR


Barton S,Heng X,Johnson BA,Summers MF




Has Abstract


2013-01-01 00:00:00












  • Facile measurement of polypeptide JHNH alpha coupling constants from HMQC-J spectra.

    abstract::A method, based on linewidth measurements, is described which permits the rapid and facile determination of JHNH alpha coupling constants from 15N labeled proteins. Using appropriately processed HMQC-J data, we have found that a simple linear relationship exists between the half-height linewidth (delta nu1/2) of 15N-1...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Wishart DS,Wang Y

    更新日期:1998-04-01 00:00:00

  • Insight into human insulin aggregation revisited using NMR derived translational diffusion parameters.

    abstract::The NMR derived translational diffusion coefficients were performed on unlabeled and uniformly labeled 13C,15N human insulin in water, both in neat, with zinc ions only, and in pharmaceutical formulation, containing only m-cresol as phenolic ligand, glycerol and zinc ions. The results show the dominant role of the pH ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Sitkowski J,Bocian W,Bednarek E,Urbańczyk M,Koźmiński W,Borowicz P,Płucienniczak G,Łukasiewicz N,Sokołowska I,Kozerski L

    更新日期:2018-06-01 00:00:00

  • Resolution and sensitivity of high field nuclear magnetic resonance spectroscopy.

    abstract::The arrival of very high field magnets and cryogenic circuitries, and the development of relaxation-optimized pulse sequences have added powerful tools for increasing sensitivity and resolution in NMR studies of biomacromolecules. The potential of these advances is not fully realized in practice, however, since curren...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章,评审


    authors: Rovnyak D,Hoch JC,Stern AS,Wagner G

    更新日期:2004-09-01 00:00:00

  • Sensitivity enhancement in NMR of macromolecules by application of optimal control theory.

    abstract::NMR of macromolecules is limited by large transverse relaxation rates. In practice, this results in low efficiency of coherence transfer steps in multidimensional NMR experiments, leading to poor sensitivity and long acquisition times. The efficiency of coherence transfer can be maximized by design of relaxation optim...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Frueh DP,Ito T,Li JS,Wagner G,Glaser SJ,Khaneja N

    更新日期:2005-05-01 00:00:00

  • Improved photo-CIDNP methods for studying protein structure and folding.

    abstract::Two new techniques offering considerable improvements in the quality of 1H photo-CIDNP spectra of proteins are demonstrated. Both focus on the problem of progressive photo-degradation of the flavin dye used to generate polarization in exposed tryptophan, tyrosine and histidine side-chains. One approach uses rapid addi...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Maeda K,Lyon CE,Lopez JJ,Cemazar M,Dobson CM,Hore PJ

    更新日期:2000-03-01 00:00:00

  • Off-resonance effects in 15N T2 CPMG measurements.

    abstract::The systematic difference between T2 values obtained from CPMG and T1p experiments was observed for backbone 15N nuclei of bacterial ribonuclease barnase. Theoretical consideration suggests that the observed difference is caused by off-resonance effects of 180 degree pulses of the CPMG pulse train. Namely, at off-reso...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Korzhnev DM,Tischenko EV,Arseniev AS

    更新日期:2000-07-01 00:00:00

  • Determination of molecular alignment tensors without backbone resonance assignment: Aid to rapid analysis of protein-protein interactions.

    abstract::Based on high-resolution structures of the free molecules accurate determination of structures of protein complexes by NMR spectroscopy is possible using residual dipolar couplings. In order, however, to be able to apply these methods, protein backbone resonances have to be assigned first. This NMR assignment process ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Zweckstetter M

    更新日期:2003-09-01 00:00:00

  • Perspectives for sensitivity enhancement in proton-detected solid-state NMR of highly deuterated proteins by preserving water magnetization.

    abstract::In this work, we show how the water flip-back approach that is widely employed in solution-state NMR can be adapted to proton-detected MAS solid-state NMR of highly deuterated proteins. The scheme allows to enhance the sensitivity of the experiment by decreasing the recovery time of the proton longitudinal magnetizati...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Chevelkov V,Xiang S,Giller K,Becker S,Lange A,Reif B

    更新日期:2015-02-01 00:00:00

  • Deleterious effects of carbon-carbon dipolar coupling on RNA NMR dynamics.

    abstract::Many regulatory RNAs undergo dynamic exchanges that are crucial for their biological functions and NMR spectroscopy is a versatile tool for monitoring dynamic motions of biomolecules. Meaningful information on biomolecular dynamics requires an accurate measurement of relaxation parameters such as longitudinal (R1) rat...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Nam H,Becette O,LeBlanc RM,Oh D,Case DA,Dayie TK

    更新日期:2020-07-01 00:00:00

  • Biosynthetically directed fractional 13C labeling facilitates identification of Phe and Tyr aromatic signals in proteins.

    abstract::Analysis of 2D [(13)C,(1)H]-HSQC spectra of biosynthetic fractionally (13)C labeled proteins is a reliable, straightforward means to obtain stereospecific assignments of Val and Leu methyl sites in proteins. Herein we show that the same fractionally labeled protein sample facilitates observation and identification of ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Jacob J,Louis JM,Nesheiwat I,Torchia DA

    更新日期:2002-11-01 00:00:00

  • Heteronuclear relayed E.COSY applied to the determination of accurate 3J(HN,C') and 3J(H beta,C') coupling constants in desulfovibrio vulgaris flavodoxin.

    abstract::A simple constant-time 3D heteronuclear NMR pulse sequence has been developed to quantitatively determine the heteronuclear three-bond couplings 3J(HN,C') and 3J(H beta,C') in uniformly 13C-enriched proteins. The protocols for measuring accurate coupling constants are based on 1H,13C-heteronuclear relayed E.COSY [Schm...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Schmidt JM,Löhr F,Rüterjans H

    更新日期:1996-03-01 00:00:00

  • PROSHIFT: protein chemical shift prediction using artificial neural networks.

    abstract::The importance of protein chemical shift values for the determination of three-dimensional protein structure has increased in recent years because of the large databases of protein structures with assigned chemical shift data. These databases have allowed the investigation of the quantitative relationship between chem...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Meiler J

    更新日期:2003-05-01 00:00:00

  • Quantitative measurement of exchange dynamics in proteins via (13)C relaxation dispersion of (13)CHD2-labeled samples.

    abstract::Methyl groups have emerged as powerful probes of protein dynamics with timescales from picoseconds to seconds. Typically, studies involving high molecular weight complexes exploit (13)CH3- or (13)CHD2-labeling in otherwise highly deuterated proteins. The (13)CHD2 label offers the unique advantage of providing (13)C, (...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Rennella E,Schuetz AK,Kay LE

    更新日期:2016-06-01 00:00:00

  • Improved NMR spectra of a protein-DNA complex through rational mutagenesis and the application of a sensitivity optimized isotope-filtered NOESY experiment.

    abstract::The NMR spectra of the complex between the DNA-binding domain of the Dead ringer protein (DRI-DBD, Gly262-Gly398) and its DNA binding site (DRI-DBD:DNA, 26 kDa) have been optimized by biochemical and spectroscopic means. First, we demonstrate the utility of a modified 2D [F1,F2] 13C-filtered NOESY experiment that empl...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Iwahara J,Wojciak JM,Clubb RT

    更新日期:2001-03-01 00:00:00

  • Isotope labeling of mammalian GPCRs in HEK293 cells and characterization of the C-terminus of bovine rhodopsin by high resolution liquid NMR spectroscopy.

    abstract::High amino acid coverage labeling of the mammalian G protein coupled receptors (GPCR) rhodopsin was established with 15N and 15N/13C isotopes. Rhodopsin was expressed at preparative scale in HEK293S cells and studied in full-length by NMR spectroscopy in detergent micelle solution. This resulted in the assignment and ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Werner K,Richter C,Klein-Seetharaman J,Schwalbe H

    更新日期:2008-01-01 00:00:00

  • Definition of a new information-based per-residue quality parameter.

    abstract::For biomolecular NMR structures typically only a poor correspondence is observed between statistics derived from the experimental input data and structural quality indicators obtained from the structure ensembles. Here, we investigate the relationship between the amount of available NMR data and structure quality. By ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Nabuurs SB,Krieger E,Spronk CA,Nederveen AJ,Vriend G,Vuister GW

    更新日期:2005-10-01 00:00:00

  • Selective excitation of intense solvent signals in the presence of radiation damping.

    abstract::Selective water excitation schemes are provided which rely on the radiation damping effect in probeheads characterized by high quality factors. The schemes are implemented in homonuclear NOE and ROE experiments, designed for the selective observation of water-protein cross peaks and their assignment using standard pro...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Otting G,Liepinsh E

    更新日期:1995-06-01 00:00:00

  • Sparse (13)C labelling for solid-state NMR studies of P. pastoris expressed eukaryotic seven-transmembrane proteins.

    abstract::We demonstrate a novel sparse (13)C labelling approach for methylotrophic yeast P. pastoris expression system, towards solid-state NMR studies of eukaryotic membrane proteins. The labelling scheme was achieved by co-utilizing natural abundance methanol and specifically (13)C labelled glycerol as carbon sources in the ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Liu J,Liu C,Fan Y,Munro RA,Ladizhansky V,Brown LS,Wang S

    更新日期:2016-05-01 00:00:00

  • Quantifying millisecond time-scale exchange in proteins by CPMG relaxation dispersion NMR spectroscopy of side-chain carbonyl groups.

    abstract::A new pulse sequence is presented for the measurement of relaxation dispersion profiles quantifying millisecond time-scale exchange dynamics of side-chain carbonyl groups in uniformly (13)C labeled proteins. The methodology has been tested using the 87-residue colicin E7 immunity protein, Im7, which is known to fold v...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Hansen AL,Kay LE

    更新日期:2011-08-01 00:00:00

  • An efficient strategy for assignment of cross-peaks in 3D heteronuclear NOESY experiments.

    abstract::The question is addressed of how maximal structural NOE data on double labelled proteins can be acquired with a minimal set of NOESY experiments. Two 3D-NOESY spectra are reported which, in concert with other commonly used spectra, provide a convenient strategy for NOE assignment. The 3D CNH-NOESY and 3D NCH-NOESY pro...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Diercks T,Coles M,Kessler H

    更新日期:1999-10-01 00:00:00

  • Solution structure of the soluble domain of the NfeD protein YuaF from Bacillus subtilis.

    abstract::The transmembrane protein YuaF from B. subtilis is a member of the NfeD-like clan with a potential role in maintaining membrane integrity during conditions of cellular stress. nfeD-genes are primarily found in highly conserved operon structures together with the gene of another membrane protein belonging to the SPFH s...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Walker CA,Hinderhofer M,Witte DJ,Boos W,Möller HM

    更新日期:2008-09-01 00:00:00

  • Measurement of 15N-13C J couplings in staphylococcal nuclease.

    abstract::15N-C alpha and 15N-C' J couplings were measured for the backbone of staphylococcal nuclease, uniformly enriched with 15N and 13C. It is found that the 1JC'N coupling is similar for beta-sheet, J = 14.8 +/- 0.5 and for alpha-helix, J = 14.8 +/- 0.4 but tends to be larger for the unstructured N- and C-terminal ends of ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Delaglio F,Torchia DA,Bax A

    更新日期:1991-11-01 00:00:00

  • Efficient DNP NMR of membrane proteins: sample preparation protocols, sensitivity, and radical location.

    abstract::Although dynamic nuclear polarization (DNP) has dramatically enhanced solid-state NMR spectral sensitivities of many synthetic materials and some biological macromolecules, recent studies of membrane-protein DNP using exogenously doped paramagnetic radicals as polarizing agents have reported varied and sometimes surpr...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Liao SY,Lee M,Wang T,Sergeyev IV,Hong M

    更新日期:2016-03-01 00:00:00

  • Automated probabilistic method for assigning backbone resonances of (13C,15N)-labeled proteins.

    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

    pub_type: 杂志文章


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

    更新日期:1997-02-01 00:00:00

  • Complete assignment of 1H, 13C and 15N chemical shifts for bovine beta-lactoglobulin: secondary structure and topology of the native state is retained in a partially unfolded form.

    abstract::Although beta-lactoglobulin (beta-LG) has been studied extensively for more than 50 years, its physical properties in solution are not yet understood fully in terms of its three-dimensional (3D) structure. For example, despite a recent high-resolution crystal structure, it is still not clear why the two common variant...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Uhrínová S,Uhrín D,Denton H,Smith M,Sawyer L,Barlow PN

    更新日期:1998-07-01 00:00:00

  • Maximum entropy approach to the determination of solution conformation of flexible polypeptides by global conformational analysis and NMR spectroscopy--application to DNS1-c-[D-A2,bu2,Trp4,Leu5]enkephalin and DNS1-c-[D-A2bu2,Trp4,D-Leu5]enkephalin.

    abstract::A method is proposed to determine the conformational equilibrium of flexible polypeptides in solution, using the data provided by NMR spectroscopy and theoretical conformational calculations. The algorithm consists of the following three steps: (i) search of the conformational space in order to find conformations with...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Groth M,Malicka J,Czaplewski C,Ołdziej S,Lankiewicz L,Wiczk W,Liwo A

    更新日期:1999-12-01 00:00:00

  • Cross-correlated spin relaxation effects in methyl 1H CPMG-based relaxation dispersion experiments: complications and a simple solution.

    abstract::Artifacts associated with the measurement of methyl (1)H single quantum CPMG-based relaxation dispersion profiles are described. These artifacts arise due to the combination of cross-correlated spin relaxation effects involving intra-methyl (1)H-(1)H dipolar interactions and imperfections in (1)H refocusing pulses tha...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Korzhnev DM,Mittermaier AK,Kay LE

    更新日期:2005-04-01 00:00:00

  • Amino acid recognition for automatic resonance assignment of intrinsically disordered proteins.

    abstract::Resonance assignment is a prerequisite for almost any NMR-based study of proteins. It can be very challenging in some cases, however, due to the nature of the protein under investigation. This is the case with intrinsically disordered proteins, for example, whose NMR spectra suffer from low chemical shifts dispersion ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Piai A,Gonnelli L,Felli IC,Pierattelli R,Kazimierczuk K,Grudziąż K,Koźmiński W,Zawadzka-Kazimierczuk A

    更新日期:2016-03-01 00:00:00

  • Determination of a complete set of coupling constants in 13C-labeled oligonucleotides.

    abstract::Three experiments are introduced to determine a complete set of coupling constants in RNA oligomers. In the HCCH-E.COSY experiment, the vicinal proton-proton coupling constants can be measured with high accuracy. In the P-FIDS-CT-HSQC experiment, vicinal proton-phosphorus and carbon-phosphorus couplings are measured t...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Schwalbe H,Marino JP,King GC,Wechselberger R,Bermel W,Griesinger C

    更新日期:1994-09-01 00:00:00

  • Redor in IS1S2 systems.

    abstract::An approach to the determination of the 2-(13)C' chemical shift (CS) tensor orientation in pyrimidine bases via heteronuclear MAS NMR spectroscopy is presented. Considering a dipolar coupled spin 1/2 network of the type S1-I-S2 consisting of directly bonded heteronuclear spins, we have carried out numerical simulation...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Leppert J,Heise B,Ramachandran R

    更新日期:2000-10-01 00:00:00