Resolution-optimized NMR measurement of (1)D(CH), (1)D(CC) and (2)D(CH) residual dipolar couplings in nucleic acid bases.


:New methods are described for accurate measurement of multiple residual dipolar couplings in nucleic acid bases. The methods use TROSY-type pulse sequences for optimizing resolution and sensitivity, and rely on the E.COSY principle to measure the relatively small two-bond (2)D(CH) couplings at high precision. Measurements are demonstrated for a 24-nt stem-loop RNA sequence, uniformly enriched in (13)C, and aligned in Pf1. The recently described pseudo-3D method is used to provide homonuclear (1)H-(1)H decoupling, which minimizes cross-correlation effects and optimizes resolution. Up to seven (1)H-(13)C and (13)C-(13)C couplings are measured for pyrimidines (U and C), including (1)D(C5H5), (1)D(C6H6), (2)D(C5H6), (2)D(C6H5), (1)D(C5C4), (1)D(C5C6), and (2)D(C4H5). For adenine, four base couplings ((1)D(C2H2), (1)D(C8H8), (1)D(C4C5), and (1)D(C5C6)) are readily measured whereas for guanine only three couplings are accessible at high relative accuracy ((1)D(C8H8), (1)D(C4C5), and (1)D(C5C6)). Only three dipolar couplings are linearly independent in planar structures such as nucleic acid bases, permitting cross validation of the data and evaluation of their accuracies. For the vast majority of dipolar couplings, the error is found to be less than +/-3% of their possible range, indicating that the measurement accuracy is not limiting when using these couplings as restraints in structure calculations. Reported isotropic values of the one- and two-bond J couplings cluster very tightly for each type of nucleotide.


J Biomol NMR


Boisbouvier J,Bryce DL,O'neil-Cabello E,Nikonowicz EP,Bax A




Has Abstract


2004-11-01 00:00:00












  • Specific binding of a naturally occurring amyloidogenic fragment of Streptococcus mutans adhesin P1 to intact P1 on the cell surface characterized by solid state NMR spectroscopy.

    abstract::The P1 adhesin (aka Antigen I/II or PAc) of the cariogenic bacterium Streptococcus mutans is a cell surface-localized protein involved in sucrose-independent adhesion and colonization of the tooth surface. The immunoreactive and adhesive properties of S. mutans suggest an unusual functional quaternary ultrastructure c...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Tang W,Bhatt A,Smith AN,Crowley PJ,Brady LJ,Long JR

    更新日期:2016-02-01 00:00:00

  • New methods for fast multidimensional NMR.

    abstract::Considerable excitement has been aroused by recent new methods for speeding up multidimensional NMR experiments by radically modifying the normal time-domain sampling protocols. These new schemes include the filter diagonalization method, GFT-NMR, the single-scan two-dimensional technique, Hadamard spectroscopy, and a...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Freeman R,Kupce E

    更新日期:2003-10-01 00:00:00

  • Structure refinement of flexible proteins using dipolar couplings: application to the protein p8MTCP1.

    abstract::The present study deals with the relevance of using mobility-averaged dipolar couplings for the structure refinement of flexible proteins. The 68-residue protein p8MTCP1 has been chosen as model for this study. Its solution state consists mainly of three alpha-helices. The two N-terminal helices are strapped in a well...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Déméné H,Ducat T,Barthe P,Delsuc MA,Roumestand C

    更新日期:2002-01-01 00:00:00

  • Complexity of aromatic ring-flip motions in proteins: Y97 ring dynamics in cytochrome c observed by cross-relaxation suppressed exchange NMR spectroscopy.

    abstract::Dynamics of large-amplitude conformational motions in proteins are complex and less understood, although these processes are intimately associated with structure, folding, stability, and function of proteins. Here, we use a large set of spectra obtained by cross-relaxation suppressed exchange NMR spectroscopy (EXSY) t...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Rao DK,Bhuyan AK

    更新日期:2007-11-01 00:00:00

  • Site-specific labeling of proteins with NMR-active unnatural amino acids.

    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

    pub_type: 杂志文章,评审


    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

  • Selective 1H- 13C NMR spectroscopy of methyl groups in residually protonated samples of large proteins.

    abstract::Methyl (13)CHD(2) isotopomers of all methyl-containing amino-acids can be observed in residually protonated samples of large proteins obtained from [U-(13)C,(1)H]-glucose/D(2)O-based bacterial media, with sensitivity sufficient for a number of NMR applications. Selective detection of some subsets of methyl groups (Ala...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Guo C,Tugarinov V

    更新日期:2010-02-01 00:00:00

  • GFT projection NMR based resonance assignment of membrane proteins: application to subunit C of E. coli F(1)F (0) ATP synthase in LPPG micelles.

    abstract::G-matrix FT projection NMR spectroscopy was employed for resonance assignment of the 79-residue subunit c of the Escherichia coli F(1)F(0) ATP synthase embedded in micelles formed by lyso palmitoyl phosphatidyl glycerol (LPPG). Five GFT NMR experiments, that is, (3,2)D HNNCO, L-(4,3)D HNNC (alphabeta) C (alpha), L-(4,...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Zhang Q,Atreya HS,Kamen DE,Girvin ME,Szyperski T

    更新日期:2008-03-01 00:00:00

  • Rapid measurement of long-range distances in proteins by multidimensional 13C-19F REDOR NMR under fast magic-angle spinning.

    abstract::The ability to simultaneously measure many long-range distances is critical to efficient and accurate determination of protein structures by solid-state NMR (SSNMR). So far, the most common distance constraints for proteins are 13C-15N distances, which are usually measured using the rotational-echo double-resonance (R...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Shcherbakov AA,Hong M

    更新日期:2018-05-01 00:00:00

  • Solution conformations of proline rings in proteins studied by NMR spectroscopy.

    abstract::Three different conformations of proline rings in a protein in solution, Up, Down and Twist, have been distinguished, and stereospecific assignments of the pyrrolidine beta-, gamma- and delta-hydrogens have been made on the basis of 1H-1H vicinal coupling constant patterns and intraresidue NOEs. For all three conforma...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Cai M,Huang Y,Liu J,Krishnamoorthi R

    更新日期:1995-09-01 00:00:00

  • NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

    abstract::The NMRPipe system is a UNIX software environment of processing, graphics, and analysis tools designed to meet current routine and research-oriented multidimensional processing requirements, and to anticipate and accommodate future demands and developments. The system is based on UNIX pipes, which allow programs runni...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Delaglio F,Grzesiek S,Vuister GW,Zhu G,Pfeifer J,Bax A

    更新日期:1995-11-01 00:00:00

  • Assignment of NMR spectra of proteins using triple-resonance two-dimensional experiments.

    abstract::Two-dimensional versions of HNCA and HNCO experiments are described, which provide essentially the same information as the 3D sequence. A multiple-quantum coherence involving either 15N and 13C alpha or 15N and 13CO is created. One of the two frequencies is given by the middle point between the two cross peaks (zero- ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Simorre JP,Brutscher B,Caffrey MS,Marion D

    更新日期:1994-05-01 00:00:00

  • Automated solvent artifact removal and base plane correction of multidimensional NMR protein spectra by AUREMOL-SSA.

    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

    pub_type: 杂志文章


    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

  • Secondary H/D isotope effect on hydrogen-bonded hydroxyl groups as a tool for recognizing distance constraints in conformational analysis of oligosaccharides.

    abstract::An 'isotopomer-selected NOE' (ISNOE) method for the unequivocal identification of mutually hydrogen-bond-linked hydroxyl groups is described. It relies on the fact that the OH group's signal patterns obtained for a partially deuterated sample originate from both isotopomers of the 'partner' hydroxyl, whereas a NOE for...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Dabrowski J,Grosskurth H,Baust C,Nifant'ev NE

    更新日期:1998-07-01 00:00:00

  • Conformational analysis of alpha-D-Fuc-(1-->4)-beta-D-GlcNAc-OMe. One-dimensional transient NOE experiments and Metropolis Monte Carlo simulations.

    abstract::One-dimensional transient NOE build-up curves were measured for the synthetic disaccharide alpha-D-Fuc-(1-->4)-beta-D-GlcNAc 1 utilizing Gaussian shaped pulses. Simulated build-up curves from Metropolis Monte Carlo simulations were compared to the experimental data. Disaccharide 1 is structurally related to methyl bet...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Weimar T,Meyer B,Peters T

    更新日期:1993-07-01 00:00:00

  • Structure and conformation in solution of the parallel-stranded hybrid alpha-d(CGCAATTCGC).beta-d(GCGTTAAGCG) by high-resolution 2D NMR.

    abstract::The unnatural duplex oligonucleotide alpha-d(CGCAATTCGC).beta-d(GCGTTAAGCG) was analyzed by high-resolution NMR methods. All of the exchangeable imino and nonexchangeable protons of the duplex were assigned. Detection of all 10 of the exchangeable imino protons confirms that a parallel, unsymmetrical duplex is formed....

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Gmeiner WH,Rayner B,Morvan F,Imbach JL,Lown JW

    更新日期:1992-05-01 00:00:00

  • TSAR: a program for automatic resonance assignment using 2D cross-sections of high dimensionality, high-resolution spectra.

    abstract::While NMR studies of proteins typically aim at structure, dynamics or interactions, resonance assignments represent in almost all cases the initial step of the analysis. With increasing complexity of the NMR spectra, for example due to decreasing extent of ordered structure, this task often becomes both difficult and ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Zawadzka-Kazimierczuk A,Koźmiński W,Billeter M

    更新日期:2012-09-01 00:00:00

  • Water-protein hydrogen exchange in the micro-crystalline protein crh as observed by solid state NMR spectroscopy.

    abstract::We report site-resolved observation of hydrogen exchange in the micro-crystalline protein Crh. Our approach is based on the use of proton T2' -selective 1H-13C-13C correlation spectra for site-specific assignments of carbons nearby labile protein protons. We compare the proton T2' selective scheme to frequency selecti...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Böckmann A,Juy M,Bettler E,Emsley L,Galinier A,Penin F,Lesage A

    更新日期:2005-07-01 00:00:00

  • NMR of bicelles: orientation and mosaic spread of the liquid-crystal director under sample rotation.

    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

    pub_type: 杂志文章


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

    更新日期:2003-02-01 00:00:00

  • High resolution 4-D spectroscopy with sparse concentric shell sampling and FFT-CLEAN.

    abstract::Recent efforts to reduce the measurement time for multidimensional NMR experiments have fostered the development of a variety of new procedures for sampling and data processing. We recently described concentric ring sampling for 3-D NMR experiments, which is superior to radial sampling as input for processing by a mul...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Coggins BE,Zhou P

    更新日期:2008-12-01 00:00:00

  • High resolution observed in 800 MHz DNP spectra of extremely rigid type III secretion needles.

    abstract::The cryogenic temperatures at which dynamic nuclear polarization (DNP) solid-state NMR experiments need to be carried out cause line-broadening, an effect that is especially detrimental for crowded protein spectra. By increasing the magnetic field strength from 600 to 800 MHz, the resolution of DNP spectra of type III...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Fricke P,Mance D,Chevelkov V,Giller K,Becker S,Baldus M,Lange A

    更新日期:2016-08-01 00:00:00

  • Determination of the equilibrium micelle-inserting position of the fusion peptide of gp41 of human immunodeficiency virus type 1 at amino acid resolution by exchange broadening of amide proton resonances.

    abstract::The exchange broadening of backbone amide proton resonances of a 23-mer fusion peptide of the transmembrane subunit of HIV-1 envelope glycoprotein gp41, gp41-FP, was investigated at pH 5 and 7 at room temperature in perdeuterated sodium dodecyl sulfate (SDS) micellar solution. Comparison of resonance peaks for these p...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Chang DK,Cheng SF

    更新日期:1998-11-01 00:00:00

  • Numerical design of RN(n)(nu) symmetry-based RF pulse schemes for recoupling and decoupling of nuclear spin interactions at high MAS frequencies.

    abstract::An approach for the efficient implementation of RN(n)(nu) symmetry-based pulse schemes that are often employed for recoupling and decoupling of nuclear spin interactions in biological solid state NMR investigations is demonstrated at high magic-angle spinning frequencies. RF pulse sequences belonging to the RN(n)(nu) ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Herbst C,Herbst J,Leppert J,Ohlenschläger O,Görlach M,Ramachandran R

    更新日期:2009-08-01 00:00:00

  • Improved three-dimensional 1H-13C-1H correlation spectroscopy of a 13C-labeled protein using constant-time evolution.

    abstract::An improved version of the three-dimensional HCCH-COSY NMR experiment is described that correlates the resonances of geminal and vicinal proton pairs with the chemical shift of the 13C nucleus attached to one of the protons. The experiment uses constant-time evolution of transverse 13C magnetization which optimizes tr...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Ikura M,Kay LE,Bax A

    更新日期:1991-09-01 00:00:00

  • Spectral densities of nitrogen nuclei in Escherichia coli ribonuclease HI obtained by 15N NMR relaxation and molecular dynamics.

    abstract::Spectral densities of the 15N amide in Escherichia coli ribonuclease HI, obtained from NMR relaxation experiments, were compared with those calculated using a molecular dynamics (MD) simulation. All calculations and comparisons assumed that the auto-correlation function describing the internal motions of the molecule ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Ishima R,Yamasaki K,Saito M,Nagayama K

    更新日期:1995-09-01 00:00:00

  • Elucidation of the origin of multiple conformations of the human alpha 3-chain type VI collagen C-terminal Kunitz domain: the reorientation of the Trp21 ring.

    abstract::The human alpha 3-chain type VI collagen C-terminal Kunitz domain fragment (alpha 3(VI)) has been studied by two dimensional 1H-1H and 1H-13C NMR spectroscopy at 303 K. It is shown that the secondary structure of the protein is strikingly similar to that of BPTI, and a number of unusual H alpha chemical shifts, which ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Sørensen MD,Kristensen SM,Bjørn S,Norris K,Olsen O,Led JJ

    更新日期:1996-12-01 00:00:00

  • SOFAST-HMQC experiments for recording two-dimensional heteronuclear correlation spectra of proteins within a few seconds.

    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

    pub_type: 杂志文章


    authors: Schanda P,Kupce E,Brutscher B

    更新日期:2005-12-01 00:00:00

  • Nucleotide-type chemical shift assignment of the encapsulated 40 kbp dsDNA in intact bacteriophage T7 by MAS solid-state NMR.

    abstract::The icosahedral bacteriophage T7 is a 50 MDa double-stranded DNA (dsDNA) virus that infects Escherichia coli. Although there is substantial information on the physical and morphological properties of T7, structural information, based mostly on Raman spectroscopy and cryo-electron microscopy, is limited. Here, we apply...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Abramov G,Goldbourt A

    更新日期:2014-08-01 00:00:00

  • Detection and characterization of serine and threonine hydroxyl protons in Bacillus circulans xylanase by NMR spectroscopy.

    abstract::Hydroxyl protons on serine and threonine residues are not well characterized in protein structures determined by both NMR spectroscopy and X-ray crystallography. In the case of NMR spectroscopy, this is in large part because hydroxyl proton signals are usually hidden under crowded regions of (1)H-NMR spectra and remai...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Brockerman JA,Okon M,McIntosh LP

    更新日期:2014-01-01 00:00:00

  • A general Monte Carlo/simulated annealing algorithm for resonance assignment in NMR of uniformly labeled biopolymers.

    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

    pub_type: 杂志文章


    authors: Hu KN,Qiang W,Tycko R

    更新日期:2011-07-01 00:00:00

  • Cell signaling, post-translational protein modifications and NMR spectroscopy.

    abstract::Post-translationally modified proteins make up the majority of the proteome and establish, to a large part, the impressive level of functional diversity in higher, multi-cellular organisms. Most eukaryotic post-translational protein modifications (PTMs) denote reversible, covalent additions of small chemical entities ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Theillet FX,Smet-Nocca C,Liokatis S,Thongwichian R,Kosten J,Yoon MK,Kriwacki RW,Landrieu I,Lippens G,Selenko P

    更新日期:2012-11-01 00:00:00