Al NMR: a novel NMR data processing program optimized for sparse sampling.


:Sparse sampling in biomolecular multidimensional NMR offers increased acquisition speed and resolution and, if appropriate conditions are met, an increase in sensitivity. Sparse sampling of indirectly detected time domains combined with the direct truly multidimensional Fourier transform has elicited particular attention because of the ability to generate a final spectrum amenable to traditional analysis techniques. A number of sparse sampling schemes have been described including radial sampling, random sampling, concentric sampling and variations thereof. A fundamental feature of these sampling schemes is that the resulting time domain data array is not amenable to traditional Fourier transform based processing and phasing correction techniques. In addition, radial sampling approaches offer a number of advantages and capabilities that are also not accessible using standard NMR processing techniques. These include sensitivity enhancement, sub-matrix processing and determination of minimal sets of sampling angles. Here we describe a new software package (Al NMR) that enables these capabilities in the context of a general NMR data processing environment.


J Biomol NMR


Gledhill JM Jr,Wand AJ




Has Abstract


2012-01-01 00:00:00












  • Partial alignment and measurement of residual dipolar couplings of proteins under high hydrostatic pressure.

    abstract::High-pressure NMR spectroscopy has emerged as a complementary approach for investigating various structural and thermodynamic properties of macromolecules. Noticeably absent from the array of experimental restraints that have been employed to characterize protein structures at high hydrostatic pressure is the residual...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Fu Y,Wand AJ

    更新日期:2013-08-01 00:00:00

  • Automated evaluation of chemical shift perturbation spectra: New approaches to quantitative analysis of receptor-ligand interaction NMR spectra.

    abstract::This paper presents new methods designed for quantitative analysis of chemical shift perturbation NMR spectra. The methods automatically trace the displacements of cross peaks between a perturbed test spectrum and the reference spectrum (or among a series of titration spectra), and measure the changes of chemical shif...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Peng C,Unger SW,Filipp FV,Sattler M,Szalma S

    更新日期:2004-08-01 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

  • Application of correlated residual dipolar couplings to the determination of the molecular alignment tensor magnitude of oriented proteins and nucleic acids.

    abstract::Residual dipolar couplings (RDC) between nuclear spins in partially aligned samples offer unique insights into biomacromolecular structure and dynamics. To fully benefit from the RDC data, accurate knowledge of the magnitude ( D (a)) and rhombicity ( R ) of the molecular alignment tensor, A, is important. An extended ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Bryce DL,Bax A

    更新日期:2004-03-01 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

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

    abstract::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. Measurem...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


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

    更新日期:2004-11-01 00:00:00

  • Amino-acid type identification in 15N-HSQC spectra by combinatorial selective 15N-labelling.

    abstract::The efficiency of cell-free protein synthesis combined with combinatorial selective 15N-labelling provides a method for the rapid assignment of 15N-HSQC cross-peaks to the 19 different non-proline amino-acid types from five 15N-HSQC spectra. This strategy was explored with two different constructs of the C-terminal do...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Wu PS,Ozawa K,Jergic S,Su XC,Dixon NE,Otting G

    更新日期:2006-01-01 00:00:00

  • Quantifying Lipari-Szabo modelfree parameters from 13CO NMR relaxation experiments.

    abstract::It is proposed to obtain effective Lipari-Szabo order parameters and local correlation times for relaxation vectors of protein (13)CO nuclei by carrying out a (13)CO-R(1) auto relaxation experiment, a transverse (13)CO CSA/13CO-13Calpha CSA/dipolar cross correlation and a transverse (13)CO CSA/(13)CO-(15)N CSA/dipolar...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Wang T,Weaver DS,Cai S,Zuiderweg ER

    更新日期:2006-10-01 00:00:00

  • Backbone dynamics of a biologically active human FGF-1 monomer, complexed to a hexasaccharide heparin-analogue, by 15N NMR relaxation methods.

    abstract::The binding site and backbone dynamics of a bioactive complex formed by the acidic fibroblast growth factor (FGF-1) and a specifically designed heparin hexasaccharide has been investigated by HSQC and relaxation NMR methods. The comparison of the relaxation data for the free and bound states has allowed showing that t...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Canales-Mayordomo A,Fayos R,Angulo J,Ojeda R,Martín-Pastor M,Nieto PM,Martín-Lomas M,Lozano R,Giménez-Gallego G,Jiménez-Barbero J

    更新日期:2006-08-01 00:00:00

  • NMR-based metabolomics of mammalian cell and tissue cultures.

    abstract::NMR spectroscopy was used to evaluate growth media and the cellular metabolome in two systems of interest to biomedical research. The first of these was a Chinese hamster ovary cell line engineered to express a recombinant protein. Here, NMR spectroscopy and a quantum mechanical total line shape analysis were utilized...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Aranibar N,Borys M,Mackin NA,Ly V,Abu-Absi N,Abu-Absi S,Niemitz M,Schilling B,Li ZJ,Brock B,Russell RJ 2nd,Tymiak A,Reily MD

    更新日期:2011-04-01 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

  • Adiabatic TOBSY in rotating solids.

    abstract::A MAS solid state NMR approach for achieving efficient scalar coupling mediated through-bond (13)C chemical shift correlations of the aliphatic carbons in uniformly labelled peptides/proteins is described. The method involves the application of a continuous train of adiabatic inversion pulses, as in the adiabatic TOCS...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


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

    更新日期:2004-06-01 00:00:00

  • 1H and 13C NMR assignments for the glycans in glycoproteins by using 2H/13C-labeled glucose as a metabolic precursor.

    abstract::In order to understand the role of the glycans in glycoproteins in solution, structural information obtained by NMR spectroscopy is obviously required. However, the assignment of the NMR signals from the glycans in larger glycoproteins is still difficult, mainly due to the lack of appropriate methods for the assignmen...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Yamaguchi Y,Takizawa T,Kato K,Arata Y,Shimada I

    更新日期:2000-12-01 00:00:00

  • Cross-correlation suppressed T1 and NOE experiments for protein side-chain 13CH2 groups.

    abstract::Relaxation measurements of side-chain 13CH2-groups of uniformly 13C labeled human ubiquitin were performed at 600 MHz and 800 MHz magnetic field strength at 30 degrees C. Dipole-dipole cross-correlated relaxation effects in T1 experiments were suppressed by the combination of radio-frequency pulses and pulsed field gr...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Jin C,Prompers JJ,Brüschweiler R

    更新日期:2003-07-01 00:00:00

  • Efficient production of a functional G protein-coupled receptor in E. coli for structural studies.

    abstract::G protein-coupled receptors (GPCRs) are transmembrane signal transducers which regulate many key physiological process. Since their discovery, their analysis has been limited by difficulties in obtaining sufficient amounts of the receptors in high-quality, functional form from heterologous expression hosts. Albeit hig...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Abiko LA,Rogowski M,Gautier A,Schertler G,Grzesiek S

    更新日期:2021-01-27 00:00:00

  • 1H NMR studies of deuterated ribonuclease HI selectively labeled with protonated amino acids.

    abstract::Two-dimensional (2D) 1H NMR experiments using deuterium labeling have been carried out to investigate the solution of ribonuclease HI (RNase HI) from Escherichia coli (E. coli), which consists of 155 amino acids. To simplify the 1H NMR spectra, two fully deuterated enzymes bearing several protonated amino acids were p...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Oda Y,Nakamura H,Yamazaki T,Nagayama K,Yoshida M,Kanaya S,Ikehara M

    更新日期:1992-03-01 00:00:00

  • Enhancement of the steady-state magnetization in TROSY experiments.

    abstract::Under the condition that the longitudinal relaxation time of spin I is shorter than the longitudinal relaxation time of spin S the steady-state magnetization in [S,I]-TROSY-type experiments can be enhanced by intermediate storage of a part of the steady-state magnetization of spin I on spin S with a pulse sequence ele...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Riek R

    更新日期:2001-10-01 00:00:00

  • Visualizing the principal component of ¹H, ¹⁵N-HSQC NMR spectral changes that reflect protein structural or functional properties: application to troponin C.

    abstract::Laboratories often repeatedly determine the structure of a given protein under a variety of conditions, mutations, modifications, or in a number of states. This approach can be cumbersome and tedious. Given then a database of structures, identifiers, and corresponding (1)H,(15)N-HSQC NMR spectra for homologous protein...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Robertson IM,Boyko RF,Sykes BD

    更新日期:2011-09-01 00:00:00

  • Solution structure of the N-terminal domain of the Staphylococcus aureus hibernation promoting factor.

    abstract::Staphylococcus aureus hibernation promoting factor (SaHPF) is a 22,2 kDa protein which plays a crucial role in 100S Staphylococcus aureus ribosome formation during stress. SaHPF consists of N-terminal domain (NTD) that prevents proteins synthesis by binding to the 30S subunit at the P- and A-sites, connected through a...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Usachev KS,Validov SZ,Khusainov IS,Varfolomeev AA,Klochkov VV,Aganov AV,Yusupov MM

    更新日期:2019-05-01 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

  • Tools for the automated assignment of high-resolution three-dimensional protein NMR spectra based on pattern recognition techniques.

    abstract::One of the major bottlenecks in the determination of proteinstructures by NMR is in the evaluation of the data produced by theexperiments. An important step in this process is assignment, where thepeaks in the spectra are assigned to specific spins within specificresidues. In this paper, we discuss a spin system assig...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Croft D,Kemmink J,Neidig KP,Oschkinat H

    更新日期:1997-10-01 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

  • Determination of the relative NH proton lifetimes of the peptide analogue viomycin in aqueous solution by NMR-based diffusion measurement.

    abstract::In aqueous solution, exchanging peptide NH protons experience two environments, that of the peptide itself with a relatively slow diffusion coefficient and that of the water solvent with a faster diffusion coefficient. Although in slow exchange on the NMR chemical shift timescale, the magnetic field gradient dependenc...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Liu M,Toms HC,Hawkes GE,Nicholson JK,Lindon JC

    更新日期:1999-01-01 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

  • 1H NMR investigation of the secondary structure, tertiary contacts and cluster environment of the four-iron ferredoxin from the hyperthermophilic archaeon Thermococcus litoralis.

    abstract::The solution molecular structure of the four-iron ferredoxin (Fd) from the hyperthermophilic archaeon Thermococcus litoralis (Tl) has been investigated by 1H NMR spectroscopy. TOCSY and NOESY experiments in H2O, tailored to detect both weakly and strongly relaxed resonances, together with steady-state NOEs in both H2O...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Donaire A,Zhou ZH,Adams MM,La Mar GN

    更新日期:1996-01-01 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

  • Comparison of amide proton exchange in reduced and oxidized Rhodobacter capsulatus cytochrome c2: a 1H-15N NMR study.

    abstract::The hydrogen-deuterium exchange rates of the reduced and oxidized forms of Rhodobacter capsulatus cytochrome c2 were studied by 1H-15N homonuclear multiple quantum correlation spectroscopy. Minimal differences were observed for the N- and C-terminal helices on changing redox state suggesting that although these helice...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Gooley PR,Zhao D,MacKenzie NE

    更新日期:1991-07-01 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

  • 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

  • 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