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.


: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-(4,3)D HNN(CO)C (alphabeta) C (alpha), (4,2)D HACA(CO)NHN and (4,3)D HCCH, were acquired along with simultaneous 3D (15)N, (13)C(aliphatic), (13)C(aromatic)-resolved [(1)H,(1)H]-NOESY with a total measurement time of approximately 43 h. Data analysis resulted in sequence specific assignments for all routinely measured backbone and (13)C(beta) shifts, and for 97% of the side chain shifts. Moreover, the use of two G(2)FT NMR experiments, that is, (5,3)D HN{N,CO}{C (alphabeta) C (alpha)} and (5,3)D {C (alphabeta) C (alpha)}{CON}HN, was explored to break the very high chemical shift degeneracy typically encountered for membrane proteins. It is shown that the 4D and 5D spectral information obtained rapidly from GFT and G(2)FT NMR experiments enables one to efficiently obtain (nearly) complete resonance assignments of membrane proteins.


J Biomol NMR


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




Has Abstract


2008-03-01 00:00:00












  • A chemical approach for site-specific identification of NMR signals from protein side-chain NH₃⁺ groups forming intermolecular ion pairs in protein-nucleic acid complexes.

    abstract::Protein-nucleic acid interactions involve intermolecular ion pairs of protein side-chain and DNA or RNA phosphate groups. Using three protein-DNA complexes, we demonstrate that site-specific oxygen-to-sulfur substitution in phosphate groups allows for identification of NMR signals from the protein side-chain NH3 (+) g...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Anderson KM,Nguyen D,Esadze A,Zandrashvili L,Gorenstein DG,Iwahara J

    更新日期:2015-05-01 00:00:00

  • HIFI-C: a robust and fast method for determining NMR couplings from adaptive 3D to 2D projections.

    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

    pub_type: 杂志文章


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

    更新日期:2007-08-01 00:00:00

  • MTH187 from Methanobacterium thermoautotrophicum has three HEAT-like repeats.

    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

    pub_type: 杂志文章


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

    更新日期:2006-06-01 00:00:00

  • Optimization of 1H decoupling eliminates sideband artifacts in 3D TROSY-based triple resonance experiments.

    abstract::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 ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Xia Y,Rossi P,Tonelli M,Huang C,Kalodimos CG,Veglia G

    更新日期:2017-09-01 00:00:00

  • Trimethylsilyl tag for probing protein-ligand interactions by NMR.

    abstract::Protein-ligand titrations can readily be monitored with a trimethylsilyl (TMS) tag. Owing to the intensity, narrow line shape and unique chemical shift of a TMS group, dissociation constants can be determined from straightforward 1D 1H-NMR spectra not only in the fast but also in the slow exchange limit. The tag is ea...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Becker W,Adams LA,Graham B,Wagner GE,Zangger K,Otting G,Nitsche C

    更新日期:2018-04-01 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

  • Narrow carbonyl resonances in proton-diluted proteins facilitate NMR assignments in the solid-state.

    abstract::HNCO/HNCACO type correlation experiments are an alternative for assignment of backbone resonances in extensively deuterated proteins in the solid-state, given the fact that line widths on the order of 14-17 Hz are achieved in the carbonyl dimension without the need of high power decoupling. The achieved resolution dem...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Linser R,Fink U,Reif B

    更新日期:2010-05-01 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

  • 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

  • Development of in vitro-grown spheroids as a 3D tumor model system for solid-state NMR spectroscopy.

    abstract::Recent advances in the field of in-cell NMR spectroscopy have made it possible to study proteins in the context of bacterial or mammalian cell extracts or even entire cells. As most mammalian cells are part of a multi-cellular complex, there is a need to develop novel NMR approaches enabling the study of proteins with...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Damman R,Lucini Paioni A,Xenaki KT,Beltrán Hernández I,van Bergen En Henegouwen PMP,Baldus M

    更新日期:2020-09-01 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

  • [13C]-constant-time [15N,1H]-TROSY-HNCA for sequential assignments of large proteins.

    abstract::The greatly improved sensitivity resulting from the use of TROSY during 15N evolution and amide proton acquisition enables the recording of HNCA spectra of large proteins with constant-time 13C alpha evolution. In [13C]-ct-[15N,1H]-TROSY-HNCA experiments with a 2H/13C/15N-labeled 110 kDa protein, 7,8-dihydroneopterin ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Salzmann M,Pervushin K,Wider G,Senn H,Wüthrich K

    更新日期:1999-05-01 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

  • RNA phosphodiester backbone dynamics of a perdeuterated cUUCGg tetraloop RNA from phosphorus-31 NMR relaxation analysis.

    abstract::We have analyzed the relaxation properties of all (31)P nuclei in an RNA cUUCGg tetraloop model hairpin at proton magnetic field strengths of 300, 600 and 900 MHz in solution. Significant H, P dipolar contributions to R (1) and R (2) relaxation are observed in a protonated RNA sample at 600 MHz. These contributions ca...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Rinnenthal J,Richter C,Nozinovic S,Fürtig B,Lopez JJ,Glaubitz C,Schwalbe H

    更新日期:2009-09-01 00:00:00

  • IBIS--a tool for automated sequential assignment of protein spectra from triple resonance experiments.

    abstract::We have developed a tool for computer-assisted assignments of protein NMR spectra from triple resonance data. The program is designed to resemble established manual assignment procedures as closely as possible. IBIS exports its results in XEASY format. Thus, using IBIS the operator has continuous visual and accounting...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Hyberts SG,Wagner G

    更新日期:2003-08-01 00:00:00

  • Heteronuclear multidimensional NMR and homology modelling studies of the C-terminal nucleotide-binding domain of the human mitochondrial ABC transporter ABCB6.

    abstract::Human ATP-binding cassette, sub-family B, member 6 (ABCB6) is a mitochondrial ABC transporter, and presumably contributes to iron homeostasis. Aimed at understanding the structural basis for the conformational changes accompanying the substrate-transportation cycle, we have studied the C-terminal nucleotide-binding do...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Kurashima-Ito K,Ikeya T,Senbongi H,Tochio H,Mikawa T,Shibata T,Ito Y

    更新日期:2006-05-01 00:00:00

  • Sequential nearest-neighbor effects on computed 13Calpha chemical shifts.

    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

    pub_type: 杂志文章


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

    更新日期:2010-09-01 00:00:00

  • Structural investigations of a GYF domain covalently linked to a proline-rich peptide.

    abstract::Protein structure determination of low affinity complexes of interacting macromolecules is often hampered by a lack of observable NOEs between the binding partners. Covalent linkage offers a way to shift the equilibrium of the interaction partners to the bound state. Here we show that a single-chain protein containing...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Freund C,Kühne R,Park S,Thiemke K,Reinherz EL,Wagner G

    更新日期:2003-10-01 00:00:00

  • A new triple-resonance experiment for the sequential assignment of backbone resonances in proteins.

    abstract::A new protocol is described for obtaining intraresidual and sequential correlations between carbonyl carbons and amide (1)H and (15)N resonances of amino acids. Frequency labeling of (13)CO spins occurs during a period required for the (13)C(α)-(15)N polarization transfer, leading to an optimized transfer efficiency. ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Löhr F,Rüterjans H

    更新日期:1995-09-01 00:00:00

  • Perspective: revisiting the field dependence of TROSY sensitivity.

    abstract::The discovery of the TROSY effect (Pervushin et al. in Proc Natl Acad Sci USA 94:12366-12371, 1997) for reducing transverse relaxation and line sharpening through selecting pathways in which dipole-dipole and CSA Hamiltonians partially cancel each other had a tremendous impact on solution NMR studies of macromolecules...

    journal_title:Journal of biomolecular NMR

    pub_type: 信件


    authors: Takeuchi K,Arthanari H,Wagner G

    更新日期:2016-12-01 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

  • 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

  • Sequential correlation of anomeric ribose protons and intervening phosphorus in RNA oligonucleotides by a 1H, 13C, 31P triple resonance experiment: HCP-CCH-TOCSY.

    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

    pub_type: 杂志文章


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

    更新日期:1995-01-01 00:00:00

  • Narrowing the conformational space sampled by two-domain proteins with paramagnetic probes in both domains.

    abstract::Calmodulin is a two-domain protein which in solution can adopt a variety of conformations upon reorientation of its domains. The maximum occurrence (MO) of a set of calmodulin conformations that are representative of the overall conformational space possibly sampled by the protein, has been calculated from the paramag...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Dasgupta S,Hu X,Keizers PH,Liu WM,Luchinat C,Nagulapalli M,Overhand M,Parigi G,Sgheri L,Ubbink M

    更新日期:2011-11-01 00:00:00

  • An improved double-tuned and isotope-filtered pulse scheme based on a pulsed field gradient and a wide-band inversion shaped pulse.

    abstract::We have developed an improved isotope-filtered pulse scheme in combination with a double-tuned filter, a hyperbolic secant inversion pulse, and a z-filter with a pulsed field gradient. These filtering pulse schemes have been incorporated into several one-, two-, and three-dimensional experiments, which were applied to...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Ogura K,Terasawa H,Inagaki F

    更新日期:1996-12-01 00:00:00

  • Characterization of the hydrogen bond network in guanosine quartets by internucleotide 3hJ(NC)' and 2hJ(NN) scalar couplings.

    abstract::Scalar coupling correlations across hydrogen bonds with carbonyl groups as acceptors have been observed in a variety of proteins, but not in nucleic acids. Here we present a pulse scheme that allows such an observation and quantification of trans-hydrogen bond 3hJ(NC)' correlations in nucleic acid base pairs, between ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Dingley AJ,Masse JE,Feigon J,Grzesiek S

    更新日期:2000-04-01 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

  • Amino-acid selective isotope labeling enables simultaneous overlapping signal decomposition and information extraction from NMR spectra.

    abstract::Signal overlapping is a major bottleneck for protein NMR analysis. We propose a new method, stable-isotope-assisted parameter extraction (SiPex), to resolve overlapping signals by a combination of amino-acid selective isotope labeling (AASIL) and tensor decomposition. The basic idea of Sipex is that overlapping signal...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Kasai T,Ono S,Koshiba S,Yamamoto M,Tanaka T,Ikeda S,Kigawa T

    更新日期:2020-03-01 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

  • Exchangeable deuterons introduce artifacts in amide 15N CEST experiments used to study protein conformational exchange.

    abstract::Protein molecules sample different conformations in solution and characterizing these conformations is crucial to understanding protein function. 15N CEST experiments are now routinely used to study slow conformational exchange of protein molecules between a 'visible' major state and 'invisible' minor states. These ex...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Tiwari VP,Pandit S,Vallurupalli P

    更新日期:2019-02-01 00:00:00