Magic-angle spinning solid-state NMR of a 144 kDa membrane protein complex: E. coli cytochrome bo3 oxidase.

Abstract:

:Recent progress in magic-angle spinning (MAS) solid-state NMR (SSNMR) has enabled multidimensional studies of large, macroscopically unoriented membrane proteins with associated lipids, without the requirement of solubility that limits other structural techniques. Here we present initial sample preparation and SSNMR studies of a 144 kDa integral membrane protein, E. coli cytochrome bo(3) oxidase. The optimized protocol for expression and purification yields approximately 5 mg of the enzymatically active, uniformly (13)C,(15)N-enriched membrane protein complex from each liter of growth medium. The preparation retains endogenous lipids and yields spectra of high sensitivity and resolution, consistent with a folded, homogenous protein. Line widths of isolated signals are less than 0.5 ppm, with a large number of individual resonances resolved in the 2D and 3D spectra. The (13)C chemical shifts, assigned by amino acid type, are consistent with the secondary structure previously observed by diffraction methods. Although the structure is predominantly helical, the percentage of non-helical signals varies among residue types; these percentages agree well between the NMR and diffraction data. Samples show minimal evidence of degradation after several weeks of NMR data acquisition. Use of a triple resonance scroll resonator probe further improves sample stability and enables higher power decoupling, higher duty cycles and more advanced 3D experiments to be performed. These initial results in cytochrome bo(3) oxidase demonstrate that multidimensional MAS SSNMR techniques have sufficient sensitivity and resolution to interrogate selected parts of a very large uniformly (13)C,(15)N-labeled membrane protein.

journal_name

J Biomol NMR

authors

Frericks HL,Zhou DH,Yap LL,Gennis RB,Rienstra CM

doi

10.1007/s10858-006-9070-5

subject

Has Abstract

pub_date

2006-09-01 00:00:00

pages

55-71

issue

1

eissn

0925-2738

issn

1573-5001

journal_volume

36

pub_type

杂志文章
  • 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

    doi:10.1023/a:1012431013082

    authors: Riek R

    更新日期:2001-10-01 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

    doi:10.1023/B:JNMR.0000019248.48726.ff

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

    更新日期:2004-06-01 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

    doi:10.1007/s10858-006-9047-4

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

    更新日期:2006-10-01 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

    doi:10.1023/B:JNMR.0000013701.16162.0c

    authors: Bryce DL,Bax A

    更新日期:2004-03-01 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

    doi:10.1007/s10858-014-9840-4

    authors: Abramov G,Goldbourt A

    更新日期:2014-08-01 00:00:00

  • The use of TROSY for detection and suppression of conformational exchange NMR line broadening in biological macromolecules.

    abstract::The interference between conformational exchange-induced time-dependent variations of chemical shifts in a pair of scalar coupled 1H and 15N spins is used to construct novel TROSY-type NMR experiments to suppress NMR signal loss in [15N,1H]-correlation spectra of a 14-mer DNA duplex free in solution and complexed with...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1023/a:1011208109853

    authors: Pervushin K

    更新日期:2001-07-01 00:00:00

  • Resolution-enhanced base-type-edited HCN experiment for RNA.

    abstract::New base-type-edited transverse-relaxation optimized CT-HCN(C) experiments are presented that yield intra-base and sugar-to-base correlations for 13C-15N labeled RNA. High spectral resolution in the 13C and 15N dimensions is achieved by constant time (CT) frequency editing. A spectral editing filter applied during the...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-005-8872-1

    authors: Van Melckebeke H,Pardi A,Boisbouvier J,Simorre JP,Brutscher B

    更新日期:2005-08-01 00:00:00

  • Nitrogen detected TROSY at high field yields high resolution and sensitivity for protein NMR.

    abstract::Detection of (15)N in multidimensional NMR experiments of proteins has sparsely been utilized because of the low gyromagnetic ratio (γ) of nitrogen and the presumed low sensitivity of such experiments. Here we show that selecting the TROSY components of proton-attached (15)N nuclei (TROSY (15)NH) yields high quality s...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-015-9991-y

    authors: Takeuchi K,Arthanari H,Shimada I,Wagner G

    更新日期:2015-12-01 00:00:00

  • Extension of the HA-detection based approach: (HCA)CON(CA)H and (HCA)NCO(CA)H experiments for the main-chain assignment of intrinsically disordered proteins.

    abstract::Extensive resonance overlap exacerbates assignment of intrinsically disordered proteins (IDPs). This issue can be circumvented by utilizing (15)N, (13)C' and (1)H(N) spins, where the chemical shift dispersion is mainly dictated by the characteristics of consecutive amino acid residues. Especially (15)N and (13)C' spin...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-011-9470-z

    authors: Mäntylahti S,Hellman M,Permi P

    更新日期:2011-02-01 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

    doi:10.1023/a:1024078926886

    authors: Hyberts SG,Wagner G

    更新日期:2003-08-01 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

    doi:10.1007/BF00182286

    authors: Otting G,Liepinsh E

    更新日期:1995-06-01 00:00:00

  • Efficient cellular solid-state NMR of membrane proteins by targeted protein labeling.

    abstract::Solid-state NMR spectroscopy (ssNMR) has made significant progress towards the study of membrane proteins in their native cellular membranes. However, reduced spectroscopic sensitivity and high background signal levels can complicate these experiments. Here, we describe a method for ssNMR to specifically label a singl...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-015-9936-5

    authors: Baker LA,Daniëls M,van der Cruijsen EA,Folkers GE,Baldus M

    更新日期:2015-06-01 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

    doi:10.1007/BF00176007

    authors: Weimar T,Meyer B,Peters T

    更新日期:1993-07-01 00:00:00

  • Determination of protein global folds using backbone residual dipolar coupling and long-range NOE restraints.

    abstract::We report the determination of the global fold of human ubiquitin using protein backbone NMR residual dipolar coupling and long-range nuclear Overhauser effect (NOE) data as conformational restraints. Specifically, by use of a maximum of three backbone residual dipolar couplings per residue (Ni-H N i, Ni-C'(i-1), H N ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1023/a:1021954812977

    authors: Giesen AW,Homans SW,Brown JM

    更新日期:2003-01-01 00:00:00

  • Applications of variable-angle sample spinning experiments to the measurement of scaled residual dipolar couplings and 15N CSA in soluble proteins.

    abstract::NMR spectra of ubiquitin in the presence of bicelles at a concentration of 32% w/v have been recorded at 700 MHz under sample spinning conditions at the magic angle (54.7 degrees ) and at an angle of 45.5 degrees . At the magic angle, the 1H-15N HSQC spectrum of ubiquitin in bicelles is virtually indistinguishable fro...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-005-3210-1

    authors: Lancelot N,Elbayed K,Piotto M

    更新日期:2005-11-01 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

    doi:10.1007/s10858-016-0023-3

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

    更新日期:2016-03-01 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

    doi:10.1007/s10858-013-9799-6

    authors: Brockerman JA,Okon M,McIntosh LP

    更新日期:2014-01-01 00:00:00

  • Automatic NOESY assignment in CS-RASREC-Rosetta.

    abstract::We have developed an approach for simultaneous structure calculation and automatic Nuclear Overhauser Effect (NOE) assignment to solve nuclear magnetic resonance (NMR) structures from unassigned NOESY data. The approach, autoNOE-Rosetta, integrates Resolution Adapted Structural RECombination (RASREC) Rosetta NMR calcu...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-014-9833-3

    authors: Lange OF

    更新日期:2014-07-01 00:00:00

  • Efficient and generalized processing of multidimensional NUS NMR data: the NESTA algorithm and comparison of regularization terms.

    abstract::The advantages of non-uniform sampling (NUS) in offering time savings and resolution enhancement in NMR experiments have been increasingly recognized. The possibility of sensitivity gain by NUS has also been demonstrated. Application of NUS to multidimensional NMR experiments requires the selection of a sampling schem...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-015-9923-x

    authors: Sun S,Gill M,Li Y,Huang M,Byrd RA

    更新日期:2015-05-01 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

    doi:10.1007/BF01875321

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

    更新日期:1992-05-01 00:00:00

  • Application of neural networks to automated assignment of NMR spectra of proteins.

    abstract::Simulated neural networks are described which aid the assignment of protein NMR spectra. A network trained to recognize amino acid type from TOCSY data was trained on 148 assigned spin systems from E. coli acyl carrier proteins (ACPs) and tested on spin systems from spinach ACP, which has a 37% sequence homology with ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/BF00178334

    authors: Hare BJ,Prestegard JH

    更新日期:1994-01-01 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

    doi:10.1007/s10858-007-9205-3

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

    更新日期:2008-01-01 00:00:00

  • NMR in target driven drug discovery: why not?

    abstract::No matter the source of compounds, drug discovery campaigns focused directly on the target are entirely dependent on a consistent stream of reliable data that reports on how a putative ligand interacts with the protein of interest. The data will derive from many sources including enzyme assays and many types of biophy...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-020-00343-9

    authors: Keiffer S,Carneiro MG,Hollander J,Kobayashi M,Pogoryelev D,Ab E,Theisgen S,Müller G,Siegal G

    更新日期:2020-11-01 00:00:00

  • Sequence-specific resonance assignment and secondary structure of (1-71) bacterioopsin.

    abstract::The conformation of chymotryptic fragment C2 of bacteriohodopsin (residues 1-71) was studied by 2D 1H NMR. The fragment was solubilized in a mixture of chloroform/methanol (1:1), 0.1 M LiClO4. Most of the resonances in 1H NMR spectra of fragment C2 were assigned using phase-sensitive DQF-COSY, TOCSY, and NOESY techniq...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/BF01875527

    authors: Sobol AG,Arseniev AS,Abdulaeva GV,Musina LYu,Bystrov VF

    更新日期:1992-03-01 00:00:00

  • An NMR method for studying the kinetics of metal exchange in biomolecular systems.

    abstract::The kinetics of lanthanide (III) exchange for calcium(II) in the C-terminal EF-hand of the protein calbindin D9k have been studied by one-dimensional (1D) stopped-flow NMR. By choosing a paramagnetic lanthanide (Ce3+), kinetics in the sub-second range can be easily measured. This is made possible by the fact that (i) ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1023/a:1020245031235

    authors: Barbieri R,Hore PJ,Luchina C,Pierattelli R

    更新日期:2002-08-01 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

    doi:10.1007/s10858-005-5021-9

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

    更新日期:2006-01-01 00:00:00

  • Ensembles of a small number of conformations with relative populations.

    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

    pub_type: 杂志文章

    doi:10.1007/s10858-015-9993-9

    authors: Vammi V,Song G

    更新日期:2015-12-01 00:00:00

  • Feasibility of trifluoromethyl TROSY NMR at high magnetic fields.

    abstract::Insights into the structure and dynamics of large biological systems has been greatly improved by two concurrent NMR approaches: the application of transverse relaxation-optimized spectroscopy (TROSY) techniques in multi-dimensional NMR, especially the methyl-TROSY, and the resurgence of 19F NMR using trifluoromethyl ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-019-00266-0

    authors: Klein BA,Sykes BD

    更新日期:2019-11-01 00:00:00

  • Solid-state NMR, electrophysiology and molecular dynamics characterization of human VDAC2.

    abstract::The voltage-dependent anion channel (VDAC) is the most abundant protein of the outer mitochondrial membrane and constitutes the major pathway for the transport of ADP, ATP, and other metabolites. In this multidisciplinary study we combined solid-state NMR, electrophysiology, and molecular dynamics simulations, to stud...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-014-9876-5

    authors: Gattin Z,Schneider R,Laukat Y,Giller K,Maier E,Zweckstetter M,Griesinger C,Benz R,Becker S,Lange A

    更新日期:2015-04-01 00:00:00

  • A microscale protein NMR sample screening pipeline.

    abstract::As part of efforts to develop improved methods for NMR protein sample preparation and structure determination, the Northeast Structural Genomics Consortium (NESG) has implemented an NMR screening pipeline for protein target selection, construct optimization, and buffer optimization, incorporating efficient microscale ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-009-9386-z

    authors: Rossi P,Swapna GV,Huang YJ,Aramini JM,Anklin C,Conover K,Hamilton K,Xiao R,Acton TB,Ertekin A,Everett JK,Montelione GT

    更新日期:2010-01-01 00:00:00