当前位置： SCI文献检索 > JOURNAL OF BIOMOLECULAR NMR期刊下所有文献 > Solution structure of the soluble domain of the NfeD protein YuaF from Bacillus subtilis.

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 superfamily, in this case YuaG. This strongly suggests a functional if not physical interaction between YuaF and YuaG. Secondary structure predictions of NfeD proteins that accompany SPFH proteins all indicate a high content of beta-sheets in the C-terminal domains indicating a conserved core structure despite very low homology at the level of primary structure. Here we report the high-resolution solution structure of YuaF's soluble C-terminal domain derived from NMR data (sYuaF, residues 97-174 of full-length YuaF). Full backbone and side chain assignments of sYuaF were obtained from triple-resonance spectra. The structure was determined from distance restraints derived from 3D NOESY spectra collected at 600 MHz and 800 MHz, together with phi, psi, and chi(1) torsion angle restraints based on the analysis of (1)H(N), (15)N, (1)H(alpha), (13)C(alpha), (13)CO, and (13)C(beta) chemical shifts, and HNHA, HNHB and HACAHB-COSY spectra. Structures were calculated using CYANA 2.0 and refined in AMBER 8. sYuaF is composed of an extended N-terminal alpha-helix and a beta-barrel formed by five beta-strands. This beta-sheet core structure is well known from the diverse class of OB-fold proteins and can also be found in the distantly related NfeD protein Ph0471 from the archaeon P. horikoshii. Despite significant differences of their amino acid sequences the structural homology of these proteins suggests a conserved function of SPFH-associated NfeD proteins.

journal_name

J Biomol NMR

journal_title

Journal of biomolecular NMR

authors

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

doi

10.1007/s10858-008-9261-3

subject

Has Abstract

pub_date

2008-09-01 00:00:00

pages

69-76

issue

1

eissn

0925-2738

issn

1573-5001

journal_volume

42

pub_type

杂志文章

相关文献

JOURNAL OF BIOMOLECULAR NMR文献大全
  • Application of virus-like particles (VLP) to NMR characterization of viral membrane protein interactions.

    abstract：:The membrane proteins of viruses play critical roles in the virus life cycle and are attractive targets for therapeutic intervention. Virus-like particles (VLP) present the possibility to study the biochemical and biophysical properties of viral membrane proteins in their native environment. Specifically, the VLP cons...

    journal_title：Journal of biomolecular NMR

    pub_type： 杂志文章

    doi：10.1007/s10858-016-0025-1

    authors： Antanasijevic A,Kingsley C,Basu A,Bowlin TL,Rong L,Caffrey M

    更新日期：2016-03-01 00:00:00

  • Efficient analysis of protein 2D NMR spectra using the software package EASY.

    abstract：:The program EASY supports the spectral analysis of biomacromolecular two-dimensional (2D) nuclear magnetic resonance (NMR) data. It provides a user-friendly, window-based environment in which to view spectra for interactive interpretation. In addition, it includes a number of automated routines for peak-picking, spin-...

    journal_title：Journal of biomolecular NMR

    pub_type： 杂志文章

    doi：10.1007/BF01877224

    authors： Eccles C,Güntert P,Billeter M,Wüthrich K

    更新日期：1991-07-01 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

    doi：10.1023/a:1024983029700

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

    更新日期：2003-10-01 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

    doi：10.1023/a:1024768328860

    authors： Zweckstetter M

    更新日期：2003-09-01 00:00:00

  • The use of chemical shift temperature gradients to establish the paramagnetic susceptibility tensor orientation: implication for structure determination/refinement in paramagnetic metalloproteins.

    abstract：:The use of dipolar shifts as important constraints in refining molecular structure of paramagnetic metalloproteins by solution NMR is now well established. A crucial initial step in this procedure is the determination of the orientation. of the anisotropic paramagnetic susceptibility tensor in the molecular frame whic...

    journal_title：Journal of biomolecular NMR

    pub_type： 杂志文章

    doi：10.1023/a:1008309121949

    authors： Xia Z,Nguyen BD,La Mar GN

    更新日期：2000-06-01 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

    doi：10.1023/a:1024960302926

    authors： Freeman R,Kupce E

    更新日期：2003-10-01 00:00:00

  • Understanding and solving abnormal peak splitting in 3D HCCH-TOCSY and HCC(CO)NH-TOCSY.

    abstract：:The 3D HCCH-TOCSY and HCC(CO)NH-TOCSY experiments provide through bond connectivity and are used for side-chain chemical shift assignment by solution-state NMR. Careful design and implementation of the pulse sequence are key to the successful application of the technique particularly when trying to extract the maximum...

    journal_title：Journal of biomolecular NMR

    pub_type： 杂志文章

    doi：10.1007/s10858-020-00310-4

    authors： Xia Y,Yuwen T,Rossi P

    更新日期：2020-05-01 00:00:00

  • Direct amide 15N to 13C transfers for solid-state assignment experiments in deuterated proteins.

    abstract：:The assignment of protein backbone and side-chain NMR chemical shifts is the first step towards the characterization of protein structure. The recent introduction of proton detection in combination with fast MAS has opened up novel opportunities for assignment experiments. However, typical 3D sequential-assignment exp...

    journal_title：Journal of biomolecular NMR

    pub_type： 杂志文章

    doi：10.1007/s10858-018-0207-0

    authors： Lends A,Ravotti F,Zandomeneghi G,Böckmann A,Ernst M,Meier BH

    更新日期：2018-10-01 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

    doi：10.1023/A:1008393202076

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

    更新日期：1999-01-01 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

    doi：10.1007/s10858-015-9909-8

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

    更新日期：2015-05-01 00:00:00

  • Comparison of the backbone dynamics of wild-type Hydrogenobacter thermophilus cytochrome c(552) and its b-type variant.

    abstract：:Cytochrome c552 from the thermophilic bacterium Hydrogenobacter thermophilus is a typical c-type cytochrome which binds heme covalently via two thioether bonds between the two heme vinyl groups and two cysteine thiol groups in a CXXCH sequence motif. This protein was converted to a b-type cytochrome by substitution of...

    journal_title：Journal of biomolecular NMR

    pub_type： 杂志文章

    doi：10.1007/s10858-015-9938-3

    authors： Tozawa K,Ferguson SJ,Redfield C,Smith LJ

    更新日期：2015-06-01 00:00:00

  • Importance of time-ordered non-uniform sampling of multi-dimensional NMR spectra of Aβ1-42 peptide under aggregating conditions.

    abstract：:Although the order of the time steps in which the non-uniform sampling (NUS) schedule is implemented when acquiring multi-dimensional NMR spectra is of limited importance when sample conditions remain unchanged over the course of the experiment, it is shown to have major impact when samples are unstable. In the latter...

    journal_title：Journal of biomolecular NMR

    pub_type： 杂志文章

    doi：10.1007/s10858-019-00235-7

    authors： Ying J,Barnes CA,Louis JM,Bax A

    更新日期：2019-09-01 00:00:00

  • 1H(C) and 1H(N) total NOE correlations in a single 3D NMR experiment. 15N and 13C time-sharing in t1 and t2 dimensions for simultaneous data acquisition.

    abstract：:Simultaneous data acquisition in time-sharing (TS) multi-dimensional NMR experiments has been shown an effective means to reduce experimental time, and thus to accelerate structure determination of proteins. This has been accomplished by spin evolution time-sharing of the X and Y heteronuclei, such as (15)N and (13)C,...

    journal_title：Journal of biomolecular NMR

    pub_type： 杂志文章

    doi：10.1023/a:1025407905478

    authors： Xia Y,Yee A,Arrowsmith CH,Gao X

    更新日期：2003-11-01 00:00:00

  • PLUSH TACSY: Homonuclear planar TACSY with two-band selective shaped pulses applied to C(α),C' transfer and C (β),C (aromatic) correlations.

    abstract：:A new homonuclear Hartmann-Hahn-type mixing scheme is introduced that effects coherence transfer between resonances in two separated frequency bands. The mixing scheme relies on the irradiation of two-band selective shaped pulses that are expanded in an MLEV-16 supercycle. Similar to heteronuclear Hartmann-Hahn experi...

    journal_title：Journal of biomolecular NMR

    pub_type： 杂志文章

    doi：10.1007/BF00211162

    authors： Carlomagno T,Maurer M,Sattler M,Schwendinger MG,Glaser SJ,Griesinger C

    更新日期：1996-09-01 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

  • 1H-1H correlations across N-H...N hydrogen bonds in nucleic acids.

    abstract：:In 2HJ(NN)-COSY experiments, which correlate protons with donor/acceptor nitrogens across Nd...HNa bonds, the receptor nitrogen needs to be assigned in order to unambiguously identify the hydrogen bond. For many situations this is a non-trivial task which is further complicated by poor dispersion of (Na,Nd) resonances...

    journal_title：Journal of biomolecular NMR

    pub_type： 杂志文章

    doi：10.1023/a:1013340227140

    authors： Majumdar A,Gosser Y,Patel DJ

    更新日期：2001-12-01 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

  • 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

    doi：10.1023/a:1013821123201

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

    更新日期：2002-01-01 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

    doi：10.1023/a:1008348827208

    authors： Korzhnev DM,Tischenko EV,Arseniev AS

    更新日期：2000-07-01 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

    doi：10.1007/BF02192865

    authors： Delaglio F,Torchia DA,Bax A

    更新日期：1991-11-01 00:00:00

  • Biomass production of site selective 13C/15N nucleotides using wild type and a transketolase E. coli mutant for labeling RNA for high resolution NMR.

    abstract：:Characterization of the structure and dynamics of nucleic acids by NMR benefits significantly from position specifically labeled nucleotides. Here an E. coli strain deficient in the transketolase gene (tktA) and grown on glucose that is labeled at different carbon sites is shown to facilitate cost-effective and large ...

    journal_title：Journal of biomolecular NMR

    pub_type： 杂志文章

    doi：10.1007/s10858-011-9586-1

    authors： Thakur CS,Luo Y,Chen B,Eldho NV,Dayie TK

    更新日期：2012-02-01 00:00:00

  • Triple resonance ¹⁵Ν NMR relaxation experiments for studies of intrinsically disordered proteins.

    abstract：:Description of protein dynamics is known to be essential in understanding their function. Studies based on a well established [Formula: see text] NMR relaxation methodology have been applied to a large number of systems. However, the low dispersion of [Formula: see text] chemical shifts very often observed within intr...

    journal_title：Journal of biomolecular NMR

    pub_type： 杂志文章

    doi：10.1007/s10858-017-0138-1

    authors： Srb P,Nováček J,Kadeřávek P,Rabatinová A,Krásný L,Žídková J,Bobálová J,Sklenář V,Žídek L

    更新日期：2017-11-01 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

    doi：10.1007/s10858-005-1846-5

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

    更新日期：2004-11-01 00:00:00

  • Breaking symmetry in the structure determination of (large) symmetric protein dimers.

    abstract：:We demonstrate a novel methodology to disrupt the symmetry in the NMR spectra of homodimers. A paramagnetic probe is introduced sub-stoichiometrically to create an asymmetric system with the paramagnetic probe residing on only one monomer within the dimer. This creates sufficient magnetic anisotropy for resolution of ...

    journal_title：Journal of biomolecular NMR

    pub_type： 杂志文章

    doi：10.1023/a:1020948529076

    authors： Gaponenko V,Altieri AS,Li J,Byrd RA

    更新日期：2002-10-01 00:00:00

  • Assignment of cytosine N3 resonances in nucleic acids via intrabase three-bond coupling to amino protons.

    abstract：:Coherences were observed between 15N3 of cytosine and its trans amino proton (H42) using a modified gradient-based heteronuclear single quantum coherence (HSQC) pulse sequence optimized for three-bond proton-nitrogen couplings. The method is demonstrated with a 22-nucleotide RNA fragment of the P5abc region of a group...

    journal_title：Journal of biomolecular NMR

    pub_type： 杂志文章

    doi：10.1023/a:1008359723515

    authors： Rüdisser S,Pelton JG,Tinoco I Jr

    更新日期：1999-10-01 00:00:00

  • Spectral editing: selection of methyl groups in multidimensional solid-state magic-angle spinning NMR.

    abstract：:A simple spectroscopic filtering technique is presented that may aid the assignment of (13)C and (15)N resonances of methyl-containing amino-acids in solid-state magic-angle spinning (MAS) NMR. A filtering block that selects methyl resonances is introduced in two-dimensional (2D) (13)C-homonuclear and (15)N-(13)C hete...

    journal_title：Journal of biomolecular NMR

    pub_type： 杂志文章

    doi：10.1007/s10858-006-9078-x

    authors： Jehle S,Hiller M,Rehbein K,Diehl A,Oschkinat H,van Rossum BJ

    更新日期：2006-11-01 00:00:00

  • Segmental isotopic labeling by asparaginyl endopeptidase-mediated protein ligation.

    abstract：:Segmental isotopic labeling can facilitate NMR studies of large proteins, multi-domain proteins, and proteins with repetitive sequences by alleviating NMR signal overlaps. Segmental isotopic labeling also allows us to investigate an individual domain in the context of a full-length protein by NMR. Several established ...

    journal_title：Journal of biomolecular NMR

    pub_type： 杂志文章

    doi：10.1007/s10858-018-0175-4

    authors： Mikula KM,Krumwiede L,Plückthun A,Iwaï H

    更新日期：2018-08-01 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

    doi：10.1007/BF00203824

    authors： Schmidt JM,Löhr F,Rüterjans H

    更新日期：1996-03-01 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

    doi：10.1007/s10858-010-9404-1

    authors： Linser R,Fink U,Reif B

    更新日期：2010-05-01 00:00:00

  • Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water.

    abstract：:The inclusion of explicit solvent water in molecular dynamics refinement of NMR structures ought to provide the most physically meaningful accounting for the effects of solvent on structure, but is computationally expensive. In order to evaluate the validity of commonly used vacuum refinements and of recently develope...

    journal_title：Journal of biomolecular NMR

    pub_type： 杂志文章

    doi：10.1023/a:1014929925008

    authors： Xia B,Tsui V,Case DA,Dyson HJ,Wright PE

    更新日期：2002-04-01 00:00:00