Removal of slow-pulsing artifacts in in-phase 15N relaxation dispersion experiments using broadband 1H decoupling.

Abstract:

:Understanding of the molecular mechanisms of protein function requires detailed insight into the conformational landscape accessible to the protein. Conformational changes can be crucial for biological processes, such as ligand binding, protein folding, and catalysis. NMR spectroscopy is exquisitely sensitive to such dynamic changes in protein conformations. In particular, Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments are a powerful tool to investigate protein dynamics on a millisecond time scale. CPMG experiments that probe the chemical shift modulation of 15N in-phase magnetization are particularly attractive, due to their high sensitivity. These experiments require high power 1H decoupling during the CPMG period to keep the 15N magnetization in-phase. Recently, an improved version of the in-phase 15N-CPMG experiment was introduced, offering greater ease of use by employing a single 1H decoupling power for all CPMG pulsing rates. In these experiments however, incomplete decoupling of off-resonance amide 1H spins introduces an artefactual dispersion of relaxation rates, the so-called slow-pulsing artifact. Here, we analyze the slow-pulsing artifact in detail and demonstrate that it can be suppressed through the use of composite pulse decoupling (CPD). We report the performances of various CPD schemes and show that CPD decoupling based on the 90x-240y-90x element results in high-quality dispersion curves free of artifacts, even for amides with high 1H offset.

journal_name

J Biomol NMR

authors

Chatterjee SD,Ubbink M,van Ingen H

doi

10.1007/s10858-018-0193-2

subject

Has Abstract

pub_date

2018-06-01 00:00:00

pages

69-77

issue

2

eissn

0925-2738

issn

1573-5001

pii

10.1007/s10858-018-0193-2

journal_volume

71

pub_type

杂志文章
  • Amino acid recognition for automatic resonance assignment of intrinsically disordered proteins.

    abstract::Resonance assignment is a prerequisite for almost any NMR-based study of proteins. It can be very challenging in some cases, however, due to the nature of the protein under investigation. This is the case with intrinsically disordered proteins, for example, whose NMR spectra suffer from low chemical shifts dispersion ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-016-0024-2

    authors: Piai A,Gonnelli L,Felli IC,Pierattelli R,Kazimierczuk K,Grudziąż K,Koźmiński W,Zawadzka-Kazimierczuk A

    更新日期:2016-03-01 00:00:00

  • Refocusing revisited: an optimized, gradient-enhanced refocused HSQC and its applications in 2D and 3D NMR and in deuterium exchange experiments.

    abstract::2D 15N-1H correlation spectra are ideal for measuring backbone amide populations to determine amide exchange protection factors in studies of protein folding or other structural features. Most protein NMR spectroscopists use HSQC, which has been shown to be generally superior to HMQC in both resolution and sensitivity...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/BF00182288

    authors: Davis JH

    更新日期:1995-06-01 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

  • 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

    doi:10.1007/s10858-010-9414-z

    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

  • Peptide self-association in aqueous trifluoroethanol monitored by pulsed field gradient NMR diffusion measurements.

    abstract::Defining the self-association state of a molecule in solution can be an important step in NMR-based structure determination. This is particularly true of peptides, where there can be a relatively small number of long-range interactions and misinterpretation of an intermolecular NOE as an intramolecular contact can hav...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1023/a:1008382624724

    authors: Yao S,Howlett GJ,Norton RS

    更新日期:2000-02-01 00:00:00

  • Predicting 13Calpha chemical shifts for validation of protein structures.

    abstract::The (13)C(alpha) chemical shifts for 16,299 residues from 213 conformations of four proteins (experimentally determined by X-ray crystallography and Nuclear Magnetic Resonance methods) were computed by using a combination of approaches that includes, but is not limited to, the use of density functional theory. Initial...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-007-9162-x

    authors: Vila JA,Villegas ME,Baldoni HA,Scheraga HA

    更新日期:2007-07-01 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

    doi:10.1007/s10858-006-9024-y

    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

  • Intensity modulated HSQC and HMQC: two simple methods to measure 3J(HNH)alpha in proteins.

    abstract::Two methods for the measurement of homonuclear 3J(HNH)alpha coupling constants are described. Both HSQC- and HMQC-type experiments employ 'quantitative J-correlation', in which the coupling constant of interest is obtained from the intensity ratio of cross peaks of two spectra. The first spectrum is acquired with 3J(H...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1023/a:1008343926502

    authors: Permi P,Kilpeläinen I,Annila A,Heikkinen S

    更新日期:2000-01-01 00:00:00

  • Improved segmental isotope labeling of proteins and application to a larger protein.

    abstract::A new isotope labeling technique for peptide segments in a protein sample was recently established using the protein splicing element intein [Yamazaki et al. (1998) J. Am. Chem. Soc., 120, 5591-5592]. This method makes it possible to observe signals of a selected amino (N-) or carboxyl (C-) terminal region along a pep...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1023/a:1008308128050

    authors: Otomo T,Teruya K,Uegaki K,Yamazaki T,Kyogoku Y

    更新日期:1999-06-01 00:00:00

  • Strategy for automated NMR resonance assignment of RNA: application to 48-nucleotide K10.

    abstract::A procedure is presented for automated sequence-specific assignment of NMR resonances of uniformly [(13)C, (15)N]-labeled RNA. The method is based on a suite of four through-bond and two through-space high-dimensional automated projection spectroscopy (APSY) experiments. The approach is exemplified with a 0.3 mM sampl...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-014-9841-3

    authors: Krähenbühl B,Lukavsky P,Wider G

    更新日期:2014-08-01 00:00:00

  • Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces.

    abstract::The key to obtaining the model-free description of the dynamics of a macromolecule is the optimisation of the model-free and Brownian rotational diffusion parameters using the collected R (1), R (2) and steady-state NOE relaxation data. The problem of optimising the chi-squared value is often assumed to be trivial, ho...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-007-9214-2

    authors: d'Auvergne EJ,Gooley PR

    更新日期:2008-02-01 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

  • Identification of solvent-exposed regions of an FK-506 analog, ascomycin, bound to FKBP using a paramagnetic probe.

    abstract::The solvent-exposed regions of (U-13C)ascomycin when bound to its putative target protein, FKBP, have been identified based on the different proton longitudinal relaxation rates (R1 = 1/T1) measured in the absence and presence of the paramagnetic relaxation reagent, 4-hydroxy-2,2,6,6-tetramethyl-piperidinyl-1-oxy (HyT...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/BF02192797

    authors: Petros AM,Neri P,Fesik SW

    更新日期:1992-01-01 00:00:00

  • Database proton NMR chemical shifts for RNA signal assignment and validation.

    abstract::The Biological Magnetic Resonance Data Bank contains NMR chemical shift depositions for 132 RNAs and RNA-containing complexes. We have analyzed the (1)H NMR chemical shifts reported for non-exchangeable protons of residues that reside within A-form helical regions of these RNAs. The analysis focused on the central bas...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-012-9683-9

    authors: Barton S,Heng X,Johnson BA,Summers MF

    更新日期:2013-01-01 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

    doi:10.1007/BF00179343

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

    更新日期:1994-05-01 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

  • Biomolecular structure refinement using the GROMOS simulation software.

    abstract::For the understanding of cellular processes the molecular structure of biomolecules has to be accurately determined. Initial models can be significantly improved by structure refinement techniques. Here, we present the refinement methods and analysis techniques implemented in the GROMOS software for biomolecular simul...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-011-9534-0

    authors: Schmid N,Allison JR,Dolenc J,Eichenberger AP,Kunz AP,van Gunsteren WF

    更新日期:2011-11-01 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

  • Adiabatic TOCSY for C,C and H,H J-transfer.

    abstract::Adiabatic pulses have been widely used for broadband decoupling and spin inversion at high magnetic fields. In this paper we propose adiabatic pulses and supercycles that can be used at high magnetic fields like 800 or 900 MHz to obtain broadband TOCSY sequences with C,C or H,H J-transfer. The new mixing sequences are...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1023/a:1026785725363

    authors: Peti W,Griesinger C,Bermel W

    更新日期:2000-11-01 00:00:00

  • Two-dimensional NMR lineshape analysis of single, multiple, zero and double quantum correlation experiments.

    abstract::NMR spectroscopy provides a powerful approach for the characterisation of chemical exchange and molecular interactions by analysis of series of experiments acquired over the course of a titration measurement. The appearance of NMR resonances undergoing chemical exchange depends on the frequency difference relative to ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-019-00297-7

    authors: Waudby CA,Ouvry M,Davis B,Christodoulou J

    更新日期:2020-01-01 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

    doi:10.1007/s10858-018-0173-6

    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

  • Advances towards resonance assignments for uniformly--13C, 15N enriched bacteriorhodopsin at 18.8 T in purple membranes.

    abstract::Solid state NMR spectra from uniformly (13)C, (15)N enriched bacteriorhodospin (bR) purified from H. salinarium were acquired at 18.8 T using magic angle spinning methods. Isolated resonances of 2D (13)C-(13)C spectra exhibited 0.50-0.55 ppm line-widths. Several amino acid types could be assigned, and at least 12 out ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-008-9235-5

    authors: Varga K,Aslimovska L,Watts A

    更新日期:2008-05-01 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

  • Single Transition-to-single Transition Polarization Transfer (ST2-PT) in [15N,1H]-TROSY.

    abstract::This paper describes the use of single transition-to-single transition polarization transfer (ST2-PT) in transverse relaxation-optimized spectroscopy (TROSY), where it affords a [Formula: see text] sensitivity enhancement for kinetically stable amide 15N-1H groups in proteins. Additional, conventional improvements of ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1023/A:1008268930690

    authors: Pervushin KV,Wider G,Wüthrich K

    更新日期:1998-08-01 00:00:00

  • Trans-hydrogen bond deuterium isotope effects of A:T base pairs in DNA.

    abstract::The chemical shifts of (13)C2 of adenosine residues of DNA were observed to experience a through-space or trans-hydrogen bond isotope effect as a result of deuterium substitution at the imino hydrogen site of base-paired thymidine residues. NMR measurements of several self-complementary DNA duplexes at natural abundan...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1023/B:JNMR.0000019507.95667.3e

    authors: Vakonakis I,LiWang AC

    更新日期:2004-05-01 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

    doi:10.1007/s10858-013-9754-6

    authors: Fu Y,Wand AJ

    更新日期:2013-08-01 00:00:00

  • The NMR structure of the domain II of a chloroplastic NifU-like protein OsNifU1A.

    abstract::NifU-like proteins are a highly conserved protein that serves as the scaffold for assembly of Fe-S clusters. Chloroplastic NifU-like proteins have tandem NifU like domains, named domain I and domain II. Although the amino acid sequences of these domains are very similar to each other, the predicted functional region f...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-007-9155-9

    authors: Kumeta H,Ogura K,Asayama M,Katoh S,Katoh E,Teshima K,Inagaki F

    更新日期:2007-06-01 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

    doi:10.1007/BF00228142

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

    更新日期:1996-12-01 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

    doi:10.1023/a:1008399304450

    authors: Chang DK,Cheng SF

    更新日期:1998-11-01 00:00:00

  • Simultaneous detection of amide and methyl correlations using a time shared NMR experiment: application to binding epitope mapping.

    abstract::Simultaneous recording of different NMR parameters is an efficient way to reduce the overall experimental time and speed up structural studies of biological macromolecules. This can especially be beneficial in the case of fast NMR-based drug screening applications or for collecting NOE restraints, where prohibitively ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-007-9178-2

    authors: Würtz P,Aitio O,Hellman M,Permi P

    更新日期:2007-10-01 00:00:00