Literature DB >> 25577242

Easy and unambiguous sequential assignments of intrinsically disordered proteins by correlating the backbone 15N or 13C' chemical shifts of multiple contiguous residues in highly resolved 3D spectra.

Yuichi Yoshimura1, Natalia V Kulminskaya, Frans A A Mulder.   

Abstract

Sequential resonance assignment strategies are typically based on matching one or two chemical shifts of adjacent residues. However, resonance overlap often leads to ambiguity in resonance assignments in particular for intrinsically disordered proteins. We investigated the potential of establishing connectivity through the three-bond couplings between sequentially adjoining backbone carbonyl carbon nuclei, combined with semi-constant time chemical shift evolution, for resonance assignments of small folded and larger unfolded proteins. Extended sequential connectivity strongly lifts chemical shift degeneracy of the backbone nuclei in disordered proteins. We show here that 3D (H)N(COCO)NH and (HN)CO(CO)NH experiments with relaxation-optimized multiple pulse mixing correlate up to seven adjacent backbone amide nitrogen or carbonyl carbon nuclei, respectively, and connections across proline residues are also obtained straightforwardly. Multiple, recurrent long-range correlations with ultra-high resolution allow backbone (1)H(N), (15)N(H), and (13)C' resonance assignments to be completed from a single pair of 3D experiments.

Entities:  

Mesh:

Substances:

Year:  2015        PMID: 25577242     DOI: 10.1007/s10858-014-9890-7

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.835


  38 in total

Review 1.  Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm.

Authors:  P E Wright; H J Dyson
Journal:  J Mol Biol       Date:  1999-10-22       Impact factor: 5.469

2.  Temperature dependence of anisotropic protein backbone dynamics.

Authors:  Tianzhi Wang; Sheng Cai; Erik R P Zuiderweg
Journal:  J Am Chem Soc       Date:  2003-07-16       Impact factor: 15.419

3.  Site-specific variations of carbonyl chemical shift anisotropies in proteins.

Authors:  Phineus R L Markwick; Michael Sattler
Journal:  J Am Chem Soc       Date:  2004-09-22       Impact factor: 15.419

Review 4.  Disordered proteins studied by chemical shifts.

Authors:  Magnus Kjaergaard; Flemming M Poulsen
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2011-10-12       Impact factor: 9.795

5.  Recommendations for the presentation of NMR structures of proteins and nucleic acids. IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy.

Authors:  J L Markley; A Bax; Y Arata; C W Hilbers; R Kaptein; B D Sykes; P E Wright; K Wüthrich
Journal:  J Biomol NMR       Date:  1998-07       Impact factor: 2.835

6.  NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

Authors:  F Delaglio; S Grzesiek; G W Vuister; G Zhu; J Pfeifer; A Bax
Journal:  J Biomol NMR       Date:  1995-11       Impact factor: 2.835

7.  NMR experiments for resonance assignments of 13C, 15N doubly-labeled flexible polypeptides: application to the human prion protein hPrP(23-230).

Authors:  A Liu; R Riek; G Wider; C von Schroetter; R Zahn; K Wüthrich
Journal:  J Biomol NMR       Date:  2000-02       Impact factor: 2.835

8.  Low-resolution structure of a vesicle disrupting α-synuclein oligomer that accumulates during fibrillation.

Authors:  Lise Giehm; Dmitri I Svergun; Daniel E Otzen; Bente Vestergaard
Journal:  Proc Natl Acad Sci U S A       Date:  2011-02-07       Impact factor: 11.205

9.  Chemical shift dispersion and secondary structure prediction in unfolded and partly folded proteins.

Authors:  J Yao; H J Dyson; P E Wright
Journal:  FEBS Lett       Date:  1997-12-15       Impact factor: 4.124

10.  A novel approach for sequential assignment of 1H, 13C, and 15N spectra of proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin.

Authors:  M Ikura; L E Kay; A Bax
Journal:  Biochemistry       Date:  1990-05-15       Impact factor: 3.162

View more
  10 in total

1.  Asynchronous through-bond homonuclear isotropic mixing: application to carbon-carbon transfer in perdeuterated proteins under MAS.

Authors:  Natalia Kulminskaya; Suresh Kumar Vasa; Karin Giller; Stefan Becker; Rasmus Linser
Journal:  J Biomol NMR       Date:  2015-08-30       Impact factor: 2.835

2.  Protein residue linking in a single spectrum for magic-angle spinning NMR assignment.

Authors:  Loren B Andreas; Jan Stanek; Tanguy Le Marchand; Andrea Bertarello; Diane Cala-De Paepe; Daniela Lalli; Magdaléna Krejčíková; Camille Doyen; Carl Öster; Benno Knott; Sebastian Wegner; Frank Engelke; Isabella C Felli; Roberta Pierattelli; Nicholas E Dixon; Lyndon Emsley; Torsten Herrmann; Guido Pintacuda
Journal:  J Biomol NMR       Date:  2015-06-16       Impact factor: 2.835

3.  MOAG-4 promotes the aggregation of α-synuclein by competing with self-protective electrostatic interactions.

Authors:  Yuichi Yoshimura; Mats A Holmberg; Predrag Kukic; Camilla B Andersen; Alejandro Mata-Cabana; S Fabio Falsone; Michele Vendruscolo; Ellen A A Nollen; Frans A A Mulder
Journal:  J Biol Chem       Date:  2017-03-23       Impact factor: 5.157

4.  15N detection harnesses the slow relaxation property of nitrogen: Delivering enhanced resolution for intrinsically disordered proteins.

Authors:  Sandeep Chhabra; Patrick Fischer; Koh Takeuchi; Abhinav Dubey; Joshua J Ziarek; Andras Boeszoermenyi; Daniel Mathieu; Wolfgang Bermel; Norman E Davey; Gerhard Wagner; Haribabu Arthanari
Journal:  Proc Natl Acad Sci U S A       Date:  2018-02-05       Impact factor: 11.205

5.  The LC8-RavP ensemble Structure Evinces A Role for LC8 in Regulating Lyssavirus Polymerase Functionality.

Authors:  Nathan E Jespersen; Cedric Leyrat; Francine C Gérard; Jean-Marie Bourhis; Danielle Blondel; Marc Jamin; Elisar Barbar
Journal:  J Mol Biol       Date:  2019-10-18       Impact factor: 5.469

6.  (13)C-detected NMR experiments for automatic resonance assignment of IDPs and multiple-fixing SMFT processing.

Authors:  Paweł Dziekański; Katarzyna Grudziąż; Patrik Jarvoll; Wiktor Koźmiński; Anna Zawadzka-Kazimierczuk
Journal:  J Biomol NMR       Date:  2015-04-23       Impact factor: 2.835

7.  Five and four dimensional experiments for robust backbone resonance assignment of large intrinsically disordered proteins: application to Tau3x protein.

Authors:  Szymon Żerko; Piotr Byrski; Paweł Włodarczyk-Pruszyński; Michał Górka; Karin Ledolter; Eliezer Masliah; Robert Konrat; Wiktor Koźmiński
Journal:  J Biomol NMR       Date:  2016-07-18       Impact factor: 2.835

8.  Six- and seven-dimensional experiments by combination of sparse random sampling and projection spectroscopy dedicated for backbone resonance assignment of intrinsically disordered proteins.

Authors:  Szymon Żerko; Wiktor Koźmiński
Journal:  J Biomol NMR       Date:  2015-09-24       Impact factor: 2.835

9.  Musashi-1: An Example of How Polyalanine Tracts Contribute to Self-Association in the Intrinsically Disordered Regions of RNA-Binding Proteins.

Authors:  Tsai-Chen Chen; Jie-Rong Huang
Journal:  Int J Mol Sci       Date:  2020-03-26       Impact factor: 5.923

10.  HACANCOi: a new Hα-detected experiment for backbone resonance assignment of intrinsically disordered proteins.

Authors:  Mikael Karjalainen; Helena Tossavainen; Maarit Hellman; Perttu Permi
Journal:  J Biomol NMR       Date:  2020-10-28       Impact factor: 2.835

  10 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.