Literature DB >> 22350953

High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins.

Anna Zawadzka-Kazimierczuk1, Wiktor Koźmiński, Hana Sanderová, Libor Krásný.   

Abstract

Four novel 5D (HACA(N)CONH, HNCOCACB, (HACA)CON(CA)CONH, (H)NCO(NCA)CONH), and one 6D ((H)NCO(N)CACONH) NMR pulse sequences are proposed. The new experiments employ non-uniform sampling that enables achieving high resolution in indirectly detected dimensions. The experiments facilitate resonance assignment of intrinsically disordered proteins. The novel pulse sequences were successfully tested using δ subunit (20 kDa) of Bacillus subtilis RNA polymerase that has an 81-amino acid disordered part containing various repetitive sequences.

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Year:  2012        PMID： 22350953      PMCID： PMC3315646          DOI： 10.1007/s10858-012-9613-x

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


  20 in total

Review 1.  Nuclear magnetic resonance methods for elucidation of structure and dynamics in disordered states.

Authors:  H J Dyson; P E Wright
Journal:  Methods Enzymol       Date:  2001       Impact factor: 1.600

2.  Speeding up three-dimensional protein NMR experiments to a few minutes.

Authors:  Paul Schanda; Hélène Van Melckebeke; Bernhard Brutscher
Journal:  J Am Chem Soc       Date:  2006-07-19       Impact factor: 15.419

3.  A set of BEST triple-resonance experiments for time-optimized protein resonance assignment.

Authors:  Ewen Lescop; Paul Schanda; Bernhard Brutscher
Journal:  J Magn Reson       Date:  2007-04-13       Impact factor: 2.229

4.  Narrow peaks and high dimensionalities: exploiting the advantages of random sampling.

Authors:  Krzysztof Kazimierczuk; Anna Zawadzka; Wiktor Koźmiński
Journal:  J Magn Reson       Date:  2009-01-13       Impact factor: 2.229

5.  H-start for exclusively heteronuclear NMR spectroscopy: the case of intrinsically disordered proteins.

Authors:  Wolfgang Bermel; Ivano Bertini; Veronika Csizmok; Isabella C Felli; Roberta Pierattelli; Peter Tompa
Journal:  J Magn Reson       Date:  2009-03-04       Impact factor: 2.229

6.  Prevalent structural disorder in E. coli and S. cerevisiae proteomes.

Authors:  Peter Tompa; Zsuzsanna Dosztanyi; Istvan Simon
Journal:  J Proteome Res       Date:  2006-08       Impact factor: 4.466

Review 7.  Intrinsically unstructured proteins and their functions.

Authors:  H Jane Dyson; Peter E Wright
Journal:  Nat Rev Mol Cell Biol       Date:  2005-03       Impact factor: 94.444

8.  Amino acid type determination in the sequential assignment procedure of uniformly 13C/15N-enriched proteins.

Authors:  S Grzesiek; A Bax
Journal:  J Biomol NMR       Date:  1993-03       Impact factor: 2.835

9.  Prediction and functional analysis of native disorder in proteins from the three kingdoms of life.

Authors:  J J Ward; J S Sodhi; L J McGuffin; B F Buxton; D T Jones
Journal:  J Mol Biol       Date:  2004-03-26       Impact factor: 5.469

10.  Optimization of random time domain sampling in multidimensional NMR.

Authors:  Krzysztof Kazimierczuk; Anna Zawadzka; Wiktor Koźmiński
Journal:  J Magn Reson       Date:  2008-02-12       Impact factor: 2.229
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  25 in total

1.  Speeding up sequence specific assignment of IDPs.

Authors:  Wolfgang Bermel; Ivano Bertini; Isabella C Felli; Leonardo Gonnelli; Wiktor Koźmiński; Alessandro Piai; Roberta Pierattelli; Jan Stanek
Journal:  J Biomol NMR       Date:  2012-06-10       Impact factor: 2.835

2.  HN-NCA heteronuclear TOCSY-NH experiment for (1)H(N) and (15)N sequential correlations in ((13)C, (15)N) labelled intrinsically disordered proteins.

Authors:  Christoph Wiedemann; Nishit Goradia; Sabine Häfner; Christian Herbst; Matthias Görlach; Oliver Ohlenschläger; Ramadurai Ramachandran
Journal:  J Biomol NMR       Date:  2015-08-18       Impact factor: 2.835

3.  Efficient protocol for backbone and side-chain assignments of large, intrinsically disordered proteins: transient secondary structure analysis of 49.2 kDa microtubule associated protein 2c.

Authors:  Jiří Nováček; Lubomír Janda; Radka Dopitová; Lukáš Žídek; Vladimír Sklenář
Journal:  J Biomol NMR       Date:  2013-07-23       Impact factor: 2.835

4.  A six-dimensional alpha proton detection-based APSY experiment for backbone assignment of intrinsically disordered proteins.

Authors:  Xuejun Yao; Stefan Becker; Markus Zweckstetter
Journal:  J Biomol NMR       Date:  2014-11-04       Impact factor: 2.835

5.  TSAR: a program for automatic resonance assignment using 2D cross-sections of high dimensionality, high-resolution spectra.

Authors:  Anna Zawadzka-Kazimierczuk; Wiktor Koźmiński; Martin Billeter
Journal:  J Biomol NMR       Date:  2012-07-18       Impact factor: 2.835

6.  Site-specific NMR mapping and time-resolved monitoring of serine and threonine phosphorylation in reconstituted kinase reactions and mammalian cell extracts.

Authors:  Francois-Xavier Theillet; Honor May Rose; Stamatios Liokatis; Andres Binolfi; Rossukon Thongwichian; Marchel Stuiver; Philipp Selenko
Journal:  Nat Protoc       Date:  2013-06-27       Impact factor: 13.491

7.  Resonance assignment of disordered protein with repetitive and overlapping sequence using combinatorial approach reveals initial structural propensities and local restrictions in the denatured state.

Authors:  Nikita Malik; Ashutosh Kumar
Journal:  J Biomol NMR       Date:  2016-09-01       Impact factor: 2.835

8.  13C APSY-NMR for sequential assignment of intrinsically disordered proteins.

Authors:  Maria Grazia Murrali; Marco Schiavina; Valerio Sainati; Wolfgang Bermel; Roberta Pierattelli; Isabella C Felli
Journal:  J Biomol NMR       Date:  2018-02-28       Impact factor: 2.835

9.  Just a Flexible Linker? The Structural and Dynamic Properties of CBP-ID4 Revealed by NMR Spectroscopy.

Authors:  Alessandro Piai; Eduardo O Calçada; Thomas Tarenzi; Alessandro Del Grande; Mihaly Varadi; Peter Tompa; Isabella C Felli; Roberta Pierattelli
Journal:  Biophys J       Date:  2016-01-19       Impact factor: 4.033

10.  Finding Our Way in the Dark Proteome.

Authors:  Asmit Bhowmick; David H Brookes; Shane R Yost; H Jane Dyson; Julie D Forman-Kay; Daniel Gunter; Martin Head-Gordon; Gregory L Hura; Vijay S Pande; David E Wemmer; Peter E Wright; Teresa Head-Gordon
Journal:  J Am Chem Soc       Date:  2016-07-19       Impact factor: 15.419
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