Literature DB >> 22580891

4D non-uniformly sampled HCBCACON and ¹J(NCα)-selective HCBCANCO experiments for the sequential assignment and chemical shift analysis of intrinsically disordered proteins.

Jiří Nováček1, Noam Y Haba, Jordan H Chill, Lukáš Zídek, Vladimír Sklenář.   

Abstract

A pair of 4D NMR experiments for the backbone assignment of disordered proteins is presented. The experiments exploit (13)C direct detection and non-uniform sampling of the indirectly detected dimensions, and provide correlations of the aliphatic proton (H(α), and H(β)) and carbon (C(α), C(β)) resonance frequencies to the protein backbone. Thus, all the chemical shifts regularly used to map the transient secondary structure motifs in the intrinsically disordered proteins (H(α), C(α), C(β), C', and N) can be extracted from each spectrum. Compared to the commonly used assignment strategy based on matching the C(α) and C(β) chemical shifts, inclusion of the H(α) and H(β) provides up to three extra resonance frequencies that decrease the chance of ambiguous assignment. The experiments were successfully applied to the original assignment of a 12.8 kDa intrinsically disordered protein having a high content of proline residues (26 %) in the sequence.

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Year:  2012        PMID: 22580891     DOI: 10.1007/s10858-012-9631-8

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


  64 in total

1.  A novel approach for the sequential backbone assignment of larger proteins: selective intra-HNCA and DQ-HNCA.

Authors:  Daniel Nietlispach; Yutaka Ito; Ernest D Laue
Journal:  J Am Chem Soc       Date:  2002-09-18       Impact factor: 15.419

2.  Accelerated acquisition of high resolution triple-resonance spectra using non-uniform sampling and maximum entropy reconstruction.

Authors:  David Rovnyak; Dominique P Frueh; Mallika Sastry; Zhen-Yu J Sun; Alan S Stern; Jeffrey C Hoch; Gerhard Wagner
Journal:  J Magn Reson       Date:  2004-09       Impact factor: 2.229

3.  Non-uniform frequency domain for optimal exploitation of non-uniform sampling.

Authors:  Krzysztof Kazimierczuk; Anna Zawadzka-Kazimierczuk; Wiktor Koźmiński
Journal:  J Magn Reson       Date:  2010-05-25       Impact factor: 2.229

4.  Spectral reconstruction methods in fast NMR: reduced dimensionality, random sampling and maximum entropy.

Authors:  Mehdi Mobli; Alan S Stern; Jeffrey C Hoch
Journal:  J Magn Reson       Date:  2006-07-11       Impact factor: 2.229

Review 5.  Regulation of cytoskeletal dynamics at the immune synapse: new stars join the actin troupe.

Authors:  Daniel D Billadeau; Janis K Burkhardt
Journal:  Traffic       Date:  2006-09-19       Impact factor: 6.215

6.  Analysis of non-uniformly sampled spectra with multi-dimensional decomposition.

Authors:  Vladislav Yu Orekhov; Victor A Jaravine
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2011-02-24       Impact factor: 9.795

7.  Maximum Entropy Spectral Reconstruction of Non-Uniformly Sampled Data.

Authors:  Mehdi Mobli; Jeffrey C Hoch
Journal:  Concepts Magn Reson Part A Bridg Educ Res       Date:  2008-11-01       Impact factor: 0.481

8.  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

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

Review 10.  Biophysical characterization of intrinsically disordered proteins.

Authors:  David Eliezer
Journal:  Curr Opin Struct Biol       Date:  2009-01-21       Impact factor: 6.809

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  18 in total

1.  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

2.  Bridge over troubled proline: assignment of intrinsically disordered proteins using (HCA)CON(CAN)H and (HCA)N(CA)CO(N)H experiments concomitantly with HNCO and i(HCA)CO(CA)NH.

Authors:  Maarit Hellman; Henni Piirainen; Veli-Pekka Jaakola; Perttu Permi
Journal:  J Biomol NMR       Date:  2013-12-18       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.  Direct correlation of consecutive C'-N groups in proteins: a method for the assignment of intrinsically disordered proteins.

Authors:  David Pantoja-Uceda; Jorge Santoro
Journal:  J Biomol NMR       Date:  2013-08-09       Impact factor: 2.835

5.  High-dimensionality 13C direct-detected NMR experiments for the automatic assignment of intrinsically disordered proteins.

Authors:  Wolfgang Bermel; Isabella C Felli; Leonardo Gonnelli; Wiktor Koźmiński; Alessandro Piai; Roberta Pierattelli; Anna Zawadzka-Kazimierczuk
Journal:  J Biomol NMR       Date:  2013-11-08       Impact factor: 2.835

6.  Taking Simultaneous Snapshots of Intrinsically Disordered Proteins in Action.

Authors:  Marco Schiavina; Maria Grazia Murrali; Letizia Pontoriero; Valerio Sainati; Rainer Kümmerle; Wolfgang Bermel; Roberta Pierattelli; Isabella C Felli
Journal:  Biophys J       Date:  2019-05-23       Impact factor: 4.033

7.  Improving the chemical shift dispersion of multidimensional NMR spectra of intrinsically disordered proteins.

Authors:  Wolfgang Bermel; Marta Bruix; Isabella C Felli; Vasantha Kumar M V; Roberta Pierattelli; Soraya Serrano
Journal:  J Biomol NMR       Date:  2013-01-12       Impact factor: 2.835

8.  New 13C-detected experiments for the assignment of intrinsically disordered proteins.

Authors:  David Pantoja-Uceda; Jorge Santoro
Journal:  J Biomol NMR       Date:  2014-04-04       Impact factor: 2.835

9.  Generating NMR chemical shift assignments of intrinsically disordered proteins using carbon-detected NMR methods.

Authors:  Debashish Sahu; Monique Bastidas; Scott A Showalter
Journal:  Anal Biochem       Date:  2013-12-10       Impact factor: 3.365

10.  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

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