Literature DB >> 22684679

Speeding up sequence specific assignment of IDPs.

Wolfgang Bermel1, Ivano Bertini, Isabella C Felli, Leonardo Gonnelli, Wiktor Koźmiński, Alessandro Piai, Roberta Pierattelli, Jan Stanek.   

Abstract

The characterization of intrinsically disordered proteins (IDPs) by NMR spectroscopy is made difficult by the extensive spectral overlaps. To overcome the intrinsic low-resolution of the spectra the introduction of high-dimensionality experiments is essential. We present here a set of high-resolution experiments based on direct (13)C-detection which proved useful in the assignment of α-synuclein, a paradigmatic IDP. In particular, we describe the implementation of 4D HCBCACON, HCCCON, HCBCANCO, 4/5D HNCACON and HNCANCO and 3/4D HCANCACO experiments, specifically tailored for spin system identification and backbone resonances sequential assignment. The use of non-uniform-sampling in the indirect dimension and of the H-flip approach to achieve longitudinal relaxation enhancement rendered the experiments very practical.

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Year:  2012        PMID: 22684679     DOI: 10.1007/s10858-012-9639-0

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


  47 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.  RefDB: a database of uniformly referenced protein chemical shifts.

Authors:  Haiyan Zhang; Stephen Neal; David S Wishart
Journal:  J Biomol NMR       Date:  2003-03       Impact factor: 2.835

3.  Optimization of 13C direct detection NMR methods.

Authors:  Nobuhisa Shimba; Helena Kovacs; Alan S Stern; Anson M Nomura; Ichio Shimada; Jeffrey C Hoch; Charles S Craik; Volker Dötsch
Journal:  J Biomol NMR       Date:  2004-10       Impact factor: 2.835

Review 4.  Atomic-level characterization of disordered protein ensembles.

Authors:  Tanja Mittag; Julie D Forman-Kay
Journal:  Curr Opin Struct Biol       Date:  2007-01-23       Impact factor: 6.809

Review 5.  Generalized Fourier transform for non-uniform sampled data.

Authors:  Krzysztof Kazimierczuk; Maria Misiak; Jan Stanek; Anna Zawadzka-Kazimierczuk; Wiktor Koźmiński
Journal:  Top Curr Chem       Date:  2012

6.  High-resolution characterization of intrinsic disorder in proteins: expanding the suite of (13)C-detected NMR spectroscopy experiments to determine key observables.

Authors:  Ivano Bertini; Isabella C Felli; Leonardo Gonnelli; M V Vasantha Kumar; Roberta Pierattelli
Journal:  Chembiochem       Date:  2011-10-17       Impact factor: 3.164

7.  A new method for purification of recombinant human alpha-synuclein in Escherichia coli.

Authors:  Chunjuan Huang; Guoping Ren; Hui Zhou; Chih-chen Wang
Journal:  Protein Expr Purif       Date:  2005-03-30       Impact factor: 1.650

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

Authors:  Anna Zawadzka-Kazimierczuk; Wiktor Koźmiński; Hana Sanderová; Libor Krásný
Journal:  J Biomol NMR       Date:  2012-02-17       Impact factor: 2.835

9.  13C direct detection experiments on the paramagnetic oxidized monomeric copper, zinc superoxide dismutase.

Authors:  Wolfgang Bermel; Ivano Bertini; Isabella C Felli; Rainer Kümmerle; Roberta Pierattelli
Journal:  J Am Chem Soc       Date:  2003-12-31       Impact factor: 15.419

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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  32 in total

1.  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

2.  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

3.  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

4.  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

5.  A reduced dimensionality NMR pulse sequence and an efficient protocol for unambiguous assignment in intrinsically disordered proteins.

Authors:  Jithender G Reddy; Ramakrishna V Hosur
Journal:  J Biomol NMR       Date:  2014-05-23       Impact factor: 2.835

6.  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

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

Authors:  Jinfa Ying; C Ashley Barnes; John M Louis; Ad Bax
Journal:  J Biomol NMR       Date:  2019-08-12       Impact factor: 2.835

8.  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

9.  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

10.  BEST-TROSY experiments for time-efficient sequential resonance assignment of large disordered proteins.

Authors:  Zsofia Solyom; Melanie Schwarten; Leonhard Geist; Robert Konrat; Dieter Willbold; Bernhard Brutscher
Journal:  J Biomol NMR       Date:  2013-02-24       Impact factor: 2.835

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