Literature DB >> 24346685

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.

Maarit Hellman1, Henni Piirainen, Veli-Pekka Jaakola, Perttu Permi.   

Abstract

NMR spectroscopy is by far the most versatile and information rich technique to study intrinsically disordered proteins (IDPs). While NMR is able to offer residue level information on structure and dynamics, assignment of chemical shift resonances in IDPs is not a straightforward process. Consequently, numerous pulse sequences and assignment protocols have been developed during past several years, targeted especially for the assignment of IDPs, including experiments that employ H(N), H(α) or (13)C detection combined with two to six indirectly detected dimensions. Here we propose two new HN-detection based pulse sequences, (HCA)CON(CAN)H and (HCA)N(CA)CO(N)H, that provide correlations with (1)H(N)(i - 1), (13)C'(i - 1) and (15)N(i), and (1)H(N)(i + 1), (13)C'(i) and (15)N(i) frequencies, respectively. Most importantly, they offer sequential links across the proline bridges and enable filling the single proline gaps during the assignment. We show that the novel experiments can efficiently complement the information available from existing HNCO and intraresidual i(HCA)CO(CA)NH pulse sequences and their concomitant usage enabled >95 % assignment of backbone resonances in cytoplasmic tail of adenosine receptor A2A in comparison to 73 % complete assignment using the HNCO/i(HCA)CO(CA)NH data alone.

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Year:  2013        PMID: 24346685     DOI: 10.1007/s10858-013-9804-0

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


  34 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.  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

3.  Optimized pathway selection in intraresidual triple-resonance experiments.

Authors:  Helena Tossavainen; Perttu Permi
Journal:  J Magn Reson       Date:  2004-10       Impact factor: 2.229

4.  HA-detected experiments for the backbone assignment of intrinsically disordered proteins.

Authors:  Sampo Mäntylahti; Olli Aitio; Maarit Hellman; Perttu Permi
Journal:  J Biomol NMR       Date:  2010-05-01       Impact factor: 2.835

5.  4D non-uniformly sampled HCBCACON and ¹J(NCα)-selective HCBCANCO experiments for the sequential assignment and chemical shift analysis of intrinsically disordered proteins.

Authors:  Jiří Nováček; Noam Y Haba; Jordan H Chill; Lukáš Zídek; Vladimír Sklenář
Journal:  J Biomol NMR       Date:  2012-05-13       Impact factor: 2.835

6.  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

7.  Sequential assignment of proline-rich regions in proteins: application to modular binding domain complexes.

Authors:  V Kanelis; L Donaldson; D R Muhandiram; D Rotin; J D Forman-Kay; L E Kay
Journal:  J Biomol NMR       Date:  2000-03       Impact factor: 2.835

8.  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

9.  Measurement of 15N-13C J couplings in staphylococcal nuclease.

Authors:  F Delaglio; D A Torchia; A Bax
Journal:  J Biomol NMR       Date:  1991-11       Impact factor: 2.835

Review 10.  A decade and a half of protein intrinsic disorder: biology still waits for physics.

Authors:  Vladimir N Uversky
Journal:  Protein Sci       Date:  2013-04-29       Impact factor: 6.725

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  7 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.  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

3.  Human adenosine A2A receptor binds calmodulin with high affinity in a calcium-dependent manner.

Authors:  Henni Piirainen; Maarit Hellman; Helena Tossavainen; Perttu Permi; Petri Kursula; Veli-Pekka Jaakola
Journal:  Biophys J       Date:  2015-02-17       Impact factor: 4.033

4.  Quarterly intrinsic disorder digest (January-February-March, 2014).

Authors:  Shelly DeForte; Krishna D Reddy; Vladimir N Uversky
Journal:  Intrinsically Disord Proteins       Date:  2016-02-12

5.  (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

6.  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

7.  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

  7 in total

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