Literature DB >> 21277815

Sparsely sampled high-resolution 4-D experiments for efficient backbone resonance assignment of disordered proteins.

Jie Wen1, Jihui Wu, Pei Zhou.   

Abstract

Intrinsically disordered proteins (IDPs) play important roles in many critical cellular processes. Due to their limited chemical shift dispersion, IDPs often require four pairs of resonance connectivities (H(α), C(α), C(β) and CO) for establishing sequential backbone assignment. Because most conventional 4-D triple-resonance experiments share an overlapping C(α) evolution period, combining existing 4-D experiments does not offer an optimal solution for non-redundant collection of a complete set of backbone resonances. Using alternative chemical shift evolution schemes, we propose a new pair of 4-D triple-resonance experiments--HA(CA)CO(CA)NH/HA(CA)CONH--that complement the 4-D HNCACB/HN(CO)CACB experiments to provide complete backbone resonance information. Collection of high-resolution 4-D spectra with sparse sampling and FFT-CLEAN processing enables efficient acquisition and assignment of complete backbone resonances of IDPs. Importantly, because the CLEAN procedure iteratively identifies resonance signals and removes their associating aliasing artifacts, it greatly reduces the dependence of the reconstruction quality on sampling schemes and produces high-quality spectra even with less-than-optimal sampling schemes.
Copyright © 2010 Elsevier Inc. All rights reserved.

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Year:  2011        PMID: 21277815      PMCID: PMC3048770          DOI: 10.1016/j.jmr.2010.12.012

Source DB:  PubMed          Journal:  J Magn Reson        ISSN: 1090-7807            Impact factor:   2.229


  27 in total

1.  (4,2)D Projection--reconstruction experiments for protein backbone assignment: application to human carbonic anhydrase II and calbindin D(28K).

Authors:  Ronald A Venters; Brian E Coggins; Doug Kojetin; John Cavanagh; Pei Zhou
Journal:  J Am Chem Soc       Date:  2005-06-22       Impact factor: 15.419

2.  Automated projection spectroscopy (APSY).

Authors:  Sebastian Hiller; Francesco Fiorito; Kurt Wüthrich; Gerhard Wider
Journal:  Proc Natl Acad Sci U S A       Date:  2005-07-25       Impact factor: 11.205

3.  Sampling of the NMR time domain along concentric rings.

Authors:  Brian E Coggins; Pei Zhou
Journal:  J Magn Reson       Date:  2006-10-27       Impact factor: 2.229

4.  Optimized 3D-NMR sampling for resonance assignment of partially unfolded proteins.

Authors:  Nicolas Pannetier; Klaartje Houben; Laurence Blanchard; Dominique Marion
Journal:  J Magn Reson       Date:  2007-01-23       Impact factor: 2.229

5.  Sequence-specific resonance assignment of soluble nonglobular proteins by 7D APSY-NMR spectroscopy.

Authors:  Sebastian Hiller; Christian Wasmer; Gerhard Wider; Kurt Wüthrich
Journal:  J Am Chem Soc       Date:  2007-08-11       Impact factor: 15.419

6.  Use of selective C alpha pulses for improvement of HN(CA)CO-D and HN(COCA)NH-D experiments.

Authors:  H Matsuo; E Kupce; H Li; G Wagner
Journal:  J Magn Reson B       Date:  1996-05

7.  Fast acquisition of high resolution 4-D amide-amide NOESY with diagonal suppression, sparse sampling and FFT-CLEAN.

Authors:  Jon W Werner-Allen; Brian E Coggins; Pei Zhou
Journal:  J Magn Reson       Date:  2010-02-21       Impact factor: 2.229

8.  A large intrinsically disordered region in SKIP and its disorder-order transition induced by PPIL1 binding revealed by NMR.

Authors:  Xingsheng Wang; Shaojie Zhang; Jiahai Zhang; Xiaojuan Huang; Chao Xu; Weiwei Wang; Zhijun Liu; Jihui Wu; Yunyu Shi
Journal:  J Biol Chem       Date:  2009-12-09       Impact factor: 5.157

9.  High resolution 4-D spectroscopy with sparse concentric shell sampling and FFT-CLEAN.

Authors:  Brian E Coggins; Pei Zhou
Journal:  J Biomol NMR       Date:  2008-10-14       Impact factor: 2.835

Review 10.  Intrinsically disordered proteins in human diseases: introducing the D2 concept.

Authors:  Vladimir N Uversky; Christopher J Oldfield; A Keith Dunker
Journal:  Annu Rev Biophys       Date:  2008       Impact factor: 12.981

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  10 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.  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

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.  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

5.  Exploring signal-to-noise ratio and sensitivity in non-uniformly sampled multi-dimensional NMR spectra.

Authors:  Sven G Hyberts; Scott A Robson; Gerhard Wagner
Journal:  J Biomol NMR       Date:  2012-12-29       Impact factor: 2.835

6.  Application of iterative soft thresholding for fast reconstruction of NMR data non-uniformly sampled with multidimensional Poisson Gap scheduling.

Authors:  Sven G Hyberts; Alexander G Milbradt; Andreas B Wagner; Haribabu Arthanari; Gerhard Wagner
Journal:  J Biomol NMR       Date:  2012-02-14       Impact factor: 2.835

7.  The Functionally Important N-Terminal Half of Fission Yeast Mid1p Anillin Is Intrinsically Disordered and Undergoes Phase Separation.

Authors:  Moon Chatterjee; Thomas D Pollard
Journal:  Biochemistry       Date:  2019-06-25       Impact factor: 3.162

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.  NMR determines transient structure and dynamics in the disordered C-terminal domain of WASp interacting protein.

Authors:  Noam Y Haba; Renana Gross; Jiri Novacek; Hadassa Shaked; Lukas Zidek; Mira Barda-Saad; Jordan H Chill
Journal:  Biophys J       Date:  2013-07-16       Impact factor: 4.033

10.  Rapid protein global fold determination using ultrasparse sampling, high-dynamic range artifact suppression, and time-shared NOESY.

Authors:  Brian E Coggins; Jonathan W Werner-Allen; Anthony Yan; Pei Zhou
Journal:  J Am Chem Soc       Date:  2012-09-21       Impact factor: 15.419

  10 in total

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