Literature DB >> 26432397

Effortless assignment with 4D covariance sequential correlation maps.

Bradley J Harden1, Subrata H Mishra1, Dominique P Frueh1.   

Abstract

Traditional Nuclear Magnetic Resonance (NMR) assignment procedures for proteins rely on preliminary peak-picking to identify and label NMR signals. However, such an approach has severe limitations when signals are erroneously labeled or completely neglected. The consequences are especially grave for proteins with substantial peak overlap, and mistakes can often thwart entire projects. To overcome these limitations, we previously introduced an assignment technique that bypasses traditional pick peaking altogether. Covariance Sequential Correlation Maps (COSCOMs) transform the indirect connectivity information provided by multiple 3D backbone spectra into direct (H, N) to (H, N) correlations. Here, we present an updated method that utilizes a single four-dimensional spectrum rather than a suite of three-dimensional spectra. We demonstrate the advantages of 4D-COSCOMs relative to their 3D counterparts. We introduce improvements accelerating their calculation. We discuss practical considerations affecting their quality. And finally we showcase their utility in the context of a 52 kDa cyclization domain from a non-ribosomal peptide synthetase.
Copyright © 2015 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  4D; Backbone assignment; COSCOM; Covariance sequential correlation maps; Peak picking

Mesh:

Substances:

Year:  2015        PMID: 26432397      PMCID: PMC4628886          DOI: 10.1016/j.jmr.2015.09.007

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


  21 in total

1.  Intraresidue HNCA and COHNCA experiments for protein backbone resonance assignment.

Authors:  Bernhard Brutscher
Journal:  J Magn Reson       Date:  2002-05       Impact factor: 2.229

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.  Covariance nuclear magnetic resonance spectroscopy.

Authors:  Rafael Brüschweiler; Fengli Zhang
Journal:  J Chem Phys       Date:  2004-03-15       Impact factor: 3.488

4.  Protein assignments without peak lists using higher-order spectra.

Authors:  Gregory Benison; Donald S Berkholz; Elisar Barbar
Journal:  J Magn Reson       Date:  2007-09-20       Impact factor: 2.229

5.  Expression, purification, and characterization of HMWP2, a 229 kDa, six domain protein subunit of Yersiniabactin synthetase.

Authors:  T A Keating; D A Miller; C T Walsh
Journal:  Biochemistry       Date:  2000-04-25       Impact factor: 3.162

6.  Assignment of methyl NMR resonances of a 52 kDa protein with residue-specific 4D correlation maps.

Authors:  Subrata H Mishra; Dominique P Frueh
Journal:  J Biomol NMR       Date:  2015-05-08       Impact factor: 2.835

7.  Intraresidual HNCA: an experiment for correlating only intraresidual backbone resonances.

Authors:  Perttu Permi
Journal:  J Biomol NMR       Date:  2002-07       Impact factor: 2.835

8.  Indirect covariance NMR spectroscopy.

Authors:  Fengli Zhang; Rafael Brüschweiler
Journal:  J Am Chem Soc       Date:  2004-10-20       Impact factor: 15.419

9.  Resolution-enhanced 4D 15N/13C NOESY protein NMR spectroscopy by application of the covariance transform.

Authors:  David A Snyder; Yingqi Xu; Daiwen Yang; Rafael Brüschweiler
Journal:  J Am Chem Soc       Date:  2007-10-31       Impact factor: 15.419

10.  Quantitative covariance NMR by regularization.

Authors:  Yanbin Chen; Fengli Zhang; David Snyder; Zhehong Gan; Lei Bruschweiler-Li; Rafael Brüschweiler
Journal:  J Biomol NMR       Date:  2007-03-10       Impact factor: 2.582

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  2 in total

1.  Covariance nuclear magnetic resonance methods for obtaining protein assignments and novel correlations.

Authors:  Aswani K Kancherla; Dominique P Frueh
Journal:  Concepts Magn Reson Part A Bridg Educ Res       Date:  2018-09-16       Impact factor: 0.481

2.  Global protein dynamics as communication sensors in peptide synthetase domains.

Authors:  Subrata H Mishra; Aswani K Kancherla; Kenneth A Marincin; Guillaume Bouvignies; Santrupti Nerli; Nikolaos Sgourakis; Daniel P Dowling; Dominique P Frueh
Journal:  Sci Adv       Date:  2022-07-15       Impact factor: 14.957

  2 in total

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