Automated amino acid side-chain NMR assignment of proteins using (13)C- and (15)N-resolved 3D [ (1)H, (1)H]-NOESY.

Journal of Biomolecular NMR
Francesco FioritoKurt Wüthrich

Abstract

ASCAN is a new algorithm for automatic sequence-specific NMR assignment of amino acid side-chains in proteins, which uses as input the primary structure of the protein, chemical shift lists of (1)H(N), (15)N, (13)C(alpha), (13)C(beta) and possibly (1)H(alpha) from the previous polypeptide backbone assignment, and one or several 3D (13)C- or (15)N-resolved [(1)H,(1)H]-NOESY spectra. ASCAN has also been laid out for the use of TOCSY-type data sets as supplementary input. The program assigns new resonances based on comparison of the NMR signals expected from the chemical structure with the experimentally observed NOESY peak patterns. The core parts of the algorithm are a procedure for generating expected peak positions, which is based on variable combinations of assigned and unassigned resonances that arise for the different amino acid types during the assignment procedure, and a corresponding set of acceptance criteria for assignments based on the NMR experiments used. Expected patterns of NOESY cross peaks involving unassigned resonances are generated using the list of previously assigned resonances, and tentative chemical shift values for the unassigned signals taken from the BMRB statistics for globular proteins. Use of this a...Continue Reading

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Citations

Jan 13, 2009·Journal of Biomolecular NMR·Mike P Williamson, C Jeremy Craven
Mar 31, 2011·Journal of Biomolecular NMR·Teppei IkeyaPeter Güntert
Jun 28, 2011·Journal of Biomolecular NMR·Jianyang ZengBruce Randall Donald
Jul 4, 2012·Journal of Biomolecular NMR·Pedro SerranoKurt Wüthrich
Oct 12, 2012·Journal of Structural and Functional Genomics·Dinesh KumarRamakrishna V Hosur
Mar 18, 2011·Quarterly Reviews of Biophysics·Paul Guerry, Torsten Herrmann
Dec 14, 2011·Nucleic Acids Research·Thomas VeithEnrico Schleiff
Jun 10, 2011·Nucleic Acids Research·Stephen Martin-TumaszSamuel E Butcher
Oct 15, 2010·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Kristaps JaudzemsKurt Wüthrich
Oct 15, 2010·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Biswaranjan MohantyKurt Wüthrich
Oct 15, 2010·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Kurt Wüthrich
Oct 15, 2010·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Pedro SerranoKurt Wüthrich
Aug 17, 2010·Journal of Molecular Biology·Margaret A JohnsonKurt Wüthrich
Aug 1, 2015·Chemistry : a European Journal·Tatiana DidenkoKurt Wüthrich
Jul 17, 2015·Protein Science : a Publication of the Protein Society·Samit Kumar DuttaKurt Wüthrich
Jul 22, 2010·Magnetic Resonance in Chemistry : MRC·Clément PontoizeauLyndon Emsley
Apr 27, 2011·Protein Science : a Publication of the Protein Society· Atia-tul-WahabKurt Wüthrich
Apr 7, 2016·Acta Crystallographica. Section D, Structural Biology·Galina A StepanyukJames R Williamson
Jun 9, 2015·Magnetic Resonance in Chemistry : MRC·Andrés M CastilloJulien Wist
Apr 17, 2009·Structure·Blair R SzymczynaJames R Williamson
May 25, 2010·Journal of Molecular Biology·Margaret A JohnsonKurt Wüthrich
May 20, 2014·Journal of Molecular Biology·Pedro SerranoKurt Wüthrich
Nov 29, 2014·Journal of Biomolecular NMR·Biswaranjan MohantyKurt Wüthrich
Apr 16, 2016·Protein Science : a Publication of the Protein Society·Christine BeuckPedro Serrano
Jun 26, 2017·Journal of Molecular Biology·Maria BirkouGeorgios A Spyroulias
May 13, 2020·Natural Product Communications·Andrew J StaupMargaret A Johnson
Nov 28, 2014·Journal of Biomolecular NMR·Samit Kumar DuttaKurt Wüthrich
Jun 6, 2017·Protein Science : a Publication of the Protein Society·Robert G HammondMargaret A Johnson

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