Automated NMR assignment of protein side chain resonances using automated projection spectroscopy (APSY)

Journal of the American Chemical Society
Sebastian HillerGerhard Wider

Abstract

This paper describes an automated method for sequence-specific NMR assignment of the aliphatic resonances of protein side chains in small- and medium-sized globular proteins in aqueous solution. The method requires the recording of a five-dimensional (5D) automated projection spectroscopy (APSY-) NMR experiment and the subsequent analysis of the APSY peak list with the algorithm ALASCA (Algorithm for local and linear assignment of side chains from APSY data). The 5D APSY-HC(CC-TOCSY)CONH experiment yields 5D chemical shift correlations of aliphatic side chain C-H moieties with the backbone atoms H(N), N, and C'. A simultaneous variation of the TOCSY mixing times and the projection angles in this APSY-type TOCSY experiment gives access to all aliphatic C-H moieties in the 20 proteinogenic amino acids. The correlation peak list resulting from the 5D APSY-HC(CC-TOCSY)CONH experiment together with the backbone assignment of the protein under study is the sole input for the algorithm ALASCA that assigns carbon and proton resonances of protein side chains. The algorithm is described, and it is shown that the aliphatic parts of 17 of the 20 common amino acid side chains are assigned unambiguously, whereas the remaining three amino aci...Continue Reading

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Citations

Sep 29, 2011·Journal of Biomolecular NMR·Barbara KrähenbühlGerhard Wider
Dec 7, 2011·Journal of Biomolecular NMR·Barbara KrähenbühlGerhard Wider
Apr 30, 2013·Journal of Biomolecular NMR·Barbara KrähenbühlGerhard Wider
Jun 6, 2014·Journal of Biomolecular NMR·Barbara KrähenbühlGerhard Wider
Jan 11, 2016·Biomolecular NMR Assignments·Andrea Gabriele FlammNicolas Coudevylle
Nov 26, 2015·Progress in Nuclear Magnetic Resonance Spectroscopy·Michał NowakowskiWiktor Koźmiński
Jan 27, 2015·Biomolecular NMR Assignments·Gerald PlatzerRobert Konrat
Feb 14, 2015·Journal of Biomolecular NMR·Takumi UedaIchio Shimada
Nov 30, 2010·Journal of Molecular Biology·Namit RanjanEilika Weber-Ban
Feb 3, 2009·Journal of Magnetic Resonance·Krzysztof KazimierczukWiktor Koźmiński
Sep 20, 2011·Journal of Magnetic Resonance·Ēriks Kupče, Ray Freeman
Jan 28, 2018·Nature Communications·Thomas EvangelidisKonstantinos Tripsianes
Jun 25, 2013·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Krzysztof KazimierczukWiktor Koźmiński
Nov 16, 2018·Journal of Biomolecular NMR·Alexander KleinRasmus Linser
Dec 18, 2010·Journal of the American Chemical Society·Alvar D GossertCésar Fernández

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