Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria

Journal of Biomolecular NMR
K J FritzschingK Schmidt-Rohr

Abstract

We have determined refined multidimensional chemical shift ranges for intra-residue correlations ((13)C-(13)C, (15)N-(13)C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 (13)C chemical shifts and >3 million chemical shifts in total); these data were originally derived from the Biological Magnetic Resonance Data Bank. Using relatively simple non-parametric statistics to find peak maxima in the distributions of helix, sheet, coil and turn chemical shifts, and without the use of limited "hand-picked" data sets, we show that ~94% of the (13)C NMR data and almost all (15)N data are quite accurately referenced and assigned, with smaller standard deviations (0.2 and 0.8 ppm, respectively) than recognized previously. On the other hand, approximately 6% of the (13)C chemical shift data in the PACSY database are shown to be clearly misreferenced, mostly by ca. -2.4 ppm. The removal of the misreferenced data and other outliers by this purging by intrinsic quality criteria (PIQC) allows for reliable identification of seco...Continue Reading

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Citations

Feb 7, 2018·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Andrzej WitkowskiGiorgio Cavigiolio
Aug 12, 2018·Journal of Biomolecular NMR·Xi ChenHunter N B Moseley
Dec 2, 2020·Proceedings of the National Academy of Sciences of the United States of America·Keith J FritzschingAnn E McDermott
Feb 18, 2021·The Journal of Physical Chemistry. B·Romeo C A DubiniPetra Rovó
Feb 13, 2021·Nature Communications·Bryan D RyderLukasz A Joachimiak
Aug 10, 2021·Nature Reviews. Methods Primers·Bernd ReifMei Hong

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