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Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution

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Abstract

Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues. The contributions from the neighboring residues are typically removed by using neighbor correction factors determined based on each residue’s effect on glycine chemical shifts. Due to its unusual conformational freedom, glycine may be particularly unrepresentative for the remaining residue types. In this study, we use random coil peptides containing glutamine instead of glycine to determine the random coil chemical shifts and the neighbor correction factors. The resulting correction factors correlate to changes in the populations of the major wells in the Ramachandran plot, which demonstrates that changes in the conformational ensemble are an important source of neighbor effects in disordered proteins. Glutamine derived random coil chemical shifts and correction factors modestly improve our ability to predict 13C chemical shifts of intrinsically disordered proteins compared to existing datasets, and may thus improve the identification of small populations of transient structure in disordered proteins.

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Acknowledgments

This work was supported by The John and Birthe Meyer Foundation, the Carlsberg Foundation grant number 2008-01-0368 and The Danish Natural Research Council grant numbers 272-08-0500 (F.M.P). We thank Kamil Tamiola and Frans Mulder (University of Groningen) for sharing their data for comparison of the random coil data sets and Gitte Wolfsberg Haxholm and Birthe B. Kragelund for valuable discussions and critical comments to the manuscript.

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Correspondence to Flemming M. Poulsen.

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Kjaergaard, M., Poulsen, F.M. Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution. J Biomol NMR 50, 157–165 (2011). https://doi.org/10.1007/s10858-011-9508-2

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