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Comparative analysis of 13C chemical shifts of β-sheet amyloid proteins and outer membrane proteins

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Abstract

Cross-β amyloid fibrils and membrane-bound β-barrels are two important classes of β-sheet proteins. To investigate whether there are systematic differences in the backbone and sidechain conformations of these two families of proteins, here we analyze the 13C chemical shifts of 17 amyloid proteins and 7 β-barrel membrane proteins whose high-resolution structures have been determined by NMR. These 24 proteins contain 373 β-sheet residues in amyloid fibrils and 521 β-sheet residues in β-barrel membrane proteins. The 13C chemical shifts are shown in 2D 13C–13C correlation maps, and the amino acid residues are categorized by two criteria: (1) whether they occur in β-strand segments or in loops and turns; (2) whether they are water-exposed or dry, facing other residues or lipids. We also examine the abundance of each amino acid in amyloid proteins and β-barrels and compare the sidechain rotameric populations. The 13C chemical shifts indicate that hydrophobic methyl-rich residues and aromatic residues exhibit larger static sidechain conformational disorder in amyloid fibrils than in β-barrels. In comparison, hydroxyl- and amide-containing polar residues have more ordered sidechains and more ordered backbones in amyloid fibrils than in β-barrels. These trends can be explained by steric zipper interactions between β-sheet planes in cross-β fibrils, and by the interactions of β-barrel residues with lipid and water in the membrane. These conformational trends should be useful for structural analysis of amyloid fibrils and β-barrels based principally on NMR chemical shifts.

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Data availability

The complete chemical shift datasets analyzed in the current study are available from Mei Hong at meihong@mit.edu upon request.

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Acknowledgements

This work is supported by NIH Grant AG059661 to M.H. and an NIH Ruth L. Kirschstein Individual National Research Service Award (1F31AI133989) to M.D.G.

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  1. Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA

    Noah H. Somberg, Martin D. Gelenter & Mei Hong

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  1. Noah H. Somberg
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  2. Martin D. Gelenter
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Correspondence to Mei Hong.

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Somberg, N.H., Gelenter, M.D. & Hong, M. Comparative analysis of 13C chemical shifts of β-sheet amyloid proteins and outer membrane proteins. J Biomol NMR 75, 151–166 (2021). https://doi.org/10.1007/s10858-021-00364-y

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