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A prevalent intraresidue hydrogen bond stabilizes proteins

Nature Chemical Biology volume 12, pages 1084–1088 (2016)Cite this article

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Abstract

Current limitations in de novo protein structure prediction and design suggest an incomplete understanding of the interactions that govern protein folding. Here we demonstrate that previously unappreciated hydrogen bonds occur within proteins between the amide proton and carbonyl oxygen of the same residue. Quantum calculations, infrared spectroscopy, and nuclear magnetic resonance spectroscopy show that these interactions share hallmark features of canonical hydrogen bonds. Biophysical analyses demonstrate that selective attenuation or enhancement of these C5 hydrogen bonds affects the stability of synthetic β-sheets. These interactions are common, affecting approximately 5% of all residues and 94% of proteins, and their cumulative impact provides several kilocalories per mole of conformational stability to a typical protein. C5 hydrogen bonds especially stabilize the flat β-sheets of the amyloid state, which is linked with Alzheimer's disease and other neurodegenerative disorders. Inclusion of these interactions in computational force fields would improve models of protein folding, function, and dysfunction.

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Figure 1: Amide carbonyl lone pairs allow for C5 hydrogen bonding.
Figure 2: C5 interactions display properties typical of hydrogen bonds.
Figure 3: Perturbation of C5 hydrogen bonds impacts β-sheet stability.
Figure 4: Energy and frequency of C5 hydrogen bonds in proteins.

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Acknowledgements

We thank G.J. Bartlett, I.C. Tanrikulu, and L.L. Kiessling for discussions, and W.M. Westler, T. Zhang, and M.T. Zanni for assistance with spectroscopy. This work was supported by grants R01 AR044276 (NIH), R01 GM044783 (NIH), and CHE-1124944 (NSF). R.W.N. was supported by Biotechnology Training Grant T32 GM008349 (NIH) and by an ACS Division of Organic Chemistry Graduate Fellowship. The National Magnetic Resonance Facility at Madison is supported by grant P41 GM103399 (NIH). High-performance computing is supported by grant CHE-0840494 (NSF). The Biophysics Instrumentation Facility at the University of Wisconsin–Madison was established with grants BIR-9512577 (NSF) and S10 RR013790 (NIH).

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Authors and Affiliations

  1. Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA

    Robert W Newberry & Ronald T Raines

  2. Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA

    Ronald T Raines

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  1. Robert W Newberry
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Contributions

R.W.N. conceived of the project. R.W.N. and R.T.R. planned the experiments. R.W.N. carried out the experiments. R.W.N. and R.T.R. analyzed the data and wrote the manuscript.

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Correspondence to Ronald T Raines.

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Supplementary Results, Supplementary Tables 1–6, Supplementary Figures 1–13 and Supplementary Note 1. (PDF 2464 kb)

Supplementary Note 2

Synthetic Procedures. (PDF 3388 kb)

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Newberry, R., Raines, R. A prevalent intraresidue hydrogen bond stabilizes proteins. Nat Chem Biol 12, 1084–1088 (2016). https://doi.org/10.1038/nchembio.2206

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