Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

A prevalent intraresidue hydrogen bond stabilizes proteins

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.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

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.

Similar content being viewed by others

References

  1. Dill, K.A. & MacCallum, J.L. The protein-folding problem, 50 years on. Science 338, 1042–1046 (2012).

    Article  CAS  Google Scholar 

  2. Dill, K.A. Dominant forces in protein folding. Biochemistry 29, 7133–7155 (1990).

    Article  CAS  Google Scholar 

  3. Pauling, L., Corey, R.B. & Branson, H.R. The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. Proc. Natl. Acad. Sci. USA 37, 205–211 (1951).

    Article  CAS  Google Scholar 

  4. Pauling, L. & Corey, R.B. The pleated sheet, a new layer configuration of polypeptide chains. Proc. Natl. Acad. Sci. USA 37, 251–256 (1951).

    Article  CAS  Google Scholar 

  5. Kabsch, W. & Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577–2637 (1983).

    Article  CAS  Google Scholar 

  6. Clauss, A.D. et al. Rabbit-ears hybrids, VSEPR sterics, and other orbital anachronisms. Chem. Educ. Res. Pract. 15, 417–434 (2014).10.1039/C4RP00057A

    Article  Google Scholar 

  7. Bartlett, G.J., Choudhary, A., Raines, R.T. & Woolfson, D.N. nπ* interactions in proteins. Nat. Chem. Biol. 6, 615–620 (2010).

    Article  CAS  Google Scholar 

  8. Bartlett, G.J. & Woolfson, D.N. On the satisfaction of backbone-carbonyl lone pairs of electrons in protein structures. Protein Sci. 25, 887–897 (2016).10.1002/pro.2896

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Avignon, M., Huong, P.V., Lascombe, J., Marraud, M. & Neel, J. Etude, par spectroscopie infra-rouge, de la conformation de quelques composés peptidiques modèles. Biopolymers 8, 69–89 (1969).

    Article  CAS  Google Scholar 

  10. Burgess, A.W. & Scheraga, H.A. Communications to the editor: Stable conformations of dipeptides. Biopolymers 12, 2177–2183 (1973).

    Article  CAS  Google Scholar 

  11. Toniolo, C. Intramolecularly hydrogen-bonded peptide conformations. CRC Crit. Rev. Biochem. 9, 1–44 (1980).

    Article  CAS  Google Scholar 

  12. Dian, B.C. et al. The infrared and ultraviolet spectra of single conformations of methyl-capped dipeptides: N-acetyl tryptophan amide and N-acetyl tryptophan methyl amide. J. Chem. Phys. 117, 10688–10702 (2002).

    Article  CAS  Google Scholar 

  13. Blanco, S., Lesarri, A., López, J.C. & Alonso, J.L. The gas-phase structure of alanine. J. Am. Chem. Soc. 126, 11675–11683 (2004).10.1021/ja048317c

    Article  CAS  PubMed  Google Scholar 

  14. González Flórez, A.I. et al. Charge-induced unzipping of isolated proteins to a defined secondary structure. Angew. Chem. Int. Ed. Engl. 55, 3295–3299 (2016).10.1002/anie.201510983

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Zimmerman, S.S., Pottle, M.S., Némethy, G. & Scheraga, H.A. Conformational analysis of the 20 naturally occurring amino acid residues using ECEPP. Macromolecules 10, 1–9 (1977).

    Article  CAS  Google Scholar 

  16. Scheiner, S. Relative strengths of NH.O and CH.O hydrogen bonds between polypeptide chain segments. J. Phys. Chem. B 109, 16132–16141 (2005).10.1021/jp053416d

    Article  CAS  PubMed  Google Scholar 

  17. Steiner, T. The hydrogen bond in the solid state. Angew. Chem. Int. Ed. Engl. 41, 48–76 (2002).

    Article  CAS  Google Scholar 

  18. McDonald, I.K. & Thornton, J.M. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238, 777–793 (1994).

    Article  CAS  Google Scholar 

  19. Rowland, R.S. & Taylor, R. Intermolecular nonbonded contact distances in organic crystal structures: comparison with distances expected from van der Waals radii. J. Phys. Chem. 100, 7384–7391 (1996).10.1021/jp953141

    Article  CAS  Google Scholar 

  20. Reed, A.E., Curtiss, L.A. & Weinhold, F. Intermolecular interactions from a natural bond orbital, donor–acceptor viewpoint. Chem. Rev. 88, 899–926 (1988).

    Article  CAS  Google Scholar 

  21. Hinderaker, M.P. & Raines, R.T. An electronic effect on protein structure. Protein Sci. 12, 1188–1194 (2003).

    Article  CAS  Google Scholar 

  22. Choudhary, A., Gandla, D., Krow, G.R. & Raines, R.T. Nature of amide carbonyl–carbonyl interactions in proteins. J. Am. Chem. Soc. 131, 7244–7246 (2009).

    Article  CAS  Google Scholar 

  23. Newberry, R.W., VanVeller, B., Guzei, I.A. & Raines, R.T. nπ* interactions of amides and thioamides: implications for protein stability. J. Am. Chem. Soc. 135, 7843–7846 (2013).10.1021/ja4033583

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Benedetti, E. et al. Structural versatility of peptides from Cα,α-dialkylated glycines. I. A conformational energy computation and X-ray diffraction study of homo-peptides from Cα,α-diethylglycine. Biopolymers 27, 357–371 (1988).10.1002/bip.360270302

    Article  CAS  Google Scholar 

  25. Toniolo, C. et al. Structural versatility of peptides from Cα,α-dialkylated glycines. II. An IR absorption and 1H-NMR study of homo-oligopeptides from Cα,α-diethylglycine. Biopolymers 27, 373–379 (1988).10.1002/bip.360270303

    Article  CAS  Google Scholar 

  26. Deechongkit, S. et al. Context-dependent contributions of backbone hydrogen bonding to β-sheet folding energetics. Nature 430, 101–105 (2004).

    Article  CAS  Google Scholar 

  27. Dado, G.P. & Gellman, S.H. Structural and thermodynamic characterization of temperature-dependent changes in the folding pattern of a synthetic triamide. J. Am. Chem. Soc. 115, 4228–4245 (1993).10.1021/ja00063a046

    Article  CAS  Google Scholar 

  28. Skinner, J.J., Lim, W.K., Bédard, S., Black, B.E. & Englander, S.W. Protein dynamics viewed by hydrogen exchange. Protein Sci. 21, 996–1005 (2012).10.1002/pro.2081

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Cochran, A.G., Skelton, N.J. & Starovasnik, M.A. Tryptophan zippers: stable, monomeric β-hairpins. Proc. Natl. Acad. Sci. USA 98, 5578–5583 (2001).

    Article  CAS  Google Scholar 

  30. Fu, Y., Gao, J., Bieschke, J., Dendle, M.A. & Kelly, J.W. Amide-to-E-olefin versus amide-to-ester backbone H-bond perturbations: evaluating the O-O repulsion for extracting H-bond energies. J. Am. Chem. Soc. 128, 15948–15949 (2006).

    Article  CAS  Google Scholar 

  31. Derewenda, Z.S., Lee, L. & Derewenda, U. The occurrence of C-H...O hydrogen bonds in proteins. J. Mol. Biol. 252, 248–262 (1995).

    Article  CAS  Google Scholar 

  32. Culik, R.M., Jo, H., DeGrado, W.F. & Gai, F. Using thioamides to site-specifically interrogate the dynamics of hydrogen bond formation in β-sheet folding. J. Am. Chem. Soc. 134, 8026–8029 (2012).10.1021/ja301681v

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Gallivan, J.P. & Dougherty, D.A. Cation-π interactions in structural biology. Proc. Natl. Acad. Sci. USA 96, 9459–9464 (1999).

    Article  CAS  Google Scholar 

  34. Shi, Z., Chen, K., Liu, Z. & Kallenbach, N.R. Conformation of the backbone in unfolded proteins. Chem. Rev. 106, 1877–1897 (2006).

    Article  CAS  Google Scholar 

  35. Richardson, J.S. & Richardson, D.C. Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation. Proc. Natl. Acad. Sci. USA 99, 2754–2759 (2002).

    Article  CAS  Google Scholar 

  36. Cheng, P.-N., Pham, J.D. & Nowick, J.S. The supramolecular chemistry of β-sheets. J. Am. Chem. Soc. 135, 5477–5492 (2013).

    Article  CAS  Google Scholar 

  37. Sawaya, M.R. et al. Atomic structures of amyloid cross-β spines reveal varied steric zippers. Nature 447, 453–457 (2007).

    Article  CAS  Google Scholar 

  38. Dobson, C.M. Protein misfolding, evolution and disease. Trends Biochem. Sci. 24, 329–332 (1999).

    Article  CAS  Google Scholar 

  39. Ohnishi, S., Kamikubo, H., Onitsuka, M., Kataoka, M. & Shortle, D. Conformational preference of polyglycine in solution to elongated structure. J. Am. Chem. Soc. 128, 16338–16344 (2006).10.1021/ja066008b

    Article  CAS  PubMed  Google Scholar 

  40. Minor, D.L. Jr. & Kim, P.S. Measurement of the β-sheet-forming propensities of amino acids. Nature 367, 660–663 (1994).

    Article  CAS  Google Scholar 

  41. Kortemme, T., Morozov, A.V. & Baker, D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J. Mol. Biol. 326, 1239–1259 (2003).

    Article  CAS  Google Scholar 

  42. Reed, A.E., Weinstock, R.B. & Weinhold, F. Natural population analysis. J. Chem. Phys. 83, 735–746 (1985).

    Article  CAS  Google Scholar 

  43. Huang, R. et al. Cross-strand coupling and site-specific unfolding thermodynamics of a trpzip β-hairpin peptide using 13C isotopic labeling and IR spectroscopy. J. Phys. Chem. B 113, 5661–5674 (2009).10.1021/jp9014299

    Article  CAS  PubMed  Google Scholar 

  44. Wang, G. & Dunbrack, R.L. Jr. PISCES: a protein sequence culling server. Bioinformatics 19, 1589–1591 (2003).

    Article  CAS  Google Scholar 

  45. Hutchinson, E.G. & Thornton, J.M. PROMOTIF--a program to identify and analyze structural motifs in proteins. Protein Sci. 5, 212–220 (1996).

    Article  CAS  Google Scholar 

Download references

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).

Author information

Authors and Affiliations

Authors

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.

Corresponding author

Correspondence to Ronald T Raines.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

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)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nchembio.2206

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing