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:

nπ* interactions in proteins

Abstract

Hydrogen bonds between backbone amides are common in folded proteins. Here, we show that an intimate interaction between backbone amides also arises from the delocalization of a lone pair of electrons (n) from an oxygen atom to the antibonding orbital (π*) of the subsequent carbonyl group. Natural bond orbital analysis predicted significant nπ* interactions in certain regions of the Ramachandran plot. These predictions were validated by a statistical analysis of a large, non-redundant subset of protein structures determined to high resolution. The correlation between these two independent studies is striking. Moreover, the nπ* interactions are abundant and especially prevalent in common secondary structures such as α-, 310- and polyproline II helices and twisted β-sheets. In addition to their evident effects on protein structure and stability, nπ* interactions could have important roles in protein folding and function, and merit inclusion in computational force fields.

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: Kinship of hydrogen bonds and nπ* interactions in an α-helix.
Figure 2: Ramachandran plots of nπ* interactions.
Figure 3: Histograms of d and θ values for Xaa-Ala, Xaa-Gly and Xaa-Pro dipeptides in α-helices, β-sheets and PII helices.
Figure 4: Values of d and θ in nπ* interactions.
Figure 5: Potential nπ* interactions in the selectivity filter of the KcsA K+ channel.

Similar content being viewed by others

Accession codes

Accessions

Protein Data Bank

References

  1. Isaacs, E.D., Shukla, A., Platzman, P.M., Hamann, D.R., Barbiellini, B. & Tulk, C.A. Covalency of the hydrogen bond in ice: a direct x-ray measurement. Phys. Rev. Lett. 82, 600–603 (1999).

    Article  CAS  Google Scholar 

  2. Weinhold, F. & Landis, C.R. Valency and Bonding: A Natural Bond Orbital Donor–Acceptor Perspective (Cambridge University Press, Cambridge, UK, 2005).

  3. Weinhold, F. Resonance character of hydrogen-bonding interactions in water and other H-bonded species. Adv. Protein Chem. 72, 121–155 (2005).

    Article  CAS  Google Scholar 

  4. Khaliullin, R.Z., Cobar, E.A., Lochan, R.C., Bell, A.T. & Head-Gordon, M. Unravelling the origin of intermolecular interactions using absolutely localized molecular orbitals. J. Phys. Chem. A 111, 8753–8765 (2007).

    Article  CAS  Google Scholar 

  5. Mirsky, A.E. & Pauling, L. On the structure of native, denatured, and coagulated proteins. Proc. Natl. Acad. Sci. USA 22, 439–447 (1936).

    Article  CAS  Google Scholar 

  6. Gray, H.B. Electrons and Chemical Bonding (W.A. Benjamin, New York, 1965).

  7. Raber, D.J., Raber, N.K., Chandrasekhar, J. & Schleyer, P.v.R. Geometries and energies of complexes between formaldehyde and first- and second-row cations. A theoretical study. Inorg. Chem. 23, 4076–4080 (1984).

    Article  CAS  Google Scholar 

  8. Laing, M. No rabbit ears on water. J. Chem. Educ. 64, 124–128 (1987).

    Article  CAS  Google Scholar 

  9. 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 

  10. DeRider, M.L. et al. Collagen stability: insights from NMR spectroscopic and hybrid density functional computational investigations of the effect of electronegative substituents on prolyl ring conformations. J. Am. Chem. Soc. 124, 2497–2505 (2002).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  12. Horng, J.-C. & Raines, R.T. Stereoelectronic effects on polyproline conformation. Protein Sci. 15, 74–83 (2006).

    Article  CAS  Google Scholar 

  13. Hodges, J.A. & Raines, R.T. Energetics of an nπ* interaction that impacts protein structure. Org. Lett. 8, 4695–4697 (2006).

    Article  CAS  Google Scholar 

  14. Gao, J. & Kelly, J.W. Toward quantification of protein backbone–backbone hydrogen bonding energies: an energetic analysis of an amide-to-ester mutation in an α-helix within a protein. Protein Sci. 17, 1096–1101 (2008).

    Article  CAS  Google Scholar 

  15. Shoulders, M.D. & Raines, R.T. Collagen structure and stability. Annu. Rev. Biochem. 78, 929–958 (2009).

    Article  CAS  Google Scholar 

  16. 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 

  17. Dai, N. & Etzkorn, F.A. Cistrans proline isomerization effects on collagen triple-helix stability are limited. J. Am. Chem. Soc. 131, 13728–13732 (2009).

    Article  CAS  Google Scholar 

  18. Gorske, B.C., Stringer, J.R., Bastian, B.L., Fowler, S.A. & Blackwell, H.E. New strategies for the design of folded peptoids revealed by a survey of noncovalent interactions in model systems. J. Am. Chem. Soc. 131, 16555–16567 (2009).

    Article  CAS  Google Scholar 

  19. Pal, T.K. & Sankararamakrishnan, R. Quantum chemical investigations on intraresidue carbonyl–carbonyl contacts in aspartates of high-resolution protein structures. J. Phys. Chem. B 114, 1038–1049 (2010).

    Article  CAS  Google Scholar 

  20. Jakobsche, C.E., Choudhary, A., Raines, R.T. & Miller, S.J. nπ* interaction and n)(π Pauli repulsion are antagonistic for protein stability. J. Am. Chem. Soc. 132, 6651–6653 (2010).

    Article  CAS  Google Scholar 

  21. Berman, H., Henrick, K., Nakamura, H. & Markley, J.L. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res. 35, D301–D303 (2007).

    Article  CAS  Google Scholar 

  22. Mahan, S.D., Ireton, G.C., Knoeber, C., Stoddard, B.L. & Black, M.E. Random mutagenesis and selection of Escherichia coli cytosine deaminase for cancer gene therapy. Protein Eng. Des. Sel. 17, 625–633 (2004).

    Article  CAS  Google Scholar 

  23. Zhou, Y., Morais-Cabral, J.H., Kaufman, A. & MacKinnon, R. Chemistry of ion coordination and hydration revealed by a K+ channel–Fab complex at 2.0 Å resolution. Nature 414, 43–48 (2001).

    Article  CAS  Google Scholar 

  24. Esposito, L., Vitagliano, L., Zagari, A. & Mazzarella, L. Pyramidalization of backbone carbonyl carbon atoms in proteins. Protein Sci. 9, 2038–2042 (2000).

    Article  CAS  Google Scholar 

  25. Lario, P.I. & Vrielink, A. Atomic resolution density maps reveal secondary structure dependent differences in electronic distribution. J. Am. Chem. Soc. 125, 12787–12794 (2003).

    Article  CAS  Google Scholar 

  26. Makhatadze, G.I. Thermodynamics of α-helix formation. Adv. Protein Chem. 72, 199–226 (2006).

    Article  CAS  Google Scholar 

  27. Yang, A.-S. & Honig, B. Free energy determinants of secondary structure formation: I. α-Helices. J. Mol. Biol. 252, 351–365 (1995).

    Article  CAS  Google Scholar 

  28. Tanaka, S. & Scheraga, H.A. Statistical mechanical treatment of protein conformation. I. Conformational properties of amino acids in proteins. Macromolecules 9, 142–159 (1976).

    Article  CAS  Google Scholar 

  29. Toniolo, C., Bonora, G.M., Mutter, M. & Pillai, V.N.R. Linear oligopeptides. 78. The effect of the insertion of a proline residue on the solution conformation of host peptides. Makromol. Chem. 182, 2007–2014 (1981).

    Article  CAS  Google Scholar 

  30. Altmann, K.-H., Wojcik, J., Vasquez, M. & Scheraga, H.A. Helix–coil stability constants for the naturally occurring amino acids in water. XXIII. Proline parameters from random poly(hydroxybutylglutamine–co–L-proline). Biopolymers 30, 107–120 (1990).

    Article  CAS  Google Scholar 

  31. Yun, R.H., Anderson, A. & Hermans, J. Proline in α-helix: stability and conformations studied by dynamics simulation. Proteins 10, 219–228 (1991).

    Article  CAS  Google Scholar 

  32. Venkatachalapathi, Y.V. & Balaram, P. An incipient 310 helix in Piv–Pro–Pro–Ala-NHMe as a model for peptide folding. Nature 281, 83–84 (1979).

    Article  CAS  Google Scholar 

  33. Tobias, D.J. & Brooks, C.L. III. Thermodynamics and mechanism of α-helix initiation in alanine and valine peptides. Biochemistry 30, 6059–6070 (1991).

    Article  CAS  Google Scholar 

  34. Sheinerman, F.B. & Brooks, C.L. III. 310 helices in peptides and proteins as studied by modified Zimm–Bragg Theory. J. Am. Chem. Soc. 117, 10098–10103 (1995).

    Article  CAS  Google Scholar 

  35. Monticelli, L.P., T.D. & Colombo, G. Mechanism of helix nucleation and propagation: Microscopic view from microsecond time scale MD simulation. J. Phys. Chem. B 109, 20064–20067 (2005).

    Article  CAS  Google Scholar 

  36. Richardson, J.S., Getzoff, E.D. & Richardson, D.C. The β-bulge: a common small unit of nonrepetitive protein structure. Proc. Natl. Acad. Sci. USA 75, 2574–2578 (1978).

    Article  CAS  Google Scholar 

  37. Chothia, C., Novotny, J., Bruccoleri, R. & Karplus, M. Domain association on immunogloblin molecules. The packing of variable domains. J. Mol. Biol. 186, 651–663 (1985).

    Article  CAS  Google Scholar 

  38. Jones, E.Y., Davis, S.J., Williams, A.F., Harlos, K. & Stuart, D.I. Crystal structure at 2.8 Å resolution of a soluble form of the cell adhesion molecule CD2. Nature 360, 232–239 (1992).

    Article  CAS  Google Scholar 

  39. Chan, A.W.E., Hutchinson, E.G., Harris, D. & Thornton, J.M. Identification, classification, and analysis of β-bulges in proteins. Protein Sci. 2, 1574–1590 (1993).

    Article  CAS  Google Scholar 

  40. 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 

  41. Lewis, P.N., Momany, F.A. & Scheraga, H.A. Folding of polypeptide chains in proteins: a proposed mechanism for folding. Proc. Natl. Acad. Sci. USA 68, 2293–2297 (1971).

    Article  CAS  Google Scholar 

  42. Zimmerman, S.S. & Scheraga, H.A. Local interactions in bends of proteins. Proc. Natl. Acad. Sci. USA 74, 4126–4129 (1977).

    Article  CAS  Google Scholar 

  43. Novotny, M. & Kleywegt, G.J. A survey of left-handed helices in protein structures. J. Mol. Biol. 347, 231–241 (2005).

    Article  CAS  Google Scholar 

  44. Farooq, A. et al. Solution structure of ERK2 binding domain of MAPK phosphatase MKP-3: Structural insights into MKP-3 activation by ERK2. Mol. Cell 7, 387–399 (2001).

    Article  CAS  Google Scholar 

  45. Gray, H.B. & Winkler, J.R. Electron flow through proteins. Chem. Phys. Lett. 483, 1–9 (2009).

    Article  CAS  Google Scholar 

  46. Frisch, M.J. et al. Gaussian 03, Revision C.02 (Gaussian, Inc., Wallingford, Connecticut, USA, 2004).

  47. Weinhold, F. Natural bond orbital methods. in Encyclopedia of Computational Chemistry (eds. Schleyer, P.v.R. et al.) 3, 792–1811 (John Wiley & Sons, Chichester, UK, 1998).

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

    Article  CAS  Google Scholar 

  49. 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 

  50. Stapley, B.J. & Creamer, T.P. A survey of left-handed polyproline II helices. Protein Sci. 8, 587–595 (1999).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank J. Spencer, J. Harvey, A. Mulholland, B. Bromley, M.D. Shoulders, B.R. Caes, C.N. Bradford, M.J. Palte and E. Moutevelis for helpful discussions. Financial support was provided by the University of Bristol and the Biotechnology and Biological Sciences Research Council of the United Kingdom (grant D003016) to D.N.W. and the US National Institutes of Health grant R01 AR044276 to R.T.R.

Author information

Authors and Affiliations

Authors

Contributions

D.N.W. and R.T.R. conceived the project. G.J.B. and D.N.W. designed the PDB analyses; G.J.B. performed the PDB analyses. A.C. and R.T.R. designed the computational analyses; A.C. performed the computational analyses. All of the coauthors wrote and edited the manuscript.

Corresponding authors

Correspondence to Ronald T Raines or Derek N Woolfson.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Tables 1–5 (PDF 482 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Bartlett, G., Choudhary, A., Raines, R. et al. nπ* interactions in proteins. Nat Chem Biol 6, 615–620 (2010). https://doi.org/10.1038/nchembio.406

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nchembio.406

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