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 n→π* 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 n→π* 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, n→π* interactions could have important roles in protein folding and function, and merit inclusion in computational force fields.
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References
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).
Weinhold, F. & Landis, C.R. Valency and Bonding: A Natural Bond Orbital Donor–Acceptor Perspective (Cambridge University Press, Cambridge, UK, 2005).
Weinhold, F. Resonance character of hydrogen-bonding interactions in water and other H-bonded species. Adv. Protein Chem. 72, 121–155 (2005).
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).
Mirsky, A.E. & Pauling, L. On the structure of native, denatured, and coagulated proteins. Proc. Natl. Acad. Sci. USA 22, 439–447 (1936).
Gray, H.B. Electrons and Chemical Bonding (W.A. Benjamin, New York, 1965).
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).
Laing, M. No rabbit ears on water. J. Chem. Educ. 64, 124–128 (1987).
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).
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).
Hinderaker, M.P. & Raines, R.T. An electronic effect on protein structure. Protein Sci. 12, 1188–1194 (2003).
Horng, J.-C. & Raines, R.T. Stereoelectronic effects on polyproline conformation. Protein Sci. 15, 74–83 (2006).
Hodges, J.A. & Raines, R.T. Energetics of an n→π* interaction that impacts protein structure. Org. Lett. 8, 4695–4697 (2006).
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).
Shoulders, M.D. & Raines, R.T. Collagen structure and stability. Annu. Rev. Biochem. 78, 929–958 (2009).
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).
Dai, N. & Etzkorn, F.A. Cis–trans proline isomerization effects on collagen triple-helix stability are limited. J. Am. Chem. Soc. 131, 13728–13732 (2009).
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).
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).
Jakobsche, C.E., Choudhary, A., Raines, R.T. & Miller, S.J. n→π* interaction and n)(π Pauli repulsion are antagonistic for protein stability. J. Am. Chem. Soc. 132, 6651–6653 (2010).
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).
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).
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).
Esposito, L., Vitagliano, L., Zagari, A. & Mazzarella, L. Pyramidalization of backbone carbonyl carbon atoms in proteins. Protein Sci. 9, 2038–2042 (2000).
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).
Makhatadze, G.I. Thermodynamics of α-helix formation. Adv. Protein Chem. 72, 199–226 (2006).
Yang, A.-S. & Honig, B. Free energy determinants of secondary structure formation: I. α-Helices. J. Mol. Biol. 252, 351–365 (1995).
Tanaka, S. & Scheraga, H.A. Statistical mechanical treatment of protein conformation. I. Conformational properties of amino acids in proteins. Macromolecules 9, 142–159 (1976).
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).
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).
Yun, R.H., Anderson, A. & Hermans, J. Proline in α-helix: stability and conformations studied by dynamics simulation. Proteins 10, 219–228 (1991).
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).
Tobias, D.J. & Brooks, C.L. III. Thermodynamics and mechanism of α-helix initiation in alanine and valine peptides. Biochemistry 30, 6059–6070 (1991).
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).
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).
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).
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).
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).
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).
Hutchinson, E.G. & Thornton, J.M. PROMOTIF—a program to identify and analyze structural motifs in proteins. Protein Sci. 5, 212–220 (1996).
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).
Zimmerman, S.S. & Scheraga, H.A. Local interactions in bends of proteins. Proc. Natl. Acad. Sci. USA 74, 4126–4129 (1977).
Novotny, M. & Kleywegt, G.J. A survey of left-handed helices in protein structures. J. Mol. Biol. 347, 231–241 (2005).
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).
Gray, H.B. & Winkler, J.R. Electron flow through proteins. Chem. Phys. Lett. 483, 1–9 (2009).
Frisch, M.J. et al. Gaussian 03, Revision C.02 (Gaussian, Inc., Wallingford, Connecticut, USA, 2004).
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).
Wang, G. & Dunbrack, R.L. PISCES: A protein sequence culling server. Bioinformatics 19, 1589–1591 (2003).
Kabsch, W. & Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577–2637 (1983).
Stapley, B.J. & Creamer, T.P. A survey of left-handed polyproline II helices. Protein Sci. 8, 587–595 (1999).
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.
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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.
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Bartlett, G., Choudhary, A., Raines, R. et al. n→π* interactions in proteins. Nat Chem Biol 6, 615–620 (2010). https://doi.org/10.1038/nchembio.406
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DOI: https://doi.org/10.1038/nchembio.406
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