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Linus Pauling and the planar peptide bond

Nature Structural Biology volume 8, pages 201–202 (2001)Cite this article

Every first year biochemistry student learns about the planarity of the peptide bond. Planarity, the result of ∼40% N–C′ double bond character arising from two dominant resonance structures, allows for a great simplification in the understanding of protein structures. Of the three repeating protein backbone dihedral angles, only φ and ψ need to be considered when assigning secondary structure, because the peptide bond dihedral angle ω is generally considered fixed at 180°. Linus Pauling's prediction of the α-helix, one of the greatest achievements in structural biology, was made by assuming (i) that the peptide bond is planar, (ii) that all amino acid residues are equivalent with respect to backbone conformations and (iii) that each amide proton is hydrogen bonded to an oxygen atom of another residue with an N–O distance of 2.72 Å (ref. 1). Similar criteria allowed Pauling to predict several other protein secondary structural elements including the γ-helix and parallel and antiparallel β-sheets, accomplishments that resulted in his 1954 Nobel Prize in Chemistry.

In 1968, Ramachandran recognized the need for nonplanar peptide bonds in cyclic peptides2. In later work, the same group argued that discrepancies in calculated values of 3JHN–Hα scalar coupling constants in peptides with bulky side chains showed the need to allow for nonplanar peptide bonds in both cyclic and linear peptides3. They also noted that most of calculations up to that time used “the standard, completely planar, trans peptide unit of dimensions given by Pauling and Corey4 as early as 1951”3. Much later and with relatively high level Hartree-Fock extended basis set ab initio calculations, Pople's group showed that the peptide bond in the gas phase has significant flexibility and rotates as much as 40° with little energetic cost5, a result subsequently verified by Edison and coworkers6. Simple geometric drawings will show that deviations of this size result from relatively small changes in interatomic distances.

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Figure 1: Peptide bond rotational energies and angular frequency distribution.

References

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Acknowledgements

I thank H. Weissig of the San Diego Supercomputer Center and Protein Data Bank for providing the dihedral angles used in Fig. 1. D. Purich, R. McKenna, M. Agbandje-McKenna, and members of my laboratory provided helpful and stimulating discussions.

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  1. the Department of Biochemistry & Molecular Biology, University of Florida, Box 100245, Gainesville, 32610-0245, Florida

    Arthur S. Edison

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Edison, A. Linus Pauling and the planar peptide bond. Nat Struct Mol Biol 8, 201–202 (2001). https://doi.org/10.1038/84921

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