Helices

Baker, E. N.

doi:10.1107/97809553602060000711

International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

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International Tables for Crystallography (2006). Vol. F. ch. 22.2, p. 548 | 1 | 2 |

Section 22.2.5.3.1. Helices

E. N. Baker^a ^*

^aSchool of Biological Sciences, University of Auckland, Private Bag 92-109, Auckland, New Zealand
Correspondence e-mail: ted.baker@auckland.ac.nz

22.2.5.3.1. Helices

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Helices have traditionally been defined in terms of their N—H···O=C hydrogen-bonding patterns as α-helices $[(i \rightarrow i - 4)]$ , 3₁₀-helices $[(i \rightarrow i - 3)]$ , or π-helices $[(i \rightarrow i - 5)]$ ; in an α-helix, for example, the peptide NH of residue 5 hydrogen bonds to the C=O of residue 1. In fact, the vast majority of helices in proteins are α-helices; 3₁₀-helices are rarely more than two turns (six residues) in length, and discrete π-helices have not been seen so far.

The residues within helices have characteristic main-chain torsion angles, (φ, ψ), of around (−63°, −40°) that cause the C=O groups to tilt outwards by about 14° from the helix axis (Baker & Hubbard, 1984). This results in somewhat less linear hydrogen bonding than in the original Pauling model (Pauling et al., 1951), with a degree of distortion towards 3₁₀-helix geometry. Thus, weak $[i \rightarrow i - 3]$ interactions are often made in addition to the more favourable $[i \rightarrow i - 4]$ hydrogen bonds, giving hydrogen-bond networks that may enhance helix elasticity (Stickle et al., 1992). Tilting outwards also makes the C=O groups more accessible for additional hydrogen bonds from side chains or water molecules. For the α-type, $[i \rightarrow i - 4]$ interactions, the hydrogen-bond angles at both donor and acceptor atoms are quite tightly clustered (N—H···O ∼157° and C=O···H ∼147°). The hydrogen-bond lengths in helices average 2.06 (16) Å (O···H) or 2.99 (14) Å (O···N) (Baker & Hubbard, 1984).

Few helices are regular throughout their length. Many are curved or kinked such that one side (often the outer, solvent-exposed side) of the helix is opened up a bit and has longer hydrogen bonds (Blundell et al., 1983; Baker & Hubbard, 1984). The bends are often associated with additional hydrogen bonds from water molecules or side chains to C=O groups that are tilted out more than usual. Curved helices are normal in coiled-coil structures and can enable long helices to pack more effectively in globular structures. Sometimes a kink can be functionally important, as in manganese superoxide dismutase, where a kink in a long helix, incorporating a π-type $[(i \rightarrow i - 5)]$ hydrogen bond, enables the optimal positioning of active-site residues (Edwards et al., 1998).

The beginnings and ends of helices are sites of hydrogen-bonding variations which can be seen as characteristic `termination motifs'. At helix N-termini, 3₁₀-type $[i\rightarrow i - 3]$ (or bifurcated $[i\rightarrow i - 3]$ and $[i\rightarrow i - 4]$ ) hydrogen bonds are often found. At C-termini, two common patterns occur. In one, labelled $[\alpha_{\rm C1}]$ by Baker & Hubbard (1984), there is a transition from α-type, $[i\rightarrow i - 4]$ to 3₁₀-type, $[{i\rightarrow i - 3}]$ hydrogen bonding, often with genuine bifurcated hydrogen bonds, as in Fig. 22.2.2.1(b), at the transition point. The other, labelled $[\alpha_{\rm C2}]$ (Baker & Hubbard, 1984) or referred to as the `Schellman motif' (Schellman, 1980), has a π-type, $[i\rightarrow i - 5]$ hydrogen bond coupled with a $[3_{10}]$ -type, $[i - 1\rightarrow i - 4]$ hydrogen bond; residue [i - 1] has a left-handed α configuration and is often Gly. The beginnings and ends of helices are also the sites of specific side-chain hydrogen-bonding patterns, referred to as N-caps and C-caps (Presta & Rose, 1988; Richardson & Richardson, 1988); these are described below.

References

Baker, E. N. & Hubbard, R. E. (1984). Hydrogen bonding in globular proteins. Prog. Biophys. Mol. Biol. 44, 97–179.Google Scholar

Blundell, T., Barlow, D., Borkakoti, N. & Thornton, J. (1983). Solvent-induced distortions and the curvature of α-helices. Nature (London), 306, 281–283.Google Scholar

Edwards, R. A., Baker, H. M., Whittaker, M. M., Whittaker, J. W. & Baker, E. N. (1998). Crystal structure of Escherichia coli manganese superoxide dismutase at 2.1 Å resolution. J. Biol. Inorg. Chem. 3, 161–171.Google Scholar

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

Presta, L. G. & Rose, G. D. (1988). Helix signals in proteins. Science, 240, 1632–1641.Google Scholar

Richardson, J. S. & Richardson, D. C. (1988). Amino acid preferences for specific locations at the ends of α-helices. Science, 240, 1648–1652.Google Scholar

Schellman, C. (1980). The alpha-L conformation at the ends of helices. In Protein folding, edited by R. Jaenicke, pp. 53–61. Amsterdam: Elsevier.Google Scholar

Stickle, D. F., Presta, L. G., Dill, K. A. & Rose, G. D. (1992). Hydrogen bonding in globular proteins. J. Mol. Biol. 226, 1143–1159.Google Scholar

International Tables for Crystallography (2006). Vol. F. ch. 22.2, p. 548