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Helix geometry in proteins

1988; Elsevier BV; Volume: 201; Issue: 3 Linguagem: Inglês

10.1016/0022-2836(88)90641-9

1089-8638

David J. Barlow, Janet M. Thornton,

Glycosylation and Glycoproteins Research

In this report we describe a general survey of all helices found in 57 of the known protein crystal structures, together with a detailed analysis of 48 α-helices found in 16 of the structures that are determined to high resolution. The survey of all helices reveals a total of 291 α-helices, 71 310-helices and no examples of π-helices. The conformations of the observed helices are significantly different from the “ideal” linear structures. The mean φ, ψ angles for the α- and 310-helices found in proteins are, respectively, (−62 °, −41 °) and (−71 °, −18 °). A computer program, HBEND, is used to characterize and to quantify the different types of helix distortion. α-Helices are classified as regular or irregular, linear, curved or kinked. Of the 48 α-helices analysed, only 15% are considered to be linear; 17% are kinked, and 58% are curved. The curvature of helices is caused by differences in the peptide hydrogen bonding on opposite faces of the helix, reflecting carbonyl-solvent/side-chain interactions for the exposed residues, and packing constraints for residues involved in the hydrophobic core. Kinked helices arise either as a result of included proline residues, or because of conflicting requirements for the optimal packing of the helix side-chains. In α-helices where there are kinks caused by proline residues, we show that the angle of kink is relatively constant (~26 °), and that there is minimal disruption of the helix hydrogen bonding. The proline residues responsible for the kinks are highly conserved, suggesting that these distortions may be structurally/functionally important.