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A survey of left-handed polyproline II helices

Published online by Cambridge University Press:  01 March 1999

BENJAMIN J. STAPLEY
Affiliation:
Kentucky Center for Structural Biology, Department of Biochemistry, University of Kentucky, 800 Rose Street, Lexington, Kentucky 40536-0298
TREVOR P. CREAMER
Affiliation:
Kentucky Center for Structural Biology, Department of Biochemistry, University of Kentucky, 800 Rose Street, Lexington, Kentucky 40536-0298
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Abstract

Left-handed polyproline II helices (PPII) are contiguous elements of protein secondary structure in which the φ and ψ angles of constituent residues are restricted to around −75° and 145°, respectively. They are important in structural proteins, in unfolded states and as ligands for signaling proteins. Here, we present a survey of 274 nonhomologous polypeptide chains from proteins of known structure for regions that form these structures. Such regions are rare, but the majority of proteins contain at least one PPII helix. Most PPII helices are shorter than five residues, although the longest found contained 12 amino acids. Proline predominates in PPII, but Gln and positively charged residues are also favored. The basis of Gln's prevalence is its ability to form an i, i + 1 side-chain to main-chain hydrogen bond with the backbone carbonyl oxygen of the proceeding residue; this helps to fix the ψ angle of the Gln and the φ and ψ of the proceeding residue in PPII conformations and explains why Gln is favored at the first position in a PPII helix. PPII helices are highly solvent exposed, which explains why apolar amino acids are disfavored despite preferring this region of φ/ψ space when in isolation. PPII helices have perfect threefold rotational symmetry and within these structures we find significant correlation between the hydrophobicity of residues at i and i + 3; thus, PPII helices in globular proteins can be considered to be amphipathic.

Type
Research Article
Copyright
© 1999 The Protein Society

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