Distinctions between hydrophobic helices in globular proteins and transmembrane segments as factors in protein sorting

Abstract

Transmembrane (TM) segments in proteins can be distinguished in amino acid sequences as continuous stretches of hydrophobic residues. However, examination of a data base of helical water-soluble (globular) proteins revealed that nearly one-third contained helices of sufficient length to span a bilayer (≥19 residues) that had mean hydrophobicity ≥actual TM segments. We now report that synthetic peptides corresponding to these globular protein sequences, which we termed "δ-helices," behave like native TM sequences and readily insert into membrane mimetic environments in helical conformations. As well, certain δ-helix sequences can integrate into the membrane bilayer when placed into a membrane-targeted chimeric protein. We establish that δ-helices can be distinguished computationally from bona fide TM segments by the decreased frequency of occurrence of Ile/Val residues and by their relatively decreased solvent accessibilities (versus other globular helices) within tertiary structure. The further observations that (i)δ-helices generally contain three or more charged residues and (ii) δ-helices display relatively even distribution of these charged residues along their lengths, rather than concentration near their N and C termini as observed for TM segments, may constitute key recognition factors in diverting δ-helices from the membrane in vivo. Although a discrete biological role for δ-helices remains to be pinpointed, our overall results suggest that such segments may be required for globular protein folding and identify additional factors that may be important in the correct selection of TM segments by the cellular machinery. © 2009 by The American Society for Biochemistry and Molecular Biology, Inc.