title: Nonpolar contributions to conformational specificity in assemblies of designed short helical peptides.
abstract: A series of designed short helical peptides was used to study the effect of nonpolar interactions on conformational specificity. The consensus sequence was designed to obtain short helices (17 residues) and to minimize the presence of interhelical polar interactions. Furthermore, the sequence contained a heptad repeat (abcdefg), where positions a and d were occupied by hydrophobic residues Leu, Ile, or Val, and positions e and g were occupied by Ala. The peptides were named according to the identities of the residues in the adeg positions, respectively. The peptides llaa, liaa, ilaa, iiaa, ivaa, viaa, lvaa, vlaa, and vvaa were synthesized, and their characterization revealed marked differences in specificity. An experimental methodology was developed to study the nine peptides and their pairwise mixtures. These peptides and their mixtures formed a vast array of structural states, which may be classified as follows: helical tetramers and pentamers, soluble and insoluble helical aggregates, insoluble unstructured aggregates, and soluble unstructured monomers. The peptide liaa formed stable helical pentamers, and iiaa and vlaa formed stable helical tetramers. Disulfide cross-linking experiments indicated the presence of an antiparallel helix alignment in the helical pentamers and tetramers. Rates of amide proton exchange of the tetrameric form of vlaa were 10-fold slower than the calculated exchange rate for unfolded vlaa. In other work, the control of specificity has been attributed to polar interactions, especially buried polar interactions; this work demonstrated that subtle changes in the configuration of nonpolar interactions resulted in a large variation in the extent of conformational specificity of assemblies of designed short helical peptides. Thus, nonpolar interactions can have a significant effect on the conformational specificity of oligomeric short helices.
authors.affiliation: Division of Molecular and Structural Biology, Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Canada.
authors.forename: C L
authors.initials: CL
authors.lastname: Boon
authors.forename: A
authors.initials: A
authors.lastname: Chakrabartty
mesh_terms: D000595:Amino Acid Sequence; D002851:Chromatography, High Pressure Liquid; D002942:Circular Dichroism; D003432:Cross-Linking Reagents; D004268:DNA-Binding Proteins; D004220:Disulfides; D004305:Dose-Response Relationship, Drug; D005656:Fungal Proteins / Q000737:chemistry; D007700:Kinetics; D008027:Light; D008956:Models, Chemical; D008969:Molecular Sequence Data; D010452:Peptide Biosynthesis; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D011494:Protein Kinases / Q000737:chemistry; D017433:Protein Structure, Secondary; D011522:Protons; D029701:Saccharomyces cerevisiae Proteins; D012542:Scattering, Radiation; D017386:Sequence Homology, Amino Acid; D012995:Solubility; D013050:Spectrometry, Fluorescence; D013997:Time Factors; D014461:Ultracentrifugation
chemical_list: D003432:Cross-Linking Reagents; D004268:DNA-Binding Proteins; D004220:Disulfides; D005656:Fungal Proteins; D010455:Peptides; D011522:Protons; D029701:Saccharomyces cerevisiae Proteins; D011494:Protein Kinases