title: Importance of environment in determining secondary structure in proteins.
abstract: We report here the effect of bulk solvent environment on the secondary structure of several peptides. In previous work, equivocal peptide sequences that are predicted to be alpha-helical from amino acid preference but are found to be beta-strand in their proteins were shown to be alpha-helical in alcohol solvents and beta-strand in nonmicellar sodium dodecyl sulfate (SDS) by circular dichroism (CD) spectroscopy [Zhong, L., & Johnson, W. C., Jr. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 4462-4465]. Here we show that equivocal sequences that are predicted to be beta-strand but are found to be alpha-helical follow the same pattern; they are alpha-helical in alcohol solvents and beta-strand in nonmicellar SDS. Furthermore, we investigated a control sequence with only a strong alpha-helical propensity and a control sequence with only a strong beta-strand propensity. Both of these well-behaved sequences followed the same pattern as the equivocal sequences. The exceptionally stable Y(EAAAK)3A is an alpha-helix in all solvents, but analyses of the CD spectra indicate the loss of helix with an increase in beta-strand and other structures on changing solvent from trifluoroethanol (TFE) to SDS, similar to the other peptides. We find that solvent is a very important factor in determining the secondary structure of an amino acid sequence in vitro and can override the propensity for a secondary structure due to sequence.(ABSTRACT TRUNCATED AT 250 WORDS)
authors.affiliation: Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331-7305.
authors.forename: D V
authors.initials: DV
authors.lastname: Waterhous
authors.forename: W C
authors.initials: WC
authors.lastname: Johnson
mesh_terms: D000595:Amino Acid Sequence; D002942:Circular Dichroism; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry; D017433:Protein Structure, Secondary; D012997:Solvents
chemical_list: D010455:Peptides; D012997:Solvents