Environment affects amino acid preference for secondary structure

Abstract

Three equivocal amino acid sequences were synthesized that are predicted to be α-helical from amino acid preference but are found to be primarily β-strand from x-ray diffraction of their respective proteins. In some solvent systems we recover the α-helical structure predicted by amino acid preference, whereas in other systems we mimic the interior of the protein and produce a β-strand. These results are experimental proof that the environment is important in determining the secondary structure formed by an amino acid sequence; therefore schemes that predict secondary structure from amino acid sequence alone can never be totally successful.