Transported proteins often contain an extension sequence called the signal peptide. The alkaline phosphatase (PhoA) signal sequence represents a typical signal peptide for comparison to idealized sequences both in vivo and in vitro. We have designed a series of idealized signal sequences which vary in amino terminal charge and core region hydrophobicity with minimal variation in amino acid composition. The idealized core regions contain different proportions of leucine and alanine residues, effectively producing hydrophobicities above and below the threshold level required for efficient secretion. The flanking amino and carboxyl termini were designed to maintain the general features and relative hydrophobicity of their counterparts in the wild-type PhoA signal sequence. Using the phoA gene, the signal peptide region was modified to generate mutants corresponding to the model sequences. Transport studies in Escherichia coli confirmed that completely idealized signal sequences, which lack a helix-breaking proline or glycine residue, can be functional if the core region is sufficiently hydrophobic and that one positively charged residue in the amino terminus is adequate for efficient transport. The corresponding peptides were chemically synthesized and exhibited HPLC retention times that reflect the relative hydrophobicities of the sequences. Structural analyses of the isolated peptides by circular dichroism demonstrate solvent dependence and exceptionally stable alpha-helix formation by the functional signal peptides in trifluoroethanol. Although leucine and alanine residues are often predicted to have similar propensities for forming an alpha-helix, considerably higher alpha-helical content is observed in the signal peptides which contain predominantly polyleucine core regions.(ABSTRACT TRUNCATED AT 250 WORDS)