Many proteins are synthesized as precursors in the form of pre-proteins or pre-pro-proteins that carry pre-sequences and or pro-sequences (see Pro-Sequence). Pre-sequences usually function as signal peptides for protein targeting, while pro-sequences play a crucial role in the folding of pro-proteins, whose examples are increasing.
Most proteins destined for protein secretion are synthesized in the cytoplasm as protein precursors (pre-proteins) containing an additional ^-terminal sequence called the signal peptide, which plays a crucial role in protein recognition of the cell secretory machinery and in initiation of protein membrane translocation (1). The signal peptides vary between 18 and 35 amino acids and have no extensive sequence homology, but share similarities in their amino acid properties. The canonical signal peptide contains three characteristic regions: an ^-terminal domain positively charged with one or two basic residues, a hydrophobic core, and a polar C-terminal domain containing the signal peptide cleavage site (2). Introduction of negatively charged and hydrophobic amino acids into the ^-terminal basic region reduces the efficiency of secretion (3), which probably interact with anionic phospholipids of the membrane (4). Substitutions of hydrophilic amino acids for hydrophobic core residues abolish protein membrane translocation, suggesting that this region is involved in the interaction with components of secretory machinery.
Upon translocation, the signal peptide is cleaved by a membrane bound signal peptidase (5), and the pre-protein precursors are converted into mature proteins. Signal peptide cleavage sites are rather regular and described by the "-3, -1 rule" (6) or "A-X-B" model (7) originally proposed by statistical evaluation of primary structures of known signal peptides. This model predicts the presence of small neutral residues at positions -3 and -1, whose structural regularity may be necessary for recognition of the signal peptide cleavage site by signal peptidase, although not essential for protein translocation itself (8). Consistently, amino acid substitutions at these positions of precursors prevent the processing.
Pre-pro-proteins have additional amino acid stretches (pro-peptides or pro-sequences) located between the signal peptide and the mature part of the protein (see Pro-Protein).
