Systematic introduction of proline in a eukaryotic signal sequence suggests asymmetry within the hydrophobic core

The hydrophobic core or h region of both prokaryotic and eukaryotic signal sequences is the predominant structural domain that controls the efficiency of protein translocation across membranes. Characteristically, hydrophobic cores appear to assume alpha-helical conformations, and studies in prokaryotes have indicated that this conformation is necessary for efficient signal sequence function. To address the conformational constraints of a eukaryotic signal sequence, we have introduced a single proline in almost each position of the signal sequence hydrophobic core of glycoprotein C (gC) of the swine herpesvirus, pseudorabies virus. When the resulting mutant virus strains were used to infect cells, we found that substitution of proline at certain positions affected gC translocation greater than its introduction at other sites within the hydrophobic core. The observed positional effects did not completely correlate with reductions in overall hydrophobicity or linear position within the hydrophobic core. Rather, it appeared that one face of the gC signal sequence alpha-helix is far more sensitive to proline disruption than the other, potentially indicating a functional asymmetry.