[en] A number of studies have introduced mutations into the yeast invertase signal peptide, using it as a model system to elucidate features for targeting, translocation and intracellular transport. Using molecular modelling of the invertase signal peptide we have analysed the hydrophobicity potential and the change in dielectric constant of the energy transfer, when the molecule moves from a hydrophobic to a hydrophilic phase at the simulated hydrophobic-hydrophilic interface. This modelling has been carried out on wild type and mutant invertase signal peptides of altered function, previously reported in the literature. While the predicted angle of insertion correlates with the measured extent of invertase secretion, with an optimum angle of 45 degrees, mutations that change the angle of orientation reduce the extent of invertase secretion. We have applied these same molecular modelling principles to the naturally occurring variants of the human apolipo-protein B (apoB) signal peptide, that confer a secretion defective phenotype when fused to yeast invertase and expressed in yeast. Our modelling thus identifies a strong correlation between the predicted angle of insertion of the signal peptide into the membrane and its ability to direct secretion.