Fusion polypeptides in gene cloning: potential problems due to conformational alterations at the junction.

Many eukaryotic genes are cloned in bacterial hosts as fusion polypeptides. Prediction of the secondary structures for some common prokaryotic fusion polypeptides shows that many junction sites correspond to important secondary structures. It is suggested that such structures could affect (hinder, etc.) the conformation or drive the folding of the neighboring eukaryotic counterparts. Thus the prokaryotic junction should be better performed in random coil regions, or short fusion prokaryotic polypeptides should be used.