Conformation of terminal regions in proteins

A carboxy-terminal helix has been observed in many proteins, suggesting that these helices confer an advantage, perhaps by providing protection against carboxypeptidase activity. To determine whether the conformational preferences of the amino- and carboxy-terminal regions are significantly different from each other and from the rest of the protein, we have analysed all proteins of known structure. We report here that the resulting distribution of the helical, beta-strand and coil conformations is significantly different for the amino- and carboxy-terminals; the former preferentially adopts an extended beta-strand while the latter is usually helical. The observed difference derives from the alpha/beta proteins, in which the helix and strand alternate along the sequence, suggesting that the origin of this preference lies, not in protection against degradation, but in the special structural topology of alpha/beta proteins and the beta alpha unit.