Generally, there are two major ways by which a mutation can affect amyloid formation and aggregation, (1) by acting on the unfolded polypeptide chain and intrinsically promoting its association or (2) by destabilizing the native, globular conformation, thereby increasing the proportion of unfolded and aggregation-competent polypeptide chains. The former effect can be predicted from the rate of aggregation
v mut and the ratio ln(
v mut/
v wt).
27 Using this correlation, the Phe540Ser mutation leads to a slightly negative value of ln(
v mut/
v wt) (−0.19) and a decelerating effect on the aggregation kinetics. Therefore, this property does not explain its amyloid-promoting effect of mutation. By contrast, there is considerable evidence that the second type of mutagenic effect applies here—namely, the destabilization of the native, globular state which makes the polypeptide main chain more competent to form intermolecular arrangements. This evidence comes from a homology model of the fourth FAS1 region of keratoepithelin
14 that has been derived from the crystal structure of its close homologue, the
Drosophila protein fasciclin 1
(Fig. 7) .
13 This model shows that the respective region forms a compact globular structure consisting of an α-helical and a β-domain and that residue Phe540 is positioned within a β-strand. This strand runs through the center of the hydrophobic core of the β-domain
(Fig. 7b) . Considering the large size of phenylalanine and its ability to make very many hydrophobic contacts, replacement of such a buried residue by the much smaller side chain of polar serine readily suggests that the thermodynamic stability of the entire protein will be decreased dramatically. For comparison, when the fully buried Phe153 of the T4 lysozyme is replaced by the small hydrophobic residue Ala, it decreases the thermodynamic stability of the protein by −3.5 kcal/mol,
28 a value that is well within the range of values known to promote aggregation and amyloid formation.
29 Indeed, amyloid structures are known to form by association of at least partly, if not entirely, unfolded polypeptide chains; and stable, globular proteins must be sufficiently unfolded to enable the polypeptide backbone to form intermolecular interactions.
30 Moreover, unfolding also favors a proteolytic cleavage reaction.