To What Extent is Anfinsen's Thermodynamic Hypothesis Consistent With the Formation and Polymorphism of Amyloid Fibrils?

For half a century, Anfinsen's Thermodynamic Hypothesis has been considered the central pillar of protein science. In Anfinsen's words, this hypothesis holds that "…the three-dimensional structure of a native protein in its normal physiological milieu…is the one in which the Gibbs free energy of the whole system is lowest; that is, that the native conformation is determined by the totality of interatomic interactions and hence by the amino acid sequence, in a given environment". Applying this hypothesis to amyloid fibril-forming proteins presents challenges, which we contemplate in four questions. First, what is the "native" structure of amyloid-forming proteins, many of which are intrinsically disordered or are proteolytic fragments of larger proteins? Second, what is the thermodynamic landscape for the conversion of native monomers to highly stable fibril assemblies? Third, how do we reconcile Anfinsen's hypothesis, that a protein's amino acid sequence determines its 3-dimensional structure, with amyloid fibrils, for which single protein sequences are capable of folding into multiple polymorphs? Fourth, what is the "physiological milieu" of amyloid fibrils? Is it increased local concentration, cofactor binding, post-translational modifications, or cellular programming of diseased tissues? We discuss answers supplied by ex vivo observations and in vitro experiments, and conclude that amyloid protein structure in vivo is determined by its sequence and its physiological milieu.