Why Prions Cannot Carry Biological Information

The prion hypothesis introduced a new system of biological information: conformational information transfer through templating. Unlike normal protein folding, which takes place spontaneously based on the primary sequence information of the protein (the thermodynamic hypothesis of protein folding or Anfinsen’s dogma), the amyloid conformation in diseases such as Creutzfeldt-Jakob disease is postulated to require a conformational template, a prion, which acts as a template to “imprint” its corrupt conformation on similar proteins [1]. Experimentally, the prion hypothesis is based on one phenomenon: seeding. This is when an amyloid fibril fragment, a seed, is added to a concentrated solution of other proteins, it catalyzes their transformation into amyloids. However, for decades it has remained unclear what exactly is the conformational information carried by prions and what is the molecular mechanism of templating. More recently, and thanks to a better understanding of the structure of amyloid fibrils, the term “conformational information” has come to designate the specific 2D cross-sectional shape, i.e., the particular cross-sectional pattern of folds and turns of protofilaments and fibrils (Figure 1A) [2]. In this framework, a prion, which is an amyloid fibril fragment, templates its cross-sectional shape on incoming protein molecules binding to its tip during elongation. The incoming molecules must accommodate the cross-sectional shape of the fibril by binding in a parallel, in-register manner (i.e., the N and C termini align in the same direction, and each amino acid of the incoming molecule stacks on top of the identical residue at the tip of the fibril) [3]. This is also the underlying principle behind the concept of prion “strains”, where different cross-sectional seed shapes are postulated to imprint their distinctive pattern of folds and turns on incoming protein molecules, leading to different disease phenotypes [2]. Similarly, prion propagation occurs via breakage or fission of a fibril with a particular cross-sectional shape into smaller fragments or seeds, which then template their shape onto incoming protein molecules. Thus, in its modern formulation, the prion templating and propagation of conformational information is based on elongation and fission.

However, for the elongation and fission mechanism to preserve and propagate specific cross-sectional shape information sustainably across generations of fibrils and across different cells, tissues, and hosts, it must fulfill some basic criteria:

However, there is an overwhelming amount of experimental evidence showing that both criteria are not fulfilled during amyloid growth:

Based on these two points alone, the prion hypothesis as it pertains to sustained conformational templating and propagation via elongation and fission is not supported by experimental evidence. Yet there are additional fundamental problems with the prion hypothesis, including:

The prion hypothesis, postulated long before the mechanistic and structural information outlined above was known, is currently in conflict with the experimental evidence accrued since its inception. It mischaracterized the phenomenon of protein phase transition as replication. What drives amyloid formation, similar to any other phase transition (crystallization, for example), is the increased probability of forming intermolecular bonds due to molecular proximity at higher protein concentrations (supersaturation). From this perspective, Anfinsen principles (the thermodynamic hypothesis) still apply to the amyloid phenomenon, where the amyloid conformation (the cross-β architecture) is spontaneously adopted under supersaturated conditions because it is more thermodynamically favorable than the native conformation, which is dependent on sequence-dependent intramolecular interactions under subsaturated conditions. In this case, no template is needed, just a nucleation catalyst, which can be any surface that lowers the thermodynamic barrier to phase transition [10]. A process that can proceed without a template is by definition a non-templated process. Thus, instead of expanding the prion hypothesis to accommodate even more diseases such as Alzheimer’s and Parkinson’s [1], we suggest extending Anfinsen’s thermodynamic hypothesis to include protein folding into the amyloid conformation under supersaturated conditions. This classical biophysical framework fits better with the experimental evidence as it includes seeding (via homologous or heterologous seeds) without excluding other pathways of amyloid induction that do not involve a proteinaceous seed component (e.g., lipid/microbial catalyzed nucleation, protein overexpression). Such framework frees the phenomenon from the unnecessary constraints of templating, enabling a better understanding of the etiological factors triggering amyloid formation and hopefully opening novel avenues for therapeutic interventions.