The process of amyloid fibril formation is causatively linked to many diseases, including Alzheimer’s disease, Parkinson’s disease, Huntingon’s disease, and familial amyloidotic polyneuropathy and cardiomyopathy. Although the exact mechanism of toxicity and the identity of the toxic species remain unknown, there is strong genetic and pathologic evidence that the process of amyloidogenesis is closely linked to these maladies. The mechanisms by which proteins assemble into amyloid vary, as do the reasons why some people are more likely to develop amyloid diseases than others. Some of the proteins that form amyloid and putatively cause amyloid disease, such as Aβ, huntingtin, and α-synuclein, are thought to be intrinsically

disordered. These assemble into amyloid in a highly concentration dependent process to form a cross β-sheet amyloid aggregate. Other amyloidogenic proteins, such as transthyretin, β₂-microglobulin, and the prion protein, exhibit well-defined native 3-dimensional structures and only form aggregates after partial unfolding or misfolding. Many amyloid diseases are familial, i.e. they are caused by mutations in genes encoding the protein that forms amyloid or a protein that is involved in the proteolytic processing of an amyloid precursor protein. For example, there are over one hundred point mutations in transthyretin that destabilize its native tetrameric fold, increasing the partially-folded monomer population and thus enhancing its amyloidogenicity, leading to familial amyloid polyneuropathy or cardiomyopathy. A point mutation at position 187 from an Asp to an Asn or Tyr in the protein gelsolin eliminates a Ca²⁺ binding site, destabilizing that protein domain and making it susceptible to aberrant cleavage first by furin in the Golgi compartment and then by a membraneassociated type I matrix metalloprotease outside the cell, yielding 8 and 5 kDa fragments. These peptide fragments then aggregate into amyloid, enabled by glycosaminoglycans, resulting in familial amyloidosis of the Finnish type or gelsolin amyloid disease. Although specific mutations in some proteins can lead to earlyonset amyloidoses, e.g. the L55P mutation in transthyretin leads to familial amyloid polyneuropathy in the second decade, much more frequently wild-type proteins will aggregate and cause sporadic disease in the aged. It remains unclear why amyloid diseases tend to affect the elderly, although it is becoming more clear that signaling pathways that maintain the proteome and strongly influence aging either share common components or in some cases are one in the same. For example, the proteostasis network capacity, which is strongly influenced by the unfolded protein response and the heat shock response, strongly influences the etiology of these diseases. Additionally, how the formation of amyloid leads to the apparently unique phenotype of each disease is still not well understood; whether deposited amyloid fibrils or intermediates leading to that deposition cause disease and how those species exhibit toxicity to cells are current topics of investigation. Understanding what triggers the onset of sporadic amyloid diseases not associated with any known mutation and the factors that hasten disease progression is of great interest. Learning more about these factors should lead to knew treatment strategies for these diseases.

Reference:

Siegel, S. J. (2008). Structure and energetics of amyloid. The Scripps Research Institute.

Bionanomaterials
Since amyloid fibrils are ordered self-assemblies, their use as bionanomaterials is of great interest. Amyloid could in principle be used as nanowires, gels, liquid crystals, and structural scaffolds. However, a better understanding of the energetics of amyloid will likely be required before any real applications result. As has been mentioned, the structure of many pathological amyloid fibrils are highly sensitive to the environment in which they are formed. Changing environmental conditions after the fibrils have formed can have a profound effect on their structure and stability, especially over a long period of time. For instance, β2-microglobulin fibrils formed at low pH dissolve when brought back to neutral conditions. Native amyloid may be better suited as a bionanomaterial because it has evolved to form amyloid, so it is likely that the structures formed are less frustrated and less susceptible to major changes in energy and structure upon an environmental change. Therefore, it is very important to carefully choose the amino acid sequences one uses to make amyloid-like bionanomaterials and to avoid using de novo designed sequences or disease-related amyloid sequences as a starting point if such sequences exhibit rough, highly concentration dependent amyloid landscapes.

Biophysics
As mentioned before, the stability of amyloid fibrils can be examined using fibril denaturation with chaotropes. To extract thermodynamic parameters from denaturation curves, approximations of two-state behavior are typically made. This type of analysis assumes there are no intermediates along the folding pathway, the folded state all adopts a single structure, and that the system is at equilibrium at the time of measurement. However, as discussed earlier, changing the environment of amyloid fibrils has a strong impact on the structure that it adopts. Adding chaotrope may change which structure is most stable, which would impact all of the assumptions made in doing this two-state approximation of amyloid denaturation. One must therefore be extremely careful when determining the stability of amyloid fibrils that these assumptions are in fact met (that the system is at equilibrium when measurements are taken and that the same structure is populated as chaotrope is added) before trying to obtain thermodynamic constants from amyloid denaturation curves.

Conclusion
It is important to understand how amyloid proteins transform from soluble monomeric units to insoluble, structured fibrils that cause disease so that viable treatment options for such maladies can be discovered. However, the polymerization mechanism most often used to describe amyloid formation, a nucleated polymerization, is likely too simplistic to describe the complexities of aggregation of pathological amyloid proteins. During a given in vitro aggregation reaction, species other than fibrils and monomers are observed, and the structures of aggregates formed depend strongly on the conditions in which the aggregation occurs and on the monomer concentration. This indicates that the folding energy landscapes of pathological amyloid proteins are not funneled, as would be the case for a typical protein; rather they are likely frustrated, containing many minima associated with different aggregate conformations that have similar energies. Therefore, slightly changing the conditions leads to a differently structured end product. For native amyloid, which has evolved its sequence to carry out its function from an amyloid structure, the folding energy landscape is likely funneled to avoid other structures that might not carry out its function properly. This has implications in the way we think about amyloid and study it biophysically, the use of amyloid fibrils for its material properties, and the design of therapeutics for treating amyloid diseases.

Reference:

Sarah J. Siegel. Structure and Energetics of Amyloid