Metastable Configurations and Nucleation of Protein Aggregation

Protein amyloid formation represents an essential feature of the polypeptide chemistry and plays a central role in human pathology and the biology of living organisms. Understanding general structural pathways in protein aggregation, as well as disease‐related specifics will aid greatly our understanding the protein folding and structure‐function relationships. Here a new emphasis is placed on the spontaneous covalent modification of polypeptide and its impact on protein aggregation. The major goal is to generate structural information on early aggregation of amyloid protein alpha‐synuclein (αS) that is involved in propagation of Parkinson's, Alzheimer's, Huntington's, Creutzfeldt‐Jakob, multiple system atrophy, Hallervorden‐Spatz syndrome, and many other neurological disorders. Biophysical assessment of the αS aggregation in vitro reveals two distinct stages. The first stage presents the slow phase separation process driven by non‐specific interactions between protein counterparts. This stage involves the formation of reversible protein aggregates ( weak flocculation ) and the growth of “protein phase”. The second stage constitutes the structural phase transition, i.e., formation of the irreversible protein aggregates such as mature fibrils ( coalescence ). Noteworthy, the macro‐crowding effects within the “protein phases” reinforce the N‐N cis‐configurations in confined proteins. These local structures become a subject of covalent modification by the same mechanism as seen for the intrinsic chromophore of 4‐(p‐hydroxybenzylidene)‐5‐imidazolinone‐type in the family of green fluorescent proteins. Importantly, this type of the covalent alterations is initiated concurrently with amyloid elongation and involves a complex multi‐step process of chain cyclization, amino acid dehydration and aerial oxidation.