Disclosing the aggregation mechanism of β2-microglobulin in amyloid disease

Protein β2-microglobulin (β2-m) is the causative agent of dialysis-related amyloidosis (DRA), a prevalent pathology affecting individuals undergoing long-term hemodialysis. The goal of this PhD project is to explore the early stage of the aggregation mechanism of β2-m with molecular simulations, using two model systems: the ΔN6 variant, a cleaved form lacking the six N-terminal residues, which is a major component of ex vivo amyloid plaques from DRA patients, and the single point D76N mutant, recently identified as the cause of an hereditary systemic amyloidosis affecting visceral organs. Methodologically, the main goal of this research project is the development of a Monte Carlo Ensemble Docking method with a cost function that considers shape, hydrophobic and electrostatic complementarity, the major drivers of protein-protein association. The D76N mutant populates two folding intermediates called I1 and I2, which display an unstructured C-terminus and two unstructured termini, respectively. The ΔN6 variant populates one folding intermediate, with an unstructured N-terminus. Protein-protein docking simulations predict an essential role for the termini and for the DE-loop (both variants), EF-loop (D76N mutant) and BC-loop (ΔN6 variant) in the dimerization mechanism of β2-m. The terminal regions are more relevant under acidic conditions while the BC-, DE- and EF-loops gain importance at physiological pH. Our results recapitulate experimental evidence according to which Phe30 and His31 (BC-loop), Arg45 (CD-loop), and Trp60 and Phe62 (DE-loop) are dimerization hotspots (i.e. residues triggering dimerization). Additionally, we predicted the involvement of new residues such as Tyr10 (A-strand), Lys75 (EF-loop), and Trp95 and Arg97 (C-terminus), thus providing new testable predictions to guide the research on β2-m amyloidogenesis. Finally we predicted that β2-m tetramerization is mainly driven by the self-association of dimers via the N- and C-terminal regions and the DE-loop, and identify Arg3 (N-terminus), Tyr10, Arg45, Phe56 (D-strand), Trp60 and Arg97 as essential residues in the process