Abstract
We use molecular dynamics simulations of a full atomistic Gō model to explore the impact of selected DE-loop mutations (D59P and W60C) on the folding space of protein human β2-microglobulin (Hβ2m), the causing agent of dialysis-related amyloidosis, a conformational disorder characterized by the deposition of insoluble amyloid fibrils in the osteoarticular system. Our simulations replicate the effect of mutations on the thermal stability that is observed in experiments in vitro. Furthermore, they predict the population of a partially folded state, with 60% of native internal free energy, which is akin to a molten globule. In the intermediate state, the solvent accessible surface area increases up to 40 times relative to the native state in 38% of the hydrophobic core residues, indicating that the identified species has aggregation potential. The intermediate state preserves the disulfide bond established between residue Cys25 and residue Cys80, which helps maintain the integrity of the core region, and is characterized by having two unstructured termini. The movements of the termini dominate the essential modes of the intermediate state, and exhibit the largest displacements in the D59P mutant, which is the most aggregation prone variant. PROPKA predictions of pKa suggest that the population of the intermediate state may be enhanced at acidic pH explaining the larger amyloidogenic potential observed in vitro at low pH for the WT protein and mutant forms.
Highlights
Human β2-microglobulin (Hβ2m) is the non-covalently bound light chain of the human class I major histocompatibility complex (MHC-I), where it chaperones the complex assembly for antigen presentation
This effect is so striking that if we had restricted ourselves to the analysis of the free energy profiles of the mutants (Figure 2c) we would have concluded that the free energy minimum located at E ~ −400 is not an intermediate state, but a highly native-like denatured state instead
We found that the intermediate exhibits the disulfide bond between residues Cys25 and Cys80 (Figure S2), a structural feature which has been proposed to be a pre-requisite for β2m fibrillogenesis at neutral pH [3]
Summary
Human β2-microglobulin (Hβ2m) is the non-covalently bound light chain of the human class I major histocompatibility complex (MHC-I), where it chaperones the complex assembly for antigen presentation. The DE-loop region is a key structural element of the protein that has been shown to be a major determinant of the kinetics of fibril formation being both involved in the nucleation and elongation phases of fibril assembly at acidic pH 2.5 [17] This segment of the polypeptide chain accommodates several aromatic bulky residues that become solvent exposed in the monomeric (free) form of β2m being able to act as sticky patches in intermolecular association. This bulky amino acid, located at the apex of the DE-loop, is highly conserved amongst vertebrates and plays a critical role in assisting the association of the β2m with the MHC-I [20] These observations have motivated a series of in vitro experiments based on mutations of Trp and other nearby residues in order to establish their relevance for biological association of β2m [20,21,22,23,24].
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