Direct Observation of β-Barrel Intermediates in the Self-Assembly of Toxic SOD128–38 and Absence in Nontoxic Glycine Mutants

• DOI: 10.1021/acs.jcim.0c01319
• Publication Date: 2021-01-15T05:02:58Z
• Authors: Yunxiang Sun; Junchao Huang; Xiangmei Duan; Feng Ding
• Keywords: aggregation intermediates; β- barrels; 0301 basic medicine; Amyloid; Chemical Sciences not elsewhere classified; Biophysics; Glycine; Biochemistry; G 33V mutants; mutants G 33V; 03 medical and health sciences; superoxide dismutase 1; Superoxide Dismutase-1; single-layer β- sheets; SOD; β- sheet-rich oligomers; Cancer; Nontoxic Glycine Mutants Soluble lo.; 0303 health sciences; Amyloid beta-Peptides; Ecology; Superoxide Dismutase; amyloid; 33W; β- barrel oligomers; two-layer β- sheets; Protein Conformation, beta-Strand; Neuroscience; Single-point glycine substitutions

Soluble low-molecular-weight oligomers formed during the early stage of amyloid aggregation are considered the major toxic species in amyloidosis. The structure-function relationship between oligomeric assemblies and the cytotoxicity in amyloid diseases are still elusive due to the heterogeneous and transient nature of these aggregation intermediates. To uncover the structural characteristics of toxic oligomeric intermediates, we compared the self-assembly dynamics and structures of SOD128-38, a cytotoxic fragment of the superoxide dismutase 1 (SOD1) associated with the amyotrophic lateral sclerosis, with its two nontoxic mutants G33V and G33W using molecular dynamics simulations. Single-point glycine substitutions in SOD128-38 have been reported to abolish the amyloid toxicity. Our simulation results showed that the toxic SOD128-38 and its nontoxic mutants followed different aggregation pathways featuring distinct aggregation intermediates. Specifically, wild-type SOD128-38 initially self-assembled into random-coil-rich oligomers, among which fibrillar aggregates composed of well-defined curved single-layer β-sheets were nucleated via coil-to-sheet conversions and the formation of β-barrels as intermediates. In contrast, the nontoxic G33V/G33W mutants readily assembled into small β-sheet-rich oligomers and then coagulated with each other into cross-β fibrils formed by two-layer β-sheets without forming β-barrels as the intermediates. The direct observation of β-barrel oligomers during the assembly of toxic SOD128-38 fragments but not the nontoxic glycine-substitution mutants strongly supports β-barrels as the toxic oligomers in amyloidosis, probably via interactions with the cell membrane and forming amyloid pores. With well-defined structures, the β-barrel might serve as a novel therapeutic target against amyloid-related diseases.