In silico investigation of the structural stability as the origin of the pathogenicity of α-synuclein protofibrils

Abstract

α-Synuclein is a presynaptic neuronal protein. The fibril form of α-synuclein is a major constituent of the intraneuronal inclusion called Lewy body, a characteristic hallmark of Parkinson’s disease. Recent ssNMR and cryo-EM experiments of wild-type α-synuclein fibrils have shown polymorphism and observed two major polymorphs, rod and twister. To associate the cytotoxicity of α-synuclein fibrils with their structural features, it is essential to understand the origins of their structural stability. In this study, we performed molecular dynamics simulations of the two major polymorphs of wild-type α-synuclein fibrils. The predominance of specific fibril polymorphs was rationalized in terms of relative structural stability in aqueous environments, which was attributed to the cooperative contributions of various stabilizing features. The results of the simulations indicated that highly stable structures in aqueous environments could be maintained by the cooperation of compact sidechain packing in the hydrophobic core, backbone geometry of the maximal β-sheet content wrapping the hydrophobic core, and solvent-exposed sidechains with large fluctuations maximizing the solvation entropy. The paired structure of the two protofilaments provides additional stability, especially at the interface region, by forming steric zipper interactions and hiding the hydrophobic residues from exposure to water. The sidechain interaction analyses and pulling simulations showed that the rod polymorph has stronger sidechain interactions and exhibits higher dissociation energy than the twister polymorph. It is expected that our study will provide a basis for understanding the pathogenic behaviors of diverse amyloid strains in terms of their structural properties.

Communicated by Ramaswamy H. Sarma

Keywords:

• Parkinson’s disease
• α-synuclein
• amyloid polymorphism
• MD simulation
• steric zipper

Authors’ contributions

S. S. and J. Y. designed the project with the discussion by K. L. The calculations and analysis were carried out by M. L. and Y. P. J. Y. and M. L. wrote the manuscript with contributions from Y. P. All authors contributed to the manuscript revision.

Disclosure statement

The authors declare no competing financial interest.

Additional information

Funding

This work was supported by the National Research Foundation of Korea (NRF) grants funded by the Korea government (MSIP): NRF-2020M3A9G7103933 and NRF-2021R1A5A1030054.