(507d) Studying Self-Assembly of Key Motifs in N-Terminal of ?-Synuclein Using Discontinuous Molecular Dynamics Simulations

The aggregation of human α-synuclein (αSyn) is associated with many neurodegenerative diseases called “synucleinopathies” such as Parkinson’s disease, dementia with Lewy bodies and multiple system atrophy. Development of treatments for these diseases, which affect millions of people worldwide, requires in-depth understanding of the self-assembly process of the αSyn protein. Both the non-amyloid component (NAC) region of αSyn (residues 61-95) and the preNAC region (residues 1-60), the latter of which contains seven familial mutations, are thought to play important roles in αSyn fibrillation. Of the sixty residues in the αSyn preNAC region, two segments P1 (residues 36-42) and P2 (residues 45-57) have been found experimentally to be modulators of the aggregation of the full length αSyn¹. Eliminating P1 resulted in inhibition of αSyn aggregation in neutral pH environments. Inhibition was observed when removing combined P1 and P2 in both neutral and acidic environments.

We have been investigating the aggregation mechanisms of motifs that contain both P1 and P2, searching for the key factors that seed or inhibit the aggregation of full length αSyn. Discontinuous molecular dynamics simulation with the PRIME20 force field was used to study self-assembly of P3 (residues 36-57), P3Plus (residues 32-61) and P3NExtend (residues 27-57). Each segment was examined at a simulation condition that supports fibril formation - a 24-peptide system at 10mM and temperature 330.5K. Our computational results predict high β-structure propensity for all three motifs, as expected based on their secondary structure propensity scores according to Kang et al.² The fibrillar structures that form in our simulations contain a preponderance of aligned β-hairpins. These findings are consistent with those of Salveson et al.³ who reported experiments showing that peptides of residues 36-55 adopt β-hairpin structures during oligomerization. Mirecka et al.⁴ successfully inhibited full length αSyn aggregation by inducing β-hairpin formation in the P3 region with a β-wrapin. These experiments suggest the essential role played by the β-hairpin structures formed by P3 region in determining whether full length αSyn aggregates or not. Our simulations of the wildtype P3, P3Plus and P3NExtend as well as their point mutations (currently L38A, L38M and V40A) have allowed us to understand the aggregation mechanisms and nucleation processes, and to identify which residues are aggregation prone. We also describe the results of an effort to design inhibitor peptides targeted to certain regions on the full-length αSyn to prevent elongation of αSyn aggregates. This is done using a highly efficient computational peptide binding design algorithm, PepBD. Based on the binding energy to the target (NAC 68-78), three prototypes have been selected; these are under further investigation in silico before being tested in vitro.

1. Doherty et al. Struct. Mol. Biol. 27, 249-259 (2020).
2. Kang et al. Protein Science. 21, 911-917 (2012).
3. Salveson et al. J. Am. Chem. Soc. 138, 4458-4467 (2016).
4. Mirecka et al. Angew. Int. Ed. 53, 4227-4230 (2014).