Local ionic conditions modulate the aggregation propensity and influence the structural polymorphism of alpha-synuclein

Parkinson’s Disease (PD) is characterized by the aggregation of alpha-synuclein (aSyn), a presynaptic protein that transitions from a disordered monomer into beta-sheet rich amyloid fibrils. The precise triggers and mechanisms underlying aSyn misfolding and aggregation remain unclear, hindering the development of effective therapeutics. Monomeric aSyn is an intrinsically disordered protein (IDP) with high conformational flexibility. Local environmental factors, such as ion concentrations, can influence the conformational ensemble of aSyn, impacting its aggregation propensity and resulting in fibril polymorphism. In this study, we explore the impact of physiologically relevant ions, mainly Ca ²⁺ and Na ⁺ , on the aggregation kinetics, monomer structural dynamics, and fibril polymorphism of aSyn. Using ThT fluorescence assays, we demonstrate that all ions accelerate aSyn aggregation, with Ca ²⁺ having the most significant effect. Using Heteronuclear Single Quantum Correlation Nuclear Magnetic Resonance ( ¹ H- ¹⁵ NHSQC NMR) spectroscopy, we validate the specific binding of Ca ²⁺ ions at the C-terminus, whereas Na ⁺ ions display non-specific interactions along the sequence of aSyn. Small-angle neutron scattering (SANS) and hydrogen-deuterium exchange mass spectrometry (HDX-MS) further reveal that Na ⁺ and Ca ²⁺ induce distinct conformational changes in the aSyn monomer, with Na ⁺ leading to more extended structures and Ca ²⁺ promoting a moderate extension of the protein. Molecular dynamics simulations (MD) corroborate these findings, showing that Na ⁺ ions increase the protein’s extension, particularly between the non-amyloid beta component (NAC) region and the C-terminus, whereas Ca ²⁺ ions bias the ensemble towards a more moderately elongated structure. Using MD, we further investigate the local environment and in particular the solvent effect and show the water persistence times in the hydration shell are also increased in the presence of Ca ²⁺ ions, indicating that the aggregation propensity of the monomer is due to a combination of conformational bias of the monomer and solvent mobility. Atomic force microscopy (AFM) of aSyn fibrils formed under these different ionic conditions reveal distinct fibril polymorphs, suggesting that ion-induced conformational biases in the monomer contribute to the diversity of fibril structures. Collectively, these findings underscore the pivotal influence of the local ionic milieu in shaping the structure and aggregation propensity of aSyn, thus offering valuable insights into the molecular underpinnings of PD and potential therapeutic avenues aimed at manipulating aSyn conformational dynamics.