Membrane Interactions of α-Synuclein Revealed by Multiscale Molecular Dynamics Simulations, Markov State Models, and NMR

Abstract

α-Synuclein is a presynaptic protein that binds to cell membranes and is linked to Parkinson's disease (PD). Whilst the normal function of remains α-synuclein remains uncertain, it is thought that oligomerization of the protein on the cell membrane contributes to cell damage.Knowledge of how α-synuclein binds to lipid bilayers is therefore of great interest as a likely first step in the molecular pathophysiology of PD, and may provide insight of the phenotype of PD-promoting mutations. We use coarse-grained and atomistic simulations in conjunction with NMR and cross-linking mass spectrometry studies of α-synuclein bound to anionic lipid bilayers to reveal a break in the helical structure of the NAC region, which may give rise to subsequent oligomer formation. Coarse-grained simulations of α-synuclein show that the interhelical region leads recognition and binding to both POPG and mixed composition bilayers and identifies important protein-lipid contacts, including those in the region between the two helices in the folded structure. We extend these simulations with all-atom simulations of the initial binding event to reveal details of the time-progression of lipid binding. We present secondary structure analysis that reveals points of possible β-strand formation in the structure, and investigate intramolecular contacts with simulations and mass-spectrometry crosslinking.Additionally we show how Markov state models can be used to investigate possible conformational changes of membrane bound α-synuclein in the NAC region, and we extract representative structures. These structural insights will aid the design and development of novel therapeutic approaches.a-syn_ms_v19 biorxiv.docx 17-Jun-20 α-Synuclein is a protein implicated in neurodegenerative disorders including Parkinson's disease and Lewy body dementia (1). Its function in healthy neurons remains uncertain (2).Lipid bilayer association of α-synuclein is thought to be important for its biological function in regulating synaptic vesicles, where it has been shown to be essential for SNARE complex assembly at the presynaptic membrane (3,4). It has been postulated to have a wide range of functions, including neuronal differentiation (4) and suppression of apoptosis (5). It is thought that toxicity towards neurones arises from the interaction of misfolded/aggregated α-synuclein with the lipid bilayer component of cell membranes (6). Thus, defining the interactions between α-synuclein and lipid bilayers is a key step in understanding the mode of action of αsynuclein, thus helping to provide a route towards drug research aimed at presenting or reversing its cellular effects .Native α-synuclein is an intrinsically disordered monomeric protein in solution (7-9). SAXS and NMR-derived experimental data suggest relatively small amounts of compaction in the ensemble of free α-synuclein (10,11). In contrast to these observations some discrete molecular dynamics (MD) simulations (12) combined with crosslinking data (13) have been interpreted as suggesting that part of the ens...

The effect of lipid composition on the dynamics of tau fibrils

“…The CG trajectories are used to model the long timescales of the binding of proteins to the lipids. The CG cutoff for the contacts are taken to be 0.7 nm according to the α ‐synuclein binding work by Sansom group 68 . The center‐of‐mass distance between the tau peptides and the lipids are computed across all the trajectories and are given in the Supporting Information (Figure S18 and S19).…”

“…The CG cutoff for the contacts are taken to be 0.7 nm according to the α-synuclein binding work by Sansom group. 68 The center-of-mass distance between the tau peptides and the lipids are computed across all the trajectories and are given in the Supporting Information (Figure S18 and S19). The highest number of contacts are observed in the system with PG lipids, and the least number of contacts in system with PC lipids.…”

The Effect of Lipid Composition on the Dynamics of Tau Fibrils

“…The CG cutoff for the contacts are taken to be 0.7 nm according to the α -synuclein binding work by Sansom group. 42 The center-of-mass distance between the tau-peptides and the lipids are computed across all the trajectories and are given in the Supporting Information (Figure S15 – S16). The highest number of contacts are observed in the system with POPG lipids, and the least number of contacts in system with POPC lipids.…”

Optimizing epitope conformational ensembles usingα-synuclein cyclic peptide “glycindel” scaffolds: A customized immunogen method for generating oligomer-selective antibodies for Parkinson’s disease

“…These monomer PDB entries are partly structured (containing α -helices) by binding to micelles (e.g. PDB 2KKW and 1XQ8), and are thought to be involved in various aspects of α -synuclein physiology ( 37 – 42 ). Thus, membrane-bound PDB monomer structures are treated separately from the unstructured isolated monomer ensemble.…”