Probing the Basis of α-Synuclein Aggregation by Comparing Simulations to Single-Molecule Experiments

Area of Science:

• Biochemistry
• Structural Biology
• Computational Biology

Background:

• Intrinsically disordered proteins (IDPs) are crucial in protein aggregation, implicated in diseases like Parkinson's.
• Determining the transient structures driving early aggregation of IDPs is challenging due to their disordered nature and heterogeneous mixtures.
• Computational methods struggle to sample relevant conformations for disordered proteins.

Purpose of the Study:

• To develop an integrated approach combining atomistic simulations and single-molecule measurements to study the early aggregation stages of IDPs.
• To identify specific residues and interactions critical for the stability of alpha-synuclein dimers.
• To discern probable structures within the disordered ensemble of alpha-synuclein dimers consistent with experimental data.

Main Methods:

• Integrated atomistic simulations with previously reported high-resolution single-molecule measurements.
• Simulated single-molecule pulling experiments (force spectroscopy) on alpha-synuclein dimers.
• Utilized Monte Carlo simulations to generate dimer structures and selected those with substantial structured content.
• Compared simulated force-extension curves with experimental optical trapping measurements.

Main Results:

• Simulated pulling curves generally aligned with experimental data, revealing a higher number of transient intermediates.
• Identified an ensemble of beta-rich dimer structures consistent with experimental findings.
• Deducted dimer interfaces from the identified beta-rich structures.
• Proposed specific druggable targets within alpha-synuclein structural motifs.

Conclusions:

• The integrated simulation and experimental approach effectively characterizes transient structures of IDPs.
• Beta-rich dimer structures of alpha-synuclein are consistent with experimental data.
• The identified structural motifs offer potential targets for therapeutic intervention against Parkinson's disease by preventing early oligomerization.