Exploring Intra- and Inter-Regional Interactions in the IDP α-Synuclein Using smFRET and MD Simulations

Theoretical concepts from polymer physics are often usedto describeintrinsically disordered proteins (IDPs). However, amino acid interactionswithin and between regions of the protein can lead to deviations fromtypical polymer scaling behavior and even to short-lived secondarystructures. To investigate the key interactions in the dynamic IDP & alpha;-synuclein (& alpha;S) at the amino acid level, we conductedsingle-molecule fluorescence resonance energy transfer (smFRET) experimentsand coarse-grained molecular dynamics (CG-MD) simulations. We findexcellent agreement between experiments and simulations. Our resultsshow that a physiological salt solution is a good solvent for & alpha;Sand that the protein is highly dynamic throughout its entire chain,with local intra- and inter-regional interactions leading to deviationsfrom global scaling. Specifically, we observe expansion in the C-terminalregion, compaction in the NAC region, and a slightly smaller distancebetween the C- and N-termini than expected. Our simulations indicatethat the compaction in the NAC region results from hydrophobic aliphaticcontacts, mostly between valine and alanine residues, and cation-& pi;interactions between lysine and tyrosine. In addition, hydrogen bondsalso seem to contribute to the compaction of the NAC region. The expansionof the C-terminal region is due to intraregional electrostatic repulsionand increased chain stiffness from several prolines. Overall, ourstudy demonstrates the effectiveness of combining smFRET experimentswith CG-MD simulations to investigate the key interactions in highlydynamic IDPs at the amino acid level.

Automated summary

Theoretical concepts from polymer physics are frequently used to describe the behavior of intrinsically disordered proteins (IDPs). However, interactions between amino acids within the protein can lead to deviations from typical polymer scaling behavior and the emergence of short-lived secondary structures. In this study, we investigated the interactions in the highly dynamic IDP α-synuclein at the amino acid level using single-molecule fluorescence resonance energy transfer experiments and molecular dynamics simulations. Our results demonstrate excellent agreement between experiments and simulations, revealing the effects of intra- and inter-regional interactions on the folding and conformation of α-synuclein. Overall, this study highlights the importance of combining experimental and computational approaches to understand the key interactions in highly dynamic IDPs.