Exploring Structural Insights of Aβ42 and α‑Synuclein Monomers and Heterodimer: A Comparative Study Using Implicit and Explicit Solvent Simulations

• Published in: The journal of physical chemistry. B 2024-05, Vol.128 (19), p.4655-4669
• Main Authors: Varenyk, Yuliia, Theodorakis, Panagiotis E., Pham, Dinh Q. H., Li, Mai Suan, Krupa, Paweł
• Format: Article
• Language: English
• Subjects: alpha-Synuclein - chemistry; alpha-Synuclein - metabolism; Amyloid beta-Peptides - chemistry; Amyloid beta-Peptides - metabolism; B: Biophysical and Biochemical Systems and Processes; Humans; Molecular Dynamics Simulation; Peptide Fragments - chemistry; Peptide Fragments - metabolism; Protein Multimerization; Solvents - chemistry
• ISSN: 1520-6106; 1520-5207; 1520-5207
• DOI: 10.1021/acs.jpcb.4c00503

Protein misfolding, aggregation, and fibril formation play a central role in the development of severe neurological disorders, including Alzheimer’s and Parkinson’s diseases. The structural stability of mature fibrils in these diseases is of great importance, as organisms struggle to effectively eliminate amyloid plaques. To address this issue, it is crucial to investigate the early stages of fibril formation when monomers aggregate into small, toxic, and soluble oligomers. However, these structures are inherently disordered, making them challenging to study through experimental approaches. Recently, it has been shown experimentally that amyloid-β 42 (Aβ42) and α-synuclein (α-Syn) can coassemble. This has motivated us to investigate the interaction between their monomers as a first step toward exploring the possibility of forming heterodimeric complexes. In particular, our study involves the utilization of various Amber and CHARMM force-fields, employing both implicit and explicit solvent models in replica exchange and conventional simulation modes. This comprehensive approach allowed us to assess the strengths and weaknesses of these solvent models and force fields in comparison to experimental and theoretical findings, ensuring the highest level of robustness. Our investigations revealed that Aβ42 and α-Syn monomers can indeed form stable heterodimers, and the resulting heterodimeric model exhibits stronger interactions compared to the Aβ42 dimer. The binding of α-Syn to Aβ42 reduces the propensity of Aβ42 to adopt fibril-prone conformations and induces significant changes in its conformational properties. Notably, in AMBER-FB15 and CHARMM36m force fields with the use of explicit solvent, the presence of Aβ42 significantly increases the β-content of α-Syn, consistent with the experiments showing that Aβ42 triggers α-Syn aggregation. Our analysis clearly shows that although the use of implicit solvent resulted in too large compactness of monomeric α-Syn, structural properties of monomeric Aβ42 and the heterodimer were preserved in explicit-solvent simulations. We anticipate that our study sheds light on the interaction between α-Syn and Aβ42 proteins, thus providing the atom-level model required to assess the initial stage of aggregation mechanisms related to Alzheimer’s and Parkinson’s diseases.