Conformational Ensemble Dynamics of Intrinsically Disordered Full-Length α- and β-Synuclein Monomers

Abnormal aggregation of α-synuclein (αS) into amyloid fibrils is a hallmark of neurodegenerative diseases such as Parkinson’s disease. In contrast, its homolog β-synuclein (βS), co-localized at presynaptic terminals, resists amyloid formation and can even inhibit αS fibrillization. However, how sequence variations affect their structural dynamics remains poorly understood. To address this, we conducted 100 independent 1000-ns atomistic discrete molecular dynamics simulations for both αS and βS monomers. Our results revealed that both proteins predominantly adopted intrinsically disordered conformations, punctuated by transient helices and β-sheets. Both αS and βS exhibited a conserved helical tendency in the first half of the N-terminal domain, while the latter half showed dynamic β-sheet characteristics, with αS displaying greater abundance. Notably, the non-amyloid component (NAC) region in αS—critical for its aggregation—frequently adopted dynamic β-sheet structures, whereas the homologous region in βS displayed a greater tendency toward dynamic helices. Despite being largely disordered, the C-terminal regions transiently interacted with β-sheet–prone segments, potentially acting as dynamic caps that limit β-sheet growth in both proteins. Free energy landscape analysis indicated a clear enthalpy–entropy trade-off: structured conformations were stabilized by lower potential energy but penalized by reduced entropy, whereas disordered states, despite higher potential energy, were entropically favored. Importantly, potential energy reduction in αS was primarily associated with β-sheet formation, while in βS it was mainly driven by helix formation. These findings offer mechanistic insight into the distinct conformational landscapes of αS and βS and establish a thermodynamic framework for understanding how sequence differences modulate their structural properties and functional roles.α-突触核蛋白（α-synuclein, αS）异常聚集形成淀粉样原纤维，是帕金森病等神经退行性疾病的标志性病理特征。与之相反，其同源蛋白β-突触核蛋白（β-synuclein, βS）可在突触前末梢共定位，不易形成淀粉样结构，甚至可抑制αS的原纤维形成。然而，序列差异如何影响二者的结构动态特性，目前仍知之甚少。为解决这一问题，我们针对αS与βS单体分别开展了100次独立的1000纳秒原子级离散分子动力学模拟。研究结果显示，两种蛋白均主要呈现内在无序构象，其间点缀着短暂存在的螺旋与β-折叠结构。αS与βS在N端结构域的前半段均表现出保守的螺旋形成倾向，而在后半段则展现出动态的β-折叠特征，且αS的β-折叠占比更高。值得注意的是，αS中与聚集密切相关的非淀粉样组分（non-amyloid component, NAC）区域常呈现动态β-折叠结构，而βS中对应的同源区域则更倾向于形成动态螺旋结构。尽管二者整体均呈无序状态，C端区域会与易形成β-折叠的片段发生瞬时相互作用，这可能作为动态“盖帽”结构限制两种蛋白的β-折叠延伸。自由能景观分析揭示了清晰的焓-熵权衡关系：有序构象的稳定依赖于更低的势能，却因熵的降低而受到制约；而无序状态虽势能更高，却在熵上更具优势。重要的是，αS的势能降低主要与β-折叠形成相关，而βS的势能降低则主要由螺旋形成驱动。本研究结果为解析αS与βS截然不同的构象图谱提供了机制层面的见解，并为理解序列差异如何调控二者的结构特性与功能角色建立了热力学框架。