分子動力學研究生物分子凝聚體中的相位調節劑

Abstract

液–液相分離（liquid–liquid phase separation, LLPS）是形成生物分子凝聚體的關鍵機制；越來越多的證據顯示，部分凝聚體可能會由液態樣狀轉變為較膠態樣（more gel-like）的組裝形式，並在如肌萎縮性側索硬化症（amyotrophic lateral sclerosis, ALS）等疾病情境下出現纖維狀結構。JSF1 被開發為一種可光控的分子，用於調控凝聚體的相態行為；在光啟動前後，完整的 JSF1 與其對應的 FUS50-60/R6 混合物呈現不同的相態特性。由於液態到膠態的成熟過程以及後續纖維形成通常發生在超出分子模擬可及的時間尺度上，本研究改以關注濃相狀態中由成分差異所驅動的重組，並將其視為可能通往成熟的早期前驅事件。本研究利用分子動力學模擬，將完整 JSF1 與不同組成調整的 FUS50-60/R6 混合物作為光啟動前後狀態的替代系統（proxies），以建立其相分離行為的分子層級模型。透過模擬共存的濃相與稀相，可萃取濃相與稀相的組成，並建構部分三元相圖，以與實驗相關條件進行比較。結果顯示，隨著 R6 濃度增加，液滴（濃相）的含水程度提高、FUS50-60 的擴散加快，且 π–π 與陽離子–π（cation–π）接觸的傾向增強。整體而言，這些模擬結果可補充實驗觀察，提供關於液滴相組成的分子層級資訊，並闡明所觀察到的相態行為與分子移動性背後的機制。

Liquid–liquid phase separation (LLPS) is essential for forming biomolecular condensates, and accumulating evidence suggests that some condensates undergo phase transitions from liquid-like states to more gel-like assemblies, with fibrillar structures emerging in disease contexts such as amyotrophic lateral sclerosis (ALS). JSF1 was developed as a light-responsive photocleavable peptide to modulate condensate phase behavior; intact JSF1 and the corresponding FUS50-60/R6 mixture after photoinitiation exhibit distinct phase properties. Because liquid-to-gel maturation and subsequent fibril formation typically occur on timescales beyond those accessible to molecular simulations, we instead focus on composition-driven reorganization within condensed states as potential early-stage precursors to maturation. Here, molecular dynamics simulations are used to model phase separation in intact JSF1 and composition-tuned FUS50-60/R6 mixtures as proxies for the pre- and post-photoinitiation states. Simulations of coexisting bulk phases enable extraction of condensed- and dilute-phase compositions and construction of part of the ternary phase diagram for comparison with experimentally relevant conditions. Increasing R6 concentration is associated with increased droplet hydration, accelerated FUS50-60 diffusion, and enhanced π–π and cation–π contact propensities. Overall, the simulations complement experimental observations by providing molecular-level insight into droplet phase composition and the mechanisms underlying observed phase behavior and mobility.