Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States.
J Am Chem Soc. 2024 Jan 10;146(1):342-357. doi: 10.1021/jacs.3c09195. Epub 2023 Dec 19.
Intrinsically disordered proteins (IDPs) frequently mediate phase separation that underlies the formation of a biomolecular condensate. Together with theory and experiment, efficient coarse-grained (CG) simulations have been instrumental in understanding the sequence-specific phase separation of IDPs. However, the widely used Cα-only models are limited in capturing the peptide nature of IDPs, particularly backbone-mediated interactions and effects of secondary structures, in phase separation. Here, we describe a hybrid resolution (HyRes) protein model toward a more accurate description of the backbone and transient secondary structures in phase separation. With an atomistic backbone and coarse-grained side chains, HyRes can semiquantitatively capture the residue helical propensity and overall chain dimension of monomeric IDPs. Using GY-23 as a model system, we show that HyRes is efficient enough for the direct simulation of spontaneous phase separation and, at the same time, appears accurate enough to resolve the effects of single His to Lys mutations. HyRes simulations also successfully predict increased β-structure formation in the condensate, consistent with available experimental CD data. We further utilize HyRes to study the phase separation of TPD-43, where several disease-related mutants in the conserved region (CR) have been shown to affect residual helicities and modulate the phase separation propensity as measured by the saturation concentration. The simulations successfully recapitulate the effect of these mutants on the helicity and phase separation propensity of TDP-43 CR. Analyses reveal that the balance between backbone and side chain-mediated interactions, but not helicity itself, actually determines phase separation propensity. These results support that HyRes represents an effective protein model for molecular simulation of IDP phase separation and will help to elucidate the coupling between transient secondary structures and phase separation.
无定形蛋白质 (IDPs) 经常介导相分离，这是生物分子凝聚体形成的基础。理论和实验相结合，高效的粗粒化 (CG) 模拟在理解 IDPs 的序列特异性相分离方面发挥了重要作用。然而，广泛使用的 Cα 仅模型在捕捉 IDPs 的肽性质方面存在局限性，特别是在相分离中无法捕捉到肽链介导的相互作用和二级结构的影响。在这里，我们描述了一种混合分辨率 (HyRes) 蛋白质模型，旨在更准确地描述相分离中肽链的构象和瞬态二级结构。HyRes 模型具有原子化的肽链主链和粗粒化的侧链，可以半定量地捕捉单体 IDPs 的残基螺旋倾向和整体链尺寸。使用 GY-23 作为模型系统，我们表明 HyRes 足够高效，可以直接模拟自发相分离，同时也足够准确，可以解析单个 His 到 Lys 突变的影响。HyRes 模拟还成功预测了凝聚体中β-结构形成的增加，与现有的实验 CD 数据一致。我们进一步利用 HyRes 研究 TPD-43 的相分离，其中保守区域 (CR) 中的几个与疾病相关的突变已被证明会影响残余螺旋度，并调节相分离倾向，这是通过饱和浓度来衡量的。模拟成功地再现了这些突变对 TDP-43 CR 螺旋度和相分离倾向的影响。分析表明，实际上决定相分离倾向的是肽链主链和侧链介导的相互作用之间的平衡，而不是螺旋度本身。这些结果支持 HyRes 是一种有效的 IDP 相分离分子模拟蛋白质模型，并将有助于阐明瞬态二级结构与相分离之间的关系。
