data for "A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway"

Protein-protein interactions are involved in a wide range of cellular processes. These interactions often involve intrinsically disordered proteins (IDPs) and protein binding domains. However, the details of IDP binding pathways are hard to characterize using experimental approaches, which can rarely capture intermediate states present at low populations. SH3 domains are common protein interaction domains that typically bind proline-rich disordered segments and are involved in cell signaling, regulation, and assembly. We hypothesized, given the flexibility of SH3 binding peptides, that their binding pathways include multiple steps important for function. Molecular dynamics simulations were used to characterize the steps of binding between the yeast Abp1p SH3 domain (AbpSH3) and a proline-rich IDP, ArkA. Before binding, the N-terminal segment 1 of ArkA is pre-structured and adopts a polyproline II helix, while segment 2 of ArkA (C-terminal) adopts a 310 helix, but is far less structured than segment 1. As segment 2 interacts with AbpSH3, it becomes more structured, but retains flexibility even in the fully engaged state. Binding simulations reveal that ArkA enters a flexible encounter complex before forming the fully engaged bound complex. In the encounter complex, transient nonspecific hydrophobic and long- range electrostatic contacts form between ArkA and the binding surface of SH3. The encounter complex ensemble includes conformations with segment 1 in both the forward and reverse orientation, suggesting that segment 2 may play a role in stabilizing the correct binding orientation. While the encounter complex forms quickly, the slow step of binding is the transition from the disordered encounter ensemble to the fully engaged state. In this transition, ArkA makes specific contacts with AbpSH3 and buries more hydrophobic surface. Simulating the binding between ApbSH3 and ArkA provides insight into the role of encounter complex intermediates and nonnative hydrophobic interactions for other SH3 domains and IDPs in general.蛋白质-蛋白质相互作用广泛参与各类细胞生命过程。这类相互作用通常涉及内在无序蛋白质（intrinsically disordered proteins, IDPs）与蛋白质结合结构域。然而，借助实验手段难以表征内在无序蛋白质结合通路的细节——这类实验方法极少能捕捉到低丰度存在的中间状态。SH3结构域（SH3 domains）是一类常见的蛋白质相互作用结构域，通常结合富含脯氨酸的无序区段，参与细胞信号转导、调控与组装过程。鉴于SH3结合肽段的柔性特征，我们推测其结合通路包含多个对功能至关重要的步骤。本研究采用分子动力学模拟（molecular dynamics simulations），表征了酵母Abp1p的SH3结构域（AbpSH3）与富含脯氨酸的内在无序蛋白质ArkA之间的结合过程。结合发生前，ArkA的N端区段1预先结构化，呈现聚脯氨酸II型螺旋（polyproline II helix）构象；而ArkA的C端区段2虽为3₁₀螺旋（3₁₀ helix）构象，但其结构化程度远低于区段1。当区段2与AbpSH3相互作用时，其结构化程度显著提升，但即便在完全结合状态下仍保留一定柔性。结合模拟结果显示，ArkA在形成完全结合的复合物前，会先形成柔性的遭遇复合物（encounter complex）。在该遭遇复合物中，ArkA与SH3的结合表面之间会形成瞬时的非特异性疏水相互作用与长程静电接触。遭遇复合物的构象集合中，区段1同时存在正向与反向两种取向，这提示区段2可能在稳定正确的结合取向中发挥作用。尽管遭遇复合物的形成速度较快，但结合过程的限速步骤是从无序的遭遇复合物集合向完全结合状态的转变。在这一转变过程中，ArkA与AbpSH3形成特异性相互作用，并掩埋了更多的疏水表面。对AbpSH3与ArkA结合过程的模拟，为理解其他SH3结构域与内在无序蛋白质的结合通路中遭遇复合物中间体与非天然疏水相互作用的作用提供了关键见解。