A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway.
A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway.
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DOI：
10.1371/journal.pcbi.1007815
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发表时间：
2020-09
影响因子：
4.3
通讯作者：
Ball KA
中科院分区：
文献类型：
--
作者：
Gerlach GJ;Carrock R;Stix R;Stollar EJ;Ball KA
蛋白质-蛋白质相互作用涉及广泛的细胞过程。这些相互作用通常涉及内在无序蛋白（IDP）和蛋白质结合结构域。然而，IDP结合途径的细节很难用实验方法来表征，这很少能捕捉到低种群存在的中间状态。SH 3结构域是常见的蛋白质相互作用结构域，其通常结合富含脯氨酸的无序片段，并参与细胞信号传导、调节和组装。我们假设，考虑到SH 3结合肽的灵活性，它们的结合途径包括对功能重要的多个步骤。分子动力学模拟被用来表征酵母Abp 1 p SH 3结构域（AbpSH 3）和富含脯氨酸的IDP，ArkA之间的结合步骤。在结合之前，ArkA的N-末端片段1是预结构化的，并采用聚脯氨酸II螺旋，而ArkA的片段2（C-末端）采用310螺旋，但远不如片段1结构化。当片段2与AbpSH 3相互作用时，它变得更加结构化，但即使在完全接合状态下也保持灵活性。绑定模拟表明，ArkA进入一个灵活的遭遇复杂的形成之前，充分参与绑定复合体。在相遇复合物中，ArkA和SH 3的结合表面之间形成瞬时非特异性疏水和长程静电接触。遇到复杂的合奏包括构象与节段1在正向和反向方向，这表明节段2可能发挥作用，稳定正确的结合方向。虽然相遇复合体快速形成，但结合的缓慢步骤是从无序相遇系综过渡到完全参与状态。在这个转变中，ArkA与AbpSH 3特异性接触，并掩埋更疏水的表面。模拟ApbSH 3和ArkA之间的结合提供了对遇到复杂中间体和其他SH 3结构域和IDP的非天然疏水相互作用的作用的了解。复杂的细胞过程是由蛋白质之间的相互作用介导的，为了确定这些相互作用如何影响细胞功能和结合动力学，我们通常必须了解蛋白质结合途径。许多蛋白质相互作用结构域，如SH 3结构域，在耦合的折叠和结合过程中与内在无序的蛋白质结合。使用分子动力学模拟，我们发现，无序的ArkA肽的结合酵母Abp 1 p SH 3结构域的收益，通过一个灵活的，无序的遭遇复杂之前，达到一个稳定的完全结合状态。相遇复合物通过肽和结构域之间的非特异性长程静电相互作用和非特异性疏水相互作用来稳定。我们的模拟突出了疏水相互作用在整个SH 3结合过程中的重要作用：在遇到复杂的非特异性疏水接触和特定的疏水接触在完全结合的复杂。相遇复合物可能是理解SH 3结构域相互作用的功能行为的关键，因为相遇复合物形成得非常快，而过渡到完全结合状态的速度较慢。在细胞中，SH 3结构域可以与许多潜在的结合伴侣快速且非特异性地形成相遇复合物，使其能够在完成结合过程之前搜索正确的识别序列。
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. Complex cellular processes are mediated by interactions between proteins, and to determine how these interactions affect cellular function and binding kinetics we often must understand the protein binding pathway. Many protein interaction domains, such as the SH3 domain, bind to intrinsically disordered proteins in a coupled folding and binding process. Using molecular dynamics simulations, we find that the binding of the disordered ArkA peptide to the yeast Abp1p SH3 domain proceeds through a flexible, disordered encounter complex before reaching a stable fully bound state. The encounter complex is stabilized by nonspecific long-range electrostatic interactions and nonspecific hydrophobic interactions between the peptide and domain. Our simulations highlight the important role of hydrophobic interactions in the entire SH3 binding process: both nonspecific hydrophobic contacts in the encounter complex and specific hydrophobic contacts in the fully bound complex. The encounter complex could be key to understanding the functional behavior of SH3 domain interactions because the encounter complex forms very quickly and the transition to the fully bound state is slower. In cells, an SH3 domain may form an encounter complex quickly and nonspecifically with many potential binding partners, allowing it to search for the correct recognition sequence before completing the binding process.
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影响因子：
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作者：
Dahal L;Shammas SL;Clarke J
通讯作者：
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