本质无序蛋白（IDP）参与各种基本生物活动，它们的行为对于更好地理解细胞中冗长但组织良好的信号转导特别重要。 IDP 表现出独特的矛盾特征，其亲和力低，但同时在识别其结合目标方面具有高特异性。转录因子 p53 在癌症抑制中发挥着至关重要的作用，利用其无序区域（例如 N 端反式激活结构域 2 (TAD2)）发挥其一些生物学功能。探索蛋白质之间的结合和解除结合过程具有挑战性，并且这些区域固有的无序特性使问题进一步复杂化。计算机模拟是补充实验的有力工具，可填补探索蛋白质之间结合/解离过程的空白。在这里，我们使用基于物理的 UNIted RESidue (UNRES) 力场和额外的 Go̅ 类势场，通过广泛的分子动力学 (MD) 模拟研究了 p300 Taz2 和 p53 TAD2 之间的结合机制。从 NMR 解析结构中提取的距离限制被施加于分子间残基对以加速结合模拟，其中 Taz2 被固定在类似天然的构象中，而无序的 TAD2 完全自由。从 TAD2 位于 Taz2 周围不同位置的六个结构开始，我们观察到亚稳态中间状态，其中 TAD2 的中间螺旋段锚定在结合口袋中，突出了 TAD2 螺旋在指导蛋白质识别中的重要性。基于物理的结合模拟表明，成功的结合是在一系列阶段之后实现的，包括（1）蛋白质碰撞以启动相遇复合物的形成，（2）TAD2的部分附着，以及最后（3）TAD2与结合物的完全附着。 Taz2 的正确装订袋。此外，基于机器学习的 PathDetect-SOM 用于识别两种结合途径、相遇复合物和中间状态。

Intrinsically disordered proteins (IDPs) engage in various fundamental biological activities, and their behavior is of particular importance for a better understanding of the verbose but well-organized signal transduction in cells. IDPs exhibit uniquely paradoxical features with low affinity but simultaneously high specificity in recognizing their binding targets. The transcription factor p53 plays a crucial role in cancer suppression, carrying out some of its biological functions using its disordered regions, such as N-terminal transactivation domain 2 (TAD2). Exploration of the binding and unbinding processes between proteins is challenging, and the inherently disordered properties of these regions further complicate the issue. Computer simulations are a powerful tool to complement the experiments to fill gaps to explore the binding/unbinding processes between proteins. Here, we investigated the binding mechanism between p300 Taz2 and p53 TAD2 through extensive molecular dynamics (MD) simulations using the physics-based UNited RESidue (UNRES) force field with additional Go̅-like potentials. Distance restraints extracted from the NMR-resolved structures were imposed on intermolecular residue pairs to accelerate binding simulations, in which Taz2 was immobilized in a native-like conformation and disordered TAD2 was fully free. Starting from six structures with TAD2 placed at different positions around Taz2, we observed a metastable intermediate state in which the middle helical segment of TAD2 is anchored in the binding pocket, highlighting the significance of the TAD2 helix in directing protein recognition. Physics-based binding simulations show that successful binding is achieved after a series of stages, including (1) protein collisions to initiate the formation of encounter complexes, (2) partial attachment of TAD2, and finally (3) full attachment of TAD2 to the correct binding pocket of Taz2. Furthermore, machine-learning-based PathDetect-SOM was used to identify two binding pathways, the encounter complexes, and the intermediate states.