Cell division control protein 42 homolog (Cdc42) protein, a Ras superfamily GTPase, regulates cellular activities, including cancer progression. Using all-atom molecular dynamics (MD) simulations and essential dynamic analysis (EDA), we investigated the structure and dynamics of the catalytic domains of GDP-bound (inactive) and GTP-bound (active) Cdc42 in solution. We discovered substantial differences in the dynamics of the inactive and active forms, particularly in the "insert region" (residues 122-135), which plays a role in Cdc42 activation and binding to effectors. The insert region has larger conformational flexibility in the GDP-bound than the GTP-bound Cdc42. The G2 loop and Switch I at the effector lobe of the catalytic domain exhibit large conformational changes in both the GDP- and GTP-bound systems, but in the GTP-bound Cdc42 the Switch I interactions with GTP are retained. Oncogenic mutations were identified in the Ras superfamily. In Cdc42, the G12V and Q61L mutations decrease the GTPase activity. We simulated these mutations in both GDP- and GTP-bound Cdc42. While the overall structural organization is quite similar between the wild-type and the mutants, there are small differences in the conformational dynamics, especially in the two Switch regions. Taken together, the G12V and Q61L mutations may play a similar role to their K-Ras counterparts in nucleotide binding and activation. The conformational differences which are mainly in the insert region and to a lesser extent in the Switch regions flanking the nucleotide binding site can shed light on binding and activation. We propose that the differences are due to a network of hydrogen bonds that gets disrupted when Cdc42 is bound to GDP, a disruption that does not exist in other Rho GTP-ases. The differences in the dynamics between the two Cdc42 states suggest that the inactive conformation has reduced ability to bind to effectors.

中文翻译：

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活性和非活性 Cdc42 的插入区域构象动力学不同


细胞分裂控制蛋白 42 同源物 (Cdc42) 蛋白是 Ras 超家族 GTP 酶，可调节细胞活动，包括癌症进展。利用全原子分子动力学 (MD) 模拟和基本动力学分析 (EDA)，我们研究了溶液中 GDP 结合（非活性）和 GTP 结合（活性）Cdc42 催化域的结构和动力学。我们发现非活性和活性形式的动力学存在显着差异，特别是在“插入区域”（残基 122-135），该区域在 Cdc42 激活和与效应器结合中发挥作用。插入区域在 GDP 结合中比 GTP 结合 Cdc42 具有更大的构象灵活性。催化结构域效应叶处的 G2 环和开关 I 在 GDP 和 GTP 结合系统中均表现出较大的构象变化，但在 GTP 结合的 Cdc42 中，开关 I 与 GTP 的相互作用得以保留。在 Ras 超家族中发现了致癌突变。在 Cdc42 中，G12V 和 Q61L 突变降低了 GTPase 活性。我们在 GDP 和 GTP 结合的 Cdc42 中模拟了这些突变。虽然野生型和突变体的整体结构组织非常相似，但构象动力学存在微小差异，特别是在两个 Switch 区域。总而言之，G12V 和 Q61L 突变可能在核苷酸结合和激活中发挥与其 K-Ras 对应物相似的作用。主要存在于插入区以及较小程度存在于核苷酸结合位点侧翼的开关区的构象差异可以揭示结合和激活。我们认为差异是由于当 Cdc42 与 GDP 结合时氢键网络受到破坏，这种破坏在其他 Rho GTP 酶中不存在。 两种 Cdc42 状态之间的动力学差异表明，非活性构象降低了与​​效应器结合的能力。