Senyuz Simge, Jang Hyunbum, Nussinov Ruth, Keskin Ozlem, Gursoy Attila
Computational Science and Engineering, Koc University, Rumelifeneri Yolu, 34450 Sariyer, Istanbul, Turkey.
Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland 21702, United States.
J Phys Chem B. 2021 Apr 22;125(15):3790-3802. doi: 10.1021/acs.jpcb.1c00883. Epub 2021 Apr 13.
Rac1 is a small GTPase that plays key roles in actin reorganization, cell motility, and cell survival/growth as well as in various cancer types and neurodegenerative diseases. Similar to other Ras superfamily GTPases, Rac1 switches between active GTP-bound and inactive GDP-bound states. Switch I and II regions open and close during GDP/GTP exchange. P29S and A159V (paralogous to K-Ras) mutations are the two most common somatic mutations of Rac1. Rac1 is a known hotspot for melanoma, whereas Rac1 most commonly occurs in head and neck cancer. To investigate how these substitutions induce the Rac1 dynamics, we used atomistic molecular dynamics simulations on the wild-type Rac1 and two mutant systems (P29S and A159V) in the GTP bound state, and on the wild-type Rac1 and P29S mutated system in the GDP bound state. Here, we show that P29S and A159V mutations activate Rac1 with different mechanisms. In Rac1-GTP, the substitution increases the flexibility of Switch I based on RMSF and dihedral angle calculations and leads to an open conformation. We propose that the open Switch I conformation is one of the underlying reasons for rapid GDP/GTP exchange of Rac1. On the other hand, in Rac1-GTP, some of the contacts of the guanosine ring of GTP with Rac1 are temporarily lost, enabling the guanosine ring to move toward Switch I and subsequently close the switch. Rac1-GTP adopts a Ras state 2 like conformation, where both switch regions are in closed conformation and Thr35 forms a hydrogen bond with the nucleotide.
Rac1是一种小GTP酶，在肌动蛋白重组、细胞运动以及细胞存活/生长中发挥关键作用，在多种癌症类型和神经退行性疾病中也有涉及。与其他Ras超家族GTP酶类似，Rac1在活性GTP结合状态和非活性GDP结合状态之间切换。在GDP/GTP交换过程中，开关I和II区域会打开和关闭。P29S和A159V（与K-Ras同源）突变是Rac1最常见的两种体细胞突变。Rac1是黑色素瘤的一个已知热点区域，而Rac1最常出现在头颈癌中。为了研究这些取代如何诱导Rac1的动力学变化，我们对处于GTP结合状态的野生型Rac1和两个突变系统（P29S和A159V）以及处于GDP结合状态的野生型Rac1和P29S突变系统进行了原子分子动力学模拟。在这里，我们表明P29S和A159V突变通过不同机制激活Rac1。在Rac1-GTP中，基于均方根波动（RMSF）和二面角计算，该取代增加了开关I的灵活性并导致开放构象。我们提出，开关I的开放构象是Rac1快速进行GDP/GTP交换的潜在原因之一。另一方面，在Rac1-GTP中，GTP的鸟苷环与Rac1的一些接触会暂时丢失，使鸟苷环能够向开关I移动并随后关闭开关。Rac1-GTP采用类似Ras状态2的构象，其中两个开关区域均处于关闭构象，且苏氨酸35与核苷酸形成氢键。
