Ngo Van A, Sarkar Sumantra, Neale Chris, Garcia Angel E
Center for Nonlinear Studies (CNLS), Los Alamos National Lab, Los Alamos, New Mexico 87545, United States.
Theoretical Biology and Biophysics Group, T-6, Los Alamos National Lab, Los Alamos, New Mexico 87545, United States.
J Phys Chem B. 2020 Jul 2;124(26):5434-5453. doi: 10.1021/acs.jpcb.0c02642. Epub 2020 Jun 8.
RAS proteins are small membrane-anchored GTPases that regulate key cellular signaling networks. It has been recently shown that different anionic lipid types can affect the spatiotemporal properties of RAS through dimerization/clustering and signaling fidelity. To understand the effects of anionic lipids on key spatiotemporal properties of RAS, we dissected 1 ms of data from all-atom molecular dynamics simulations for KRAS4B on two model anionic lipid membranes that have 30% of POPS mixed with neutral POPC and 8% of PIP2 mixed with POPC. We unveiled the orientation space of KRAS4B, whose kinetics were slower and more distinguishable on the membrane containing PIP2 than the membrane containing POPS. Particularly, the PIP2-mixed membrane can differentiate a third kinetic orientation state from the other two known orientation states. We observed that each orientation state may yield different binding modes with an RAF kinase, which is required for activating the MAPK/ERK signaling pathway. However, an overall occluded probability, for which RAF kinases cannot bind KRAS4B, remains unchanged on the two different membranes. We identified rare fast diffusion modes of KRAS4B that appear coupled with orientations exposed to cytosolic RAF. Particularly, on the membrane having PIP2, we found nonlinear correlations between the orientation states and the conformations of the cationic farnesylated hypervariable region, which acts as an anchor in the membrane. Using diffusion coefficients estimated from the all-atom simulations, we quantified the effect of PIP2 and POPS on the KRAS4B dimerization via Green's function reaction dynamics simulations, in which the averaged dimerization rate is 12.5% slower on PIP2-mixed membranes.
RAS蛋白是一类小型膜锚定GTP酶，可调节关键的细胞信号网络。最近的研究表明，不同类型的阴离子脂质可通过二聚化/聚集以及信号保真度来影响RAS的时空特性。为了了解阴离子脂质对RAS关键时空特性的影响，我们从全原子分子动力学模拟中提取了1毫秒的数据，该模拟针对的是KRAS4B在两种模型阴离子脂质膜上的情况，一种膜含有30%的POPS与中性POPC混合，另一种膜含有8%的PIP2与POPC混合。我们揭示了KRAS4B的取向空间，其动力学在含有PIP2的膜上比含有POPS的膜上更慢且更具可区分性。特别地，含有PIP2的混合膜能够区分出一种与其他两种已知取向状态不同的第三种动力学取向状态。我们观察到，每种取向状态可能会产生与RAF激酶不同的结合模式，而RAF激酶是激活MAPK/ERK信号通路所必需的。然而，RAF激酶无法结合KRAS4B的总体封闭概率在两种不同的膜上保持不变。我们确定了KRAS4B罕见的快速扩散模式，这些模式似乎与暴露于胞质RAF的取向相关联。特别是，在含有PIP2的膜上，我们发现了取向状态与阳离子法尼基化高变区构象之间的非线性相关性，该高变区在膜中起锚定作用。利用从全原子模拟中估计的扩散系数，我们通过格林函数反应动力学模拟量化了PIP2和POPS对KRAS4B二聚化的影响，其中在含有PIP2的混合膜上平均二聚化速率慢12.5%。
