Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas 77030, United States.
J Phys Chem B. 2022 Jun 23;126(24):4491-4500. doi: 10.1021/acs.jpcb.2c01253. Epub 2022 Jun 10.
The intrinsically disordered C-terminus of the prominent oncogenic protein KRAS-4B (KRAS) selectively interacts and clusters with phosphatidylserine (PS) lipids in the plasma membrane (PM). This 11-residue segment, called tK, contains a polybasic domain (PBD) of six contiguous lysine residues and a farnesylated cysteine. Previous molecular dynamics (MD) simulation studies of tK in phosphatidylcholine (PC)/PS bilayers have suggested that backbone conformational dynamics modulate tK-PS interactions. These simulations have been conducted in symmetric membranes whereas the PM is compositionally asymmetric, with the inner leaflet, where KRAS is localized, being enriched with PS and phosphatidylethanolamine (PE) lipids. To examine if bilayer asymmetry affects tK conformational dynamics and interaction with lipids, we conducted two 10 μs long MD simulations of tK bound to a PC/PS and a PC/PS/PE bilayer in which the PS and PE lipids are distributed in one leaflet. We found that, first, these compositional asymmetries caused differences in acyl chain dynamics between leaflets, but the equilibrium structural and dynamic properties of the two asymmetric bilayers are similar; second, in both systems tK is highly dynamic and samples at least two distinct conformational states; third, PS-tK hydrogen-bonding interactions vary with peptide backbone conformations, and lysine side chains in the PBD predominantly interact with the serine oxygens of PS. These results are in good agreement with previous observations of tK in symmetric membranes. The effects of POPS asymmetry or the presence of POPE on tK are limited to modulating the relative contribution of individual side chains to interactions with lipids and redistributing conformational substates. Additional observations include the larger flexibility of tK in the current simulations, which we attribute to the longer duration of the simulations and the use of the CHARMM36m force field, which more accurately models intrinsically disordered peptides such as tK.
致癌蛋白 KRAS-4B（KRAS）的无规则 C 端选择性地与质膜（PM）中的磷脂酰丝氨酸（PS）脂质相互作用并聚集。这个 11 个残基的片段，称为 tK，包含一个由六个连续赖氨酸残基组成的多碱性结构域（PBD）和一个法呢基化半胱氨酸。先前关于 tK 在磷脂酰胆碱（PC）/PS 双层中的分子动力学（MD）模拟研究表明，骨架构象动力学调节 tK-PS 相互作用。这些模拟是在对称膜中进行的，而 PM 在组成上是不对称的，其中 KRAS 定位的内叶富含 PS 和磷脂酰乙醇胺（PE）脂质。为了研究双层不对称性是否影响 tK 构象动力学及其与脂质的相互作用，我们对与 PC/PS 和 PC/PS/PE 双层结合的 tK 进行了两次 10 μs 长的 MD 模拟，其中 PS 和 PE 脂质分布在一个叶中。我们发现，首先，这些组成不对称性导致了双层之间的酰基链动力学的差异，但两个不对称双层的平衡结构和动态特性是相似的；其次，在这两种系统中，tK 高度动态，至少有两种不同的构象状态；第三，PS-tK 氢键相互作用随肽骨架构象而变化，PBD 中的赖氨酸侧链主要与 PS 的丝氨酸氧相互作用。这些结果与以前在对称膜中观察到的 tK 结果一致。POPS 不对称性或 POPE 的存在对 tK 的影响仅限于调节单个侧链与脂质相互作用的相对贡献，并重新分配构象亚态。其他观察结果包括在当前模拟中 tK 更大的灵活性，我们将其归因于模拟时间的延长和使用 CHARMM36m 力场，该力场更准确地模拟了 tK 等内源性无序肽。
