PDF(Pubmed)
Abstract：
Anchoring of coagulation factors to anionic regions of the membrane involves the C2 domain as a key player. The rate of enzymatic reactions of the coagulation factors is increased by several orders of magnitude upon membrane binding. However, the precise mechanisms behind the rate acceleration remain unclear, primarily because of a lack of understanding of the conformational dynamics of the C2-containing factors and corresponding complexes. We elucidate the membrane-bound form of the C2 domain from human coagulation factor V (FV-C2) by characterizing its membrane binding the specific lipid-protein interactions. Employing all-atom molecular dynamics simulations and leveraging the highly mobile membrane-mimetic (HMMM) model, we observed spontaneous binding of FV-C2 to a phosphatidylserine (PS)-containing membrane within 2-25 ns across twelve independent simulations. FV-C2 interacted with the membrane through three loops (spikes 1-3), achieving a converged, stable orientation. Multiple HMMM trajectories of the spontaneous membrane binding provided extensive sampling and ample data to examine the membrane-induced effects on the conformational dynamics of C2 as well as specific lipid-protein interactions. Despite existing crystal structures representing presumed \"open\" and \"closed\" states of FV-C2, our results revealed a continuous distribution of structures between these states, with the most populated structures differing from both \"open\" and \"closed\" states observed in crystal environments. Lastly, we characterized a putative PS-specific binding site formed by K23, Q48, and S78 located in the groove enclosed by spikes 1-3 (PS-specificity pocket), suggesting a different orientation of a bound headgroup moiety compared to previous proposals based upon analysis of static crystal structures.
摘要：
将凝血因子锚定到膜的阴离子区域涉及C2域作为关键角色。在膜结合时，凝血因子的酶促反应速率增加了几个数量级。然而,速率加速背后的确切机制尚不清楚，主要是因为缺乏对含C2因子和相应复合物的构象动力学的理解。我们通过表征其膜结合特异性脂质-蛋白质相互作用来阐明人凝血因子V（FV-C2）的C2结构域的膜结合形式。采用全原子分子动力学模拟并利用高流动性膜模拟（HMMM）模型，在12次独立模拟中，我们观察到FV-C2与含磷脂酰丝氨酸（PS）的膜在2-25ns内的自发结合。FV-C2通过三个回路与膜相互作用（尖峰1-3），实现融合，方向稳定。自发膜结合的多个HMMM轨迹提供了广泛的采样和充足的数据，以检查膜诱导的对C2构象动力学的影响以及特定的脂质-蛋白质相互作用。尽管现有的晶体结构代表FV-C2的假定“开放”和“封闭”状态，我们的结果表明这些状态之间的结构的连续分布，在晶体环境中观察到的最密集的结构与“开放”和“封闭”状态不同。最后,我们表征了由K23，Q48和S78形成的推定的PS特异性结合位点，位于由尖峰1-3（PS特异性口袋）包围的凹槽中，根据静态晶体结构的分析，与先前的提议相比，提出了结合的头基部分的不同取向。
