Inter-domain Communication Mechanisms in an ABC Importer: A Molecular Dynamics Study of the MalFGK₂E Complex

ATP-Binding Cassette transporters are ubiquitous membrane proteins that convert the energy from ATP-binding and hydrolysis into conformational changes of the transmembrane region to allow the translocation of substrates against their concentration gradient. Despite the large amount of structural and biochemical data available for this family, it is still not clear how the energy obtained from ATP hydrolysis in the ATPase domains is “transmitted” to the transmembrane domains. In this work, we focus our attention on the consequences of hydrolysis and inorganic phosphate exit in the maltose uptake system (MalFGK2E) from Escherichia coli. The prime goal is to identify and map the structural changes occurring during an ATP-hydrolytic cycle. For that, we use extensive molecular dynamics simulations to study three potential intermediate states (with 10 replicates each): an ATP-bound, an ADP plus inorganic phosphate-bound and an ADP-bound state. Our results show that the residues presenting major rearrangements are located in the A-loop, in the helical sub-domain, and in the “EAA motif” (especially in the “coupling helices” region). Additionally, in one of the simulations with ADP we were able to observe the opening of the NBD dimer accompanied by the dissociation of ADP from the ABC signature motif, but not from its corresponding P-loop motif. This work, together with several other MD studies, suggests a common communication mechanism both for importers and exporters, in which ATP-hydrolysis induces conformational changes in the helical sub-domain region, in turn transferred to the transmembrane domains via the “coupling helices”.ATP结合盒（ATP-Binding Cassette, ABC）转运蛋白是一类广泛分布的膜蛋白，能够将ATP结合与水解过程中释放的能量转化为跨膜区域的构象变化，从而实现底物逆浓度梯度的跨膜转运。尽管目前针对该家族已积累了海量结构与生化研究数据，但ATP酶结构域中ATP水解所产生的能量如何“传递”至跨膜结构域，其具体机制仍未阐明。本研究聚焦于大肠杆菌麦芽糖摄取系统（MalFGK2E）中ATP水解与无机磷酸释放所引发的效应，核心目标是识别并定位ATP水解循环过程中发生的结构变化。为此，我们采用大规模分子动力学模拟，对三种潜在中间态开展研究，每组设置10次重复模拟：ATP结合态、ADP结合无机磷酸态，以及ADP结合态。研究结果显示，发生显著构象重排的氨基酸残基主要位于A环、螺旋亚结构域以及EAA基序（EAA motif）区域，尤其是偶联螺旋（coupling helices）区段。此外，在一次ADP结合态的模拟中，我们观察到核苷酸结合结构域二聚体（Nucleotide-Binding Domain dimer, NBD dimer）发生打开，同时ADP从ABC特征基序（ABC signature motif）上脱离，但并未从对应的P环基序（P-loop motif）上解离。本研究结合其他多项分子动力学研究成果，提示输入型与输出型ABC转运蛋白存在共通的通讯机制：ATP水解诱导螺旋亚结构域区域发生构象变化，进而通过偶联螺旋将信号传递至跨膜结构域。