Gyimesi Gergely, Ramachandran Srinivas, Kota Pradeep, Dokholyan Nikolay V, Sarkadi Balázs, Hegedus Tamás
Membrane Research Group, Hungarian Academy of Sciences, Budapest, Hungary.
Biochim Biophys Acta. 2011 Dec;1808(12):2954-64. doi: 10.1016/j.bbamem.2011.07.038. Epub 2011 Aug 3.
ABC transporters play important roles in all types of organisms by participating in physiological and pathological processes. In order to modulate the function of ABC transporters, detailed knowledge regarding their structure and dynamics is necessary. Available structures of ABC proteins indicate three major conformations, a nucleotide-bound "bottom-closed" state with the two nucleotide binding domains (NBDs) tightly closed, and two nucleotide-free conformations, the "bottom-closed" and the "bottom-open", which differ in the extent of separation of the NBDs. However, it remains a question how the widely open conformation should be interpreted, and whether hydrolysis at one of the sites can drive conformational transitions while the NBDs remain in contact. To extend our knowledge, we have investigated the dynamic properties of the Sav1866 transporter using molecular dynamics (MD) simulations. We demonstrate that the replacement of one ATP by ADP alters the correlated motion patterns of the NBDs and the transmembrane domains (TMD). The results suggest that the hydrolysis of a single nucleotide could lead to extracellular closure, driving the transport cycle. Essential dynamics analysis of simulations suggests that single nucleotide hydrolysis can drive the system toward a "bottom-closed" apo conformation similar to that observed in the structure of the MsbA transporter. We also found significant structural instability of the "bottom-open" form of the transporters in simulations. Our results suggest that ATP hydrolysis at one of the sites promotes transport related conformational changes leading to the "bottom-closed" apo conformation, which could thus be physiologically more relevant for describing the structure of the apo state.
ABC转运蛋白通过参与生理和病理过程在所有类型的生物体中发挥重要作用。为了调节ABC转运蛋白的功能，有必要详细了解其结构和动力学。ABC蛋白的现有结构表明存在三种主要构象，一种是核苷酸结合的“底部关闭”状态，两个核苷酸结合结构域（NBDs）紧密关闭，以及两种无核苷酸构象，即“底部关闭”和“底部打开”，它们在NBDs的分离程度上有所不同。然而，如何解释广泛开放的构象以及在一个位点的水解是否能在NBDs保持接触的情况下驱动构象转变仍然是一个问题。为了扩展我们的知识，我们使用分子动力学（MD）模拟研究了Sav1866转运蛋白的动力学特性。我们证明用ADP替代一个ATP会改变NBDs和跨膜结构域（TMDs）的相关运动模式。结果表明，单个核苷酸的水解可能导致细胞外关闭，驱动转运循环。模拟的主成分动力学分析表明，单个核苷酸水解可以驱动系统朝着类似于在MsbA转运蛋白结构中观察到的“底部关闭”无配体构象转变。我们还在模拟中发现转运蛋白“底部打开”形式存在显著的结构不稳定性。我们的结果表明，在一个位点的ATP水解促进了与转运相关的构象变化，导致“底部关闭”无配体构象，因此从生理学角度来看，这种构象可能更适合描述无配体状态的结构。
