Fernández-de Gortari Eli, Espinoza-Fonseca L Michel
Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
Phys Chem Chem Phys. 2017 Apr 12;19(15):10153-10162. doi: 10.1039/c7cp00243b.
We have performed microsecond molecular dynamics (MD) simulations to determine the mechanism for protonation-dependent structural transitions of the sarco/endoplasmic reticulum Ca-ATPase (SERCA), one of the most prominent members of the large P-type ATPase superfamily that transports ions across biological membranes. The release of two H from the transport sites activates SERCA by inducing a structural transition between low (E2) and high (E1) Ca-affinity states (E2-to-E1 transition), but the structural mechanism by which transport site deprotonation facilitates this transition is unknown. We performed microsecond all-atom MD simulations to determine the effects of transport site protonation on the structural dynamics of the E2 state in solution. We found that the protonated E2 state has structural characteristics that are similar to those observed in crystal structures of E2. Upon deprotonation, a single Na ion rapidly (<10 ns) binds to the transmembrane transport sites and induces a kink in M5, disrupts the M3-M5 interface, and increases the mobility of the M3/A-M3 linker. Principal component analysis showed that counter-rotation of the cytosolic N-A domains about the membrane normal axis, which is the primary motion driving the E2-to-E1 transition, is present in both protonated and deprotonated E2 states; however, protonation-dependent structural changes in the transmembrane domain control the hierarchical organization and amplitude of this motion. We propose that preexisting rigid-body domain motions underlie structural transitions of SERCA, where the functionally important directionality is preserved while transport site protonation controls the dominance and amplitude of motion to shift the equilibrium between the E1 and E2 states. We conclude that ligand-induced modulation of preexisting domain motions is likely a common theme in structural transitions of the P-type ATPase superfamily.
我们进行了微秒级分子动力学（MD）模拟，以确定肌浆网/内质网Ca-ATP酶（SERCA）质子化依赖性结构转变的机制。SERCA是大型P型ATP酶超家族中最突出的成员之一，负责跨生物膜运输离子。从运输位点释放两个H通过诱导低（E2）和高（E1）钙亲和力状态之间的结构转变（E2到E1转变）来激活SERCA，但运输位点去质子化促进这种转变的结构机制尚不清楚。我们进行了微秒级全原子MD模拟，以确定运输位点质子化对溶液中E2状态结构动力学的影响。我们发现质子化的E2状态具有与E2晶体结构中观察到的相似的结构特征。去质子化后，单个Na离子迅速（<10 ns）结合到跨膜运输位点，诱导M5出现扭结，破坏M3-M5界面，并增加M3/A-M3连接子的流动性。主成分分析表明，胞质N-A结构域围绕膜法线轴的反向旋转是驱动E2到E1转变的主要运动，在质子化和去质子化的E2状态中均存在；然而，跨膜结构域中质子化依赖性的结构变化控制了这种运动的层次组织和幅度。我们提出，预先存在的刚体结构域运动是SERCA结构转变的基础，其中功能上重要的方向性得以保留，而运输位点质子化控制运动的主导性和幅度，以改变E1和E2状态之间的平衡。我们得出结论，配体诱导的预先存在的结构域运动的调节可能是P型ATP酶超家族结构转变中的一个共同主题。
