Helix Unfolding/Refolding Characterizes the Functional Dynamics of Staphylococcus aureus Clp Protease*
Helix Unfolding/Refolding Characterizes the Functional Dynamics of Staphylococcus aureus Clp Protease*
复制标题
DOI：
10.1074/jbc.m113.452714
复制
发表时间：
2013-04
期刊：
影响因子：
--
通讯作者：
F. Ye;Jie Zhang;Hongchuan Liu;R. Hilgenfeld;Ruihan Zhang;X. Kong;Lianchun Li;Junyan Lu;Xinlei Zh
中科院分区：
文献类型：
--
作者：
F. Ye;Jie Zhang;Hongchuan Liu;R. Hilgenfeld;Ruihan Zhang;X. Kong;Lianchun Li;Junyan Lu;Xinlei Zh
背景：ClpP在不同构象之间动态转换的分子机制知之甚少。结果：分子动力学模拟描述了SaClpP三种构象之间转变的分子途径。结论：抑制性去折叠/重折叠是ClpP的功能动力学和作用机制。意义：这项研究提供了一般ClpP的动力学和机制的分子见解。ATP依赖性Clp蛋白酶（ClpP）不仅在控制蛋白质质量方面而且在调节细菌病原体毒力方面发挥重要作用，使其成为抗菌治疗的有吸引力的靶标。我们先前已经确定了金黄色葡萄球菌ClpP（SaClpP）在两种不同状态下的晶体结构，扩展和压缩。为了研究ClpP在这些状态之间的动态切换，我们进行了一系列的分子动力学模拟。在结构转变过程中，延长的SaClpP单体中的长而直的螺旋E经历了去折叠/再折叠过程，导致与压缩单体中的螺旋非常相似的扭结螺旋。作为分子动力学模拟中的稳定中间体，致密态被提出并随后在X射线晶体学实验中被证实。我们的综合研究还确定，Ala 140作为一个“铰链”之间的延伸和压缩状态的过渡，和Glu 137是必不可少的稳定的压缩状态。总体而言，这项研究提供了分子的见解的动力学和机制的功能构象变化的SaClpP。由于ClpP蛋白在不同物种中的高度保守序列，这些发现可能反映了整个ClpP家族中共享的动态过程的开关机制，从而有助于更好地理解Clp蛋白酶组装和功能的原理。
Background: The molecular mechanism of ClpP dynamic switching between different conformations is poorly understood. Results: MD simulations describe the molecular pathway of the transition between three conformations of SaClpP. Conclusion: Helix unfolding/refolding characterizes the functional dynamics and mechanism of ClpP. Significance: This study provides molecular insights into the dynamics and mechanism of ClpP in general. The ATP-dependent Clp protease (ClpP) plays an essential role not only in the control of protein quality but also in the regulation of bacterial pathogen virulence, making it an attractive target for antibacterial treatment. We have previously determined the crystal structures of Staphylococcus aureus ClpP (SaClpP) in two different states, extended and compressed. To investigate the dynamic switching of ClpP between these states, we performed a series of molecular dynamics simulations. During the structural transition, the long and straight helix E in the extended SaClpP monomer underwent an unfolding/refolding process, resulting in a kinked helix very similar to that in the compressed monomer. As a stable intermediate in the molecular dynamics simulation, the compact state was suggested and subsequently identified in x-ray crystallographic experiment. Our combined studies also determined that Ala140 acted as a “hinge” during the transition between the extended and compressed states, and Glu137 was essential for stabilizing the compressed state. Overall, this study provides molecular insights into the dynamics and mechanism of the functional conformation changes of SaClpP. Given the highly conserved sequences of ClpP proteins among different species, these findings potentially reflect a switching mechanism for the dynamic process shared in the whole ClpP family in general and thus aid in better understand the principles of Clp protease assembly and function.