Li Congcong, Chen Siao, Huang Tianci, Zhang Fangning, Yuan Jiawei, Chang Hao, Li Wannan, Han Weiwei
Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, China.
Jilin Province TeyiFood Biotechnology Company Limited, Changchun, China.
Front Chem. 2021 Feb 26;9:640994. doi: 10.3389/fchem.2021.640994. eCollection 2021.
Glutamine 5'-phosphoribosylpyrophosphate amidotransferase (GPATase) catalyzes the synthesis of phosphoribosylamine, pyrophosphate, and glutamate from phosphoribosylpyrophosphate, as well as glutamine at two sites (i.e., glutaminase and phosphoribosylpyrophosphate sites), through a 20 Å NH channel. In this study, conventional molecular dynamics (cMD) simulations and enhanced sampling accelerated molecular dynamics (aMD) simulations were integrated to characterize the mechanism for coordination catalysis at two separate active sites in the enzyme. Results of cMD simulations illustrated the mechanism by which two substrate analogues, namely, DON and cPRPP, affect the structural stability of GPATase from the perspective of dynamic behavior. aMD simulations obtained several key findings. First, a comparison of protein conformational changes in the complexes of GPATase-DON and GPATase-DON-cPRPP showed that binding cPRPP to the PRTase flexible loop (K326 to L350) substantially effected the formation of the R73-DON salt bridge. Moreover, only the PRTase flexible loop in the GPATase-DON-cPRPP complex could remain closed and had sufficient space for cPRPP binding, indicating that binding of DON to the glutamine loop had an impact on the PRTase flexible loop. Finally, both DON and cPRPP tightly bonded to the two domains, thereby inducing the glutamine loop and the PRTase flexible loop to move close to each other. This movement facilitated the transfer of NH3 via the NH3 channel. These theoretical results are useful to the ongoing research on efficient inhibitors related to GPATase.
谷氨酰胺5'-磷酸核糖焦磷酸酰胺转移酶（GPATase）通过一个20埃的NH通道，在两个位点（即谷氨酰胺酶位点和磷酸核糖焦磷酸位点）催化由磷酸核糖焦磷酸、谷氨酰胺合成磷酸核糖胺、焦磷酸和谷氨酸。在本研究中，结合传统分子动力学（cMD）模拟和增强采样加速分子动力学（aMD）模拟，以表征该酶两个独立活性位点的协同催化机制。cMD模拟结果从动态行为角度阐明了两种底物类似物DON和cPRPP影响GPATase结构稳定性的机制。aMD模拟得出了几个关键发现。首先，对GPATase-DON和GPATase-DON-cPRPP复合物中蛋白质构象变化的比较表明，将cPRPP与PRTase柔性环（K326至L350）结合显著影响了R73-DON盐桥的形成。此外，只有GPATase-DON-cPRPP复合物中的PRTase柔性环能够保持闭合，并有足够空间结合cPRPP，这表明DON与谷氨酰胺环的结合对PRTase柔性环有影响。最后，DON和cPRPP都紧密结合到两个结构域，从而诱导谷氨酰胺环和PRTase柔性环彼此靠近移动。这种移动促进了NH3通过NH3通道的转移。这些理论结果对正在进行的与GPATase相关的高效抑制剂研究很有用。
