Computationally exploring the mechanism of bacteriophage T7 gp4 helicase translocating along ssDNA.
Computationally exploring the mechanism of bacteriophage T7 gp4 helicase translocating along ssDNA.
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DOI：
10.1073/pnas.2202239119
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发表时间：
2022-08-09
影响因子：
11.1
通讯作者：
中科院分区：
文献类型：
--
作者：
六元解旋酶是DNA复制的核心成分，许多复制型解旋酶已被提出作为疾病治疗的药物靶点。了解复制解旋酶的结构及其易位机制对于更好地理解DNA复制和复制应激反应以及解旋酶的治疗靶向是至关重要的。解旋酶的大尺寸和解旋酶转位过程中发生的大规模构象变化阻碍了解旋酶结构和动力学的研究。我们新开发的粗粒蛋白质单链DNA力场的模拟概括了gp 4亚基的大规模易位与有限的计算成本，并揭示了许多关于gp 4解旋酶易位的机械细节。噬菌体T7 gp 4解旋酶作为一个模型系统，了解六聚体复制解旋酶易位的机制。核苷5′-三磷酸水解和gp 4解旋酶转位如何耦合的机理基础尚未完全解决。在这里，我们使用了一个以生物学为基准的粗粒度蛋白质力场，联想记忆，水介导的结构和能量模型（AWSEM），与单链DNA（ssDNA）力场3SPN. 2C来研究gp 4易位。我们发现，在亚基界面的腺苷5′-三磷酸（ATP）稳定的亚基-亚基相互作用，抑制亚基易位。ATP水解为腺苷5′-二磷酸使得一个亚基能够移位，并且新的ATP结合在新的亚基界面处完成亚基移位。LoopD 2和N-末端引发酶结构域提供瞬时蛋白质-蛋白质和蛋白质-DNA相互作用，促进大规模亚基运动。gp 4解旋酶的模拟验证了我们的粗粒蛋白质-ssDNA力场，并阐明了复制解旋酶易位的分子基础。
Hexametric helicase is a central component in DNA replication and many replicative helicases have been proposed as drug targets for disease treatment. Knowledge of both the structures of replicative helicases and their mechanisms of translocation is essential for a better understanding of DNA replication and replication stress response, as well as for therapeutic targeting of helicases. The very large size of the helicase and the large-scale conformational changes that occur during helicase translocation have hindered investigations of helicase structure and dynamics. Simulations with our newly developed coarse-grained protein–single-stranded DNA force field recapitulated the large-scale translocation of the gp4 subunit with limited computational cost and revealed numerous mechanistic details about gp4 helicase translocation. Bacteriophage T7 gp4 helicase has served as a model system for understanding mechanisms of hexameric replicative helicase translocation. The mechanistic basis of how nucleoside 5′-triphosphate hydrolysis and translocation of gp4 helicase are coupled is not fully resolved. Here, we used a thermodynamically benchmarked coarse-grained protein force field, Associative memory, Water mediated, Structure and Energy Model (AWSEM), with the single-stranded DNA (ssDNA) force field 3SPN.2C to investigate gp4 translocation. We found that the adenosine 5′-triphosphate (ATP) at the subunit interface stabilizes the subunit–subunit interaction and inhibits subunit translocation. Hydrolysis of ATP to adenosine 5′-diphosphate enables the translocation of one subunit, and new ATP binding at the new subunit interface finalizes the subunit translocation. The LoopD2 and the N-terminal primase domain provide transient protein–protein and protein–DNA interactions that facilitate the large-scale subunit movement. The simulations of gp4 helicase both validate our coarse-grained protein–ssDNA force field and elucidate the molecular basis of replicative helicase translocation.
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影响因子：
5.5
作者：
Jin, Shikai;Chen, Mingchen;Wolynes, Peter G.
通讯作者：
Wolynes, Peter G.
影响因子：
14.9
作者：
Jin, Shikai;Contessoto, Vinicius G.;Wolynes, Peter G.
通讯作者：
Wolynes, Peter G.
影响因子：
15
作者：
Kim, Dorothy M.;Zheng, Haiyan;Hunt, John F.
通讯作者：
Hunt, John F.
影响因子：
3.3
作者：
Chen, Mingchen;Chen, Xun;Wolynes, Peter G.
通讯作者：
Wolynes, Peter G.
DOI：
10.1073/pnas.1119057109
发表时间：
2012-01-17
影响因子：
11.1
作者：
Chen, Huimin;Meisburger, Steve P.;Pollack, Lois
通讯作者：
Pollack, Lois