Investigating the Conformational Dynamics of a Y-Family DNA Polymerase during Its Folding and Binding to DNA and a Nucleotide.
Investigating the Conformational Dynamics of a Y-Family DNA Polymerase during Its Folding and Binding to DNA and a Nucleotide.
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作者：
Chu X;Suo Z;Wang J
在DNA聚合过程中，Y家族DNA聚合酶能够绕过各种DNA损伤，从而延缓复制分叉的进程。众所周知，Y家族DNA聚合酶的结构是自然进化而来的，以承担这一重要任务。然而，这些蛋白质如何利用其独特的结构和构象动力学特征进行跨损伤DNA合成的机制尚不清楚。在这里，我们开发了基于结构的模型来研究前催化DNA聚合过程，包括DNA和核苷酸与DPO4的结合，DPO4是来自Sulfolobus solfararicus的一个聚合的Y家族聚合酶。我们研究了DPO4的折叠和构象动力学之间的相互作用，发现DPO4经历了先解离(去折叠)再折叠的过程，完成了功能上的“由开到闭”的构象转变。DNA结合通过不同类型的相互作用在逐步结合过程中动态地调节DPO4的构象平衡，导致DPO4在不同的DNA结合阶段的构象分布不同。我们观察到，核苷酸结合诱导了DPO4-DNA复合体活性部位周围的几个接触的调制，与高自由能垒相关。我们的模拟结果与实验证据相一致，即核苷酸引起的活性部位的构象变化是核苷酸掺入的限速步骤。结合局部受挫分析，我们强调了DPO4构象动力学和波动在促进DNA和核苷酸结合方面的重要性。我们的发现提供了与底物结合相关的DPO4构象动力学过程的机械性见解，并有助于理解Y-家族DNA聚合酶的“结构-动力学-功能”关系。
During DNA polymerization, the Y-family DNA polymerases are capable of bypassing various DNA damage, which can stall the replication fork progression. It has been well acknowledged that the structures of the Y-family DNA polymerases have been naturally evolved to undertake this vital task. However, the mechanisms of how these proteins utilize their unique structural and conformational dynamical features to perform the translesion DNA synthesis are less understood. Here, we developed structure-based models to study the precatalytic DNA polymerization process, including DNA and nucleotide binding to DPO4, a paradigmatic Y-family polymerase from Sulfolobus solfataricus. We studied the interplay between the folding and the conformational dynamics of DPO4 and found that DPO4 undergoes first unraveling (unfolding) and then folding for accomplishing the functional “open-to-closed” conformational transition. DNA binding dynamically modulates the conformational equilibrium in DPO4 during the stepwise binding through different types of interactions, leading to different conformational distributions of DPO4 at different DNA binding stages. We observed that nucleotide binding induces modulation of a few contacts surrounding the active site of the DPO4–DNA complex associated with a high free energy barrier. Our simulation results resonate with the experimental evidence that the conformational change at the active site led by nucleotide is the rate-limiting step of nucleotide incorporation. In combination with localized frustration analyses, we underlined the importance of DPO4 conformational dynamics and fluctuations in facilitating DNA and nucleotide binding. Our findings offer mechanistic insights into the processes of DPO4 conformational dynamics associated with the substrate binding and contribute to the understanding of the “structure–dynamics–function” relationship in the Y-family DNA polymerases.
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影响因子：
2.9
作者：
Cao, Huaiqing;Huang, Yongqi;Liu, Zhirong
通讯作者：
Liu, Zhirong
DOI：
10.1073/pnas.0709915104
发表时间：
2007-12-11
影响因子：
11.1
作者：
Ferreiro, Diego U.;Hegler, Joseph A.;Wolynes, Peter G.
通讯作者：
Wolynes, Peter G.
DOI：
10.1073/pnas.84.21.7524
发表时间：
1987-11-01
影响因子：
11.1
作者：
BRYNGELSON, JD;WOLYNES, PG
通讯作者：
WOLYNES, PG
影响因子：
5.6
作者：
Clementi, C;Nymeyer, H;Onuchic, JN
通讯作者：
Onuchic, JN
影响因子：
14.9
作者：
Brenlla A;Markiewicz RP;Rueda D;Romano LJ
通讯作者：
Romano LJ