Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India.
Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia.
Int J Biol Macromol. 2022 May 31;208:11-19. doi: 10.1016/j.ijbiomac.2022.03.021. Epub 2022 Mar 8.
Clamp loaders ensure processive DNA replication by loading the toroidal shaped sliding clamps onto the DNA. The sliding clamps serve as a platform for the attachment of polymerases and several other proteins associated with the regulation of various cellular processes. Clamp loaders are fascinating as nanomachines that engage in protein-protein and protein-DNA interactions. The loading mechanism of the clamp around dsDNA at the atomic level has not yet been fully explored. We performed microsecond timescale molecular dynamics simulations to reveal the dynamics of two different intermediate complexes involved in loading of the clamps around DNA. We conducted various time-dependent MD-driven analyses including the highly robust Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) calculations to observe changes in the structural elements of the clamp loader-clamp-DNA complexes in open and closed states. Our studies revealed the structural consequences of ATP hydrolysis events at different subunits of the clamp loader. This study would help in a better understanding of the clamp loading mechanism and would allow tackling various complications that might arise due to irregularities in this process.
夹钳加载器通过将环型滑动夹钳加载到 DNA 上来确保连续的 DNA 复制。滑动夹钳作为附着聚合酶和几种与各种细胞过程调节相关的其他蛋白质的平台。夹钳加载器作为参与蛋白质-蛋白质和蛋白质-DNA 相互作用的纳米机器非常有趣。夹钳在 dsDNA 周围的加载机制在原子水平上尚未得到充分探索。我们进行了微秒时间尺度的分子动力学模拟，以揭示涉及夹钳在 DNA 周围加载的两种不同中间复合物的动力学。我们进行了各种时变 MD 驱动的分析，包括高度稳健的分子力学泊松-玻尔兹曼表面积（MMPBSA）计算，以观察夹钳加载器-夹钳-DNA 复合物在打开和关闭状态下结构元件的变化。我们的研究揭示了夹钳加载器不同亚基中 ATP 水解事件的结构后果。这项研究将有助于更好地理解夹钳加载机制，并允许解决由于该过程不规则性可能导致的各种并发症。
