关键锚定残基被保守疏水性口袋识别,确保 DNA 夹的亚基界面完整性。

Recognition of a Key Anchor Residue by a Conserved Hydrophobic Pocket Ensures Subunit Interface Integrity in DNA Clamps.

机构信息

Department of Chemistry, 414 Wartik Laboratory, The Pennsylvania State University, University Park, PA 16802, USA.

Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302, USA.

出版信息

J Mol Biol. 2019 Jun 28;431(14):2493-2510. doi: 10.1016/j.jmb.2019.04.035. Epub 2019 Apr 30.

Abstract

Sliding clamp proteins encircle duplex DNA and are involved in processive DNA replication and the DNA damage response. Clamp proteins are ring-shaped oligomers (dimers or trimers) and are loaded onto DNA by an ATP-dependent clamp loader complex that ruptures the interface between two adjacent subunits. Here we measured the solution dynamics of the human clamp protein, proliferating cell nuclear antigen, by monitoring the change in the fluorescence of a site-specifically labeled. To unravel the origins of clamp subunit interface stability, we carried out comprehensive comparative analysis of the interfaces of seven sliding clamps. We used computational modeling (molecular dynamic simulations and MM/GBSA binding energy decomposition analyses) to identify conserved networks of hydrophobic residues critical for clamp stability and ring-opening dynamics. The hydrophobic network is shared among clamp proteins and exhibits a "key in a keyhole" pattern where a bulky aromatic residue from one clamp subunit is anchored into a hydrophobic pocket of the opposing subunit. Bioinformatics and dynamic network analyses showed that this oligomeric latch is conserved across DNA sliding clamps from all domains of life and dictates the dynamics of clamp opening and closing.

摘要

滑动夹钳蛋白环绕双链 DNA,并参与连续 DNA 复制和 DNA 损伤反应。夹钳蛋白是环形寡聚体(二聚体或三聚体),并通过 ATP 依赖性夹钳加载器复合物加载到 DNA 上,该复合物会破坏两个相邻亚基之间的界面。在这里,我们通过监测特异性标记的位点的荧光变化来测量人夹钳蛋白增殖细胞核抗原的溶液动力学。为了解开夹钳亚基界面稳定性的起源,我们对七种滑动夹钳的界面进行了全面的比较分析。我们使用计算建模(分子动力学模拟和 MM/GBSA 结合能分解分析)来识别对夹钳稳定性和环开动力学至关重要的保守疏水残基网络。该疏水网络在夹钳蛋白之间共享,并表现出“钥匙在锁孔”的模式,其中一个夹钳亚基的大体积芳基残基锚定到相反亚基的疏水性口袋中。生物信息学和动态网络分析表明,这种寡聚闩锁在所有生命领域的 DNA 滑动夹钳中都保守存在,并决定了夹钳打开和关闭的动力学。

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