Kantarci Nigar, Doruker Pemra, Haliloglu Turkan
Department of Chemical Engineering and Polymer Research Center, Bogazici University, Istanbul, Turkey.
Biophys J. 2006 Jul 15;91(2):421-32. doi: 10.1529/biophysj.106.077800.
Elastic network models are used for investigation of the p53 core domain functional dynamics. Global modes of motion indicate high positive correlations for residue fluctuations across the A-B interface, which are not observed at the B-C interface. Major hinge formation is observed at the A-B interface upon dimerization indicating stability of the A-B dimer. These findings imply A-B as the native dimerization interface, whereas B-C is the crystal interface. The A-B dimer exhibits an opening-closing motion about DNA, supporting the previously suggested clamp-like model of nonspecific DNA binding followed by diffusion. Monomer A has limited positive correlations with DNA, while monomer B exhibits high positive correlations with DNA in the functionally significant slow modes. Thus, monomer B might seem to maintain the stability of the dimer-DNA complex by forming the relatively fixed arm of the dimer clamp, whereas the other arm of the clamp, monomer A, might allow sliding via continuous association/dissociation mechanisms.
弹性网络模型用于研究p53核心结构域的功能动力学。全局运动模式表明，A - B界面处残基波动具有高度正相关，而在B - C界面未观察到这种情况。二聚化时在A - B界面观察到主要的铰链形成，表明A - B二聚体的稳定性。这些发现意味着A - B是天然二聚化界面，而B - C是晶体界面。A - B二聚体围绕DNA表现出开闭运动，支持了先前提出的非特异性DNA结合后扩散的钳状模型。单体A与DNA的正相关性有限，而单体B在功能上重要的慢模式下与DNA表现出高度正相关。因此，单体B似乎通过形成二聚体钳的相对固定臂来维持二聚体 - DNA复合物的稳定性，而钳的另一臂单体A可能通过连续的缔合/解离机制允许滑动。
