Conformational elasticity can facilitate TALE-DNA recognition.
Conformational elasticity can facilitate TALE-DNA recognition.
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DOI：
10.1016/b978-0-12-800168-4.00009-3
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发表时间：
2014
影响因子：
--
通讯作者：
Duan, Yong
中科院分区：
文献类型：
--
作者：
Lei, Hongxing;Sun, Jiya;Baldwin, Enoch P.;Segal, David J.;Duan, Yong
序列可编程转录激活因子样效应子（TALE）蛋白已成为基因组工程的高效工具。最近的晶体结构描绘了开放的未结合螺线管和由34个氨基酸重复形成的更紧凑的DNA结合螺线管之间的过渡。TALE如何在这两种形式之间转换构象而没有实质性的能量补偿，以及重复可变双残基（RVD）如何区分同源碱基和其他碱基仍然不清楚。对TALE与DNA相互作用机理的这两个方面进行了计算分析，以便更好地理解能量学。在无DNA TALE结构的分子动力学模拟中观察到高弹性，所述无DNA TALE结构从结合构象开始，其中其对广泛的构象进行采样，包括实验确定的脱辅基构象和结合构象。在从apo形式开始的模拟中也观察到这种弹性特征，这表明两种构象之间的自由能垒低，结合时需要小的补偿。为了分析结合特异性，我们使用Poisson-Boltzmann/表面积（PBSA）和其他方法对RVD和碱基的各种组合进行了自由能计算。PBSA计算表明，天然RVD基础结构具有较低的结合自由能比失配结构的RVD检查。我们的理论分析提供了新的见解的动力学和能量的TALE-DNA结合机制。
Sequence-programmable transcription activator-like effector (TALE) proteins have emerged as a highly efficient tool for genome engineering. Recent crystal structures depict a transition between an open unbound solenoid and more compact DNA-bound solenoid formed by the 34 amino acid repeats. How TALEs switch conformation between these two forms without substantial energetic compensation, and how the repeat-variable di-residues (RVDs) discriminate between the cognate base and other bases still remain unclear. Computational analysis on these two aspects of TALE-DNA interaction mechanism has been conducted in order to achieve a better understanding of the energetics. High elasticity was observed in the molecular dynamics simulations of DNA-free TALE structure that started from the bound conformation where it sampled a wide range of conformations including the experimentally determined apo- and bound- conformations. This elastic feature was also observed in the simulations starting from the apo form which suggests low free energy barrier between the two conformations and small compensation required upon binding. To analyze binding specificity, we performed free energy calculations of various combinations of RVDs and bases using Poisson-Boltzmann/surface area (PBSA) and other approaches. The PBSA calculations indicated that the native RVD-base structures had lower binding free energy than mismatched structures for most of the RVDs examined. Our theoretical analyses provided new insight on the dynamics and energetics of TALE-DNA binding mechanism.