Molecular Dynamics Simulations of DNA-Free and DNA-Bound TAL Effectors

TAL (transcriptional activator-like) effectors (TALEs) are DNA-binding proteins, containing a modular central domain that recognizes specific DNA sequences. Recently, the crystallographic studies of TALEs revealed the structure of DNA-recognition domain. In this article, molecular dynamics (MD) simulations are employed to study two crystal structures of an 11.5-repeat TALE, in the presence and absence of DNA, respectively. The simulated results indicate that the specific binding of RVDs (repeat-variable diresidues) with DNA leads to the markedly reduced fluctuations of tandem repeats, especially at the two ends. In the DNA-bound TALE system, the base-specific interaction is formed mainly by the residue at position 13 within a TAL repeat. Tandem repeats with weak RVDs are unfavorable for the TALE-DNA binding. These observations are consistent with experimental studies. By using principal component analysis (PCA), the dominant motions are open-close movements between the two ends of the superhelical structure in both DNA-free and DNA-bound TALE systems. The open-close movements are found to be critical for the recognition and binding of TALE-DNA based on the analysis of free energy landscape (FEL). The conformational analysis of DNA indicates that the 5′ end of DNA target sequence has more remarkable structural deformability than the other sites. Meanwhile, the conformational change of DNA is likely associated with the specific interaction of TALE-DNA. We further suggest that the arrangement of N-terminal repeats with strong RVDs may help in the design of efficient TALEs. This study provides some new insights into the understanding of the TALE-DNA recognition mechanism.转录激活因子样效应物（transcriptional activator-like effectors，TALEs）是一类DNA结合蛋白，其含有可识别特定DNA序列的模块化中央结构域。近年来，针对TALEs的晶体学研究已阐明其DNA识别结构域的三维构象。本文采用分子动力学（molecular dynamics，MD）模拟方法，分别研究了结合DNA与未结合DNA的11.5重复序列TALE蛋白的两种晶体结构。模拟结果显示，重复可变双残基（repeat-variable diresidues，RVDs）与DNA的特异性结合可显著降低串联重复单元的构象波动，尤其在其两端区域。在结合DNA的TALE体系中，碱基特异性相互作用主要由TAL重复单元内第13位残基介导形成。携带弱结合型RVD的串联重复单元不利于TALE与DNA的结合，上述观测结果与实验研究结论相符。通过主成分分析（principal component analysis，PCA），研究发现无论是否结合DNA，TALE体系的超螺旋结构两端均存在显著的开合运动，这是体系的主要运动模式。结合自由能景观（free energy landscape，FEL）分析结果可知，该开合运动对TALE与DNA的识别及结合过程至关重要。DNA构象分析结果显示，靶DNA序列的5′端相较于其他位点具有更强的结构形变能力。与此同时，DNA的构象变化可能与TALE-DNA的特异性相互作用密切相关。本研究进一步提出，在N端串联排布强结合型RVD重复单元，可为高效TALE蛋白的设计提供新思路。本研究为深入解析TALE-DNA的识别机制提供了全新的理论视角。