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BioMed Research International
Volume 2016, Article ID 8036450, 11 pages
http://dx.doi.org/10.1155/2016/8036450
Research Article

Potential Role of the Last Half Repeat in TAL Effectors Revealed by a Molecular Simulation Study

1College of Mathematics and Informatics, South China Agricultural University, Guangzhou, China
2School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
3Faculty of Biotechnology Industry, Chengdu University, Chengdu, China

Received 20 May 2016; Revised 16 August 2016; Accepted 24 August 2016

Academic Editor: Zhongjie Liang

Copyright © 2016 Hua Wan et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

TAL effectors (TALEs) contain a modular DNA-binding domain that is composed of tandem repeats. In all naturally occurring TALEs, the end of tandem repeats is invariantly a truncated half repeat. To investigate the potential role of the last half repeat in TALEs, we performed comparative molecular dynamics simulations for the crystal structure of DNA-bound TALE AvrBs3 lacking the last half repeat and its modeled structure having the last half repeat. The structural stability analysis indicates that the modeled system is more stable than the nonmodeled system. Based on the principle component analysis, it is found that the AvrBs3 increases its structural compactness in the presence of the last half repeat. The comparison of DNA groove parameters of the two systems implies that the last half repeat also causes the change of DNA major groove binding efficiency. The following calculation of hydrogen bond reveals that, by stabilizing the phosphate binding with DNA at the C-terminus, the last half repeat helps to adopt a compact conformation at the protein-DNA interface. It further mediates more contacts between TAL repeats and DNA nucleotide bases. Finally, we suggest that the last half repeat is required for the high-efficient recognition of DNA by TALE.