Potential Role of the Last Half Repeat in TAL Effectors Revealed by a Molecular Simulation Study.
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.
College of Mathematics and Informatics, South China Agricultural University, Guangzhou, China.
Hua
H
Wan
School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China.
Shan
S
Chang
Faculty of Biotechnology Industry, Chengdu University, Chengdu, China.
Jian-Ping
JP
Hu
College of Mathematics and Informatics, South China Agricultural University, Guangzhou, China.
Xu-Hong
XH
Tian
College of Mathematics and Informatics, South China Agricultural University, Guangzhou, China.
Mei-Hua
0000-0003-3727-1552
MH
Wang
D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000648:ultrastructure*; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D017433:Protein Structure, Secondary; D020080:Tandem Repeat Sequences; D000071336:Transcription Activator-Like Effectors / Q000737:chemistry* / Q000235:genetics / Q000648:ultrastructure*
D000071336:Transcription Activator-Like Effectors; D004247:DNA