In silico analysis on structure and DNA binding mode of AtNAC1, a NAC transcription factor from Arabidopsis thaliana
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- 作者：Qiankun Zhu (1)
Jiaxin Zou (1)
Mengli Zhu (1)
Zubi Liu (1)
Peichun Feng (1)
Gaotao Fan (1)
Wanjun Wang (1)
Hai Liao (1) - 关键词：Arabidopsis thaliana ; AtNAC1 ; DNA binding ; Molecular modeling ; NAC transcription factor
- 刊名：Journal of Molecular Modeling
- 出版年：2014
- 出版时间：March 2014
- 年：2014
- 卷：20
- 期：3
- 全文大小：2,368 KB
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Jiaxin Zou (1)
Mengli Zhu (1)
Zubi Liu (1)
Peichun Feng (1)
Gaotao Fan (1)
Wanjun Wang (1)
Hai Liao (1)
1. School of Life Science and Engineering, Southwest Jiaotong University, No. 111 Erhuanlu Beiyiduan, Chengdu, 610031, China - ISSN：0948-5023
文摘
NAC (NAM/ATAF/CUC) transcription factors regulate the expression of the target genes by formation of NAC-DNA complex, which are involved in development, stress responses and nutrient distribution in many metaphyta plants. AtNAC1, a NAC transcription factor from Arabidopsis thaliana, plays an important role in auxin signaling and root development. In order to understand the structure and DNA binding model of AtNAC1, the 3D structure model of AtNAC1 was constructed and docked with its target DNA. The structure of AtNAC1 monomer contained four α-helices and eight β-sheets. Two homo monomers of AtNAC1 formed a homo-dimer. The N-terminal sheet S1, Arg24 and Glu31 played an important role in forming AtNAC1 homo-dimer. AtNAC1 dimer interacted with DNA via its core β-sheet (S5) which contained WKATGKD motif inserting into the major groove of DNA and formed a tight AtNAC1-DNA complex. The DNA sites for AtNAC1 binding were 5-CTGACGTA-3-and 5-GATGACGC-3- Lys102, Ala103, Thr104, Gly105, Lys106, and Asp107 interacting with sugars/bases of DNA were probably responsible for specific recognition of DNA sites. Meanwhile, Arg91, Lys135, and Lys171 binding with phosphate groups of DNA backbone might be the key residues for affinity with DNA. The study provided the in silico framework to understand the interactions of AtNAC1 with DNA at the molecular level.