title: In silico analysis on structure and DNA binding mode of AtNAC1, a NAC transcription factor from Arabidopsis thaliana.
abstract: 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.
authors.affiliation: School of Life Science and Engineering, Southwest Jiaotong University, No. 111 Erhuanlu Beiyiduan, Chengdu, 610031, China.
authors.forename: Qiankun
authors.initials: Q
authors.lastname: Zhu
authors.forename: Jiaxin
authors.initials: J
authors.lastname: Zou
authors.forename: Mengli
authors.initials: M
authors.lastname: Zhu
authors.forename: Zubi
authors.initials: Z
authors.lastname: Liu
authors.forename: Peichun
authors.initials: P
authors.lastname: Feng
authors.forename: Gaotao
authors.initials: G
authors.lastname: Fan
authors.forename: Wanjun
authors.initials: W
authors.lastname: Wang
authors.forename: Hai
authors.initials: H
authors.lastname: Liao
mesh_terms: D020816:Amino Acid Motifs / Q000235:genetics; D000595:Amino Acid Sequence; D029681:Arabidopsis Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D003198:Computer Simulation; D018744:DNA, Plant / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D055503:Protein Multimerization; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D014157:Transcription Factors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; D018744:DNA, Plant; D014157:Transcription Factors