title: Molecular dynamics simulations reveal the disparity in specific recognition of GCC-box by AtERFs transcription factors super family in Arabidopsis.
abstract: Arabidopsis ethylene responsive element binding factors (AtERFs) form a transcription factor super family. While the functions of most AtERFs are unknown, a number of AtERFs appear to be involved in regulation of stress-related genes through their DNA binding domains (DBD), namely ERF domains, which recognize a consensus motif GCC-box at the regulatory region. In this study, molecular dynamics simulations were performed on the four ERF domain-GCC-box complexes, AtERF1, AtERF4, AtEBP and CFBF1, to determine disparity in specific binding to the GCC-box by the AtERFs. Our results suggested that three amino acid residues Arg29, Glu39 and Arg41, played a vital role in direct readout of DNA. The position of the consensus sequence GCCGCC has an intrinsic disparity on binding with ERF domains. The third C, fourth G and the last C in the GCC motif was compulsory for recognition by ERF domains. Our results provide structural evidence for a sequence-dependent recognition mechanism for AtERFs.
authors.affiliation: Key Lab for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun, 130023, P.R. China.
authors.forename: Shichen
authors.initials: S
authors.lastname: Wang
authors.forename: Shuo
authors.initials: S
authors.lastname: Yang
authors.forename: Yuejia
authors.initials: Y
authors.lastname: Yin
authors.forename: Jinghui
authors.initials: J
authors.lastname: Xi
authors.forename: Shanyu
authors.initials: S
authors.lastname: Li
authors.forename: Dongyun
authors.initials: D
authors.lastname: Hao
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D004247:DNA / Q000737:chemistry; D018506:Gene Expression Regulation, Plant; D008958:Models, Molecular; D008969:Molecular Sequence Data; D005810:Multigene Family; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D013997:Time Factors; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D014157:Transcription Factors; D004247:DNA