scholarly journals Identification of DNA Recognition Sequences and Protein Interaction Domains of the Multiple-Zn-Finger Protein Roaz

1998 ◽  
Vol 18 (11) ◽  
pp. 6447-6456 ◽  
Author(s):  
Robert Y. L. Tsai ◽  
Randall R. Reed
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Binding Site ◽  
Zinc Finger ◽  
Protein Interaction ◽  
Inverted Repeat ◽  
Finger Protein ◽  
Zinc Finger Motifs ◽  
Half Site

ABSTRACT Roaz, a rat C2H2 zinc finger protein, plays a role in the regulation of olfactory neuronal differentiation through its interaction with the Olf-1/EBF transcription factor family. An additional role for the Roaz/Olf-1/EBF heterodimeric protein is suggested by its ability to regulate gene activation at a distinct promoter lacking Olf-1/EBF-binding sites. Using an in vitro binding-site selection assay (Selex), we demonstrate that Roaz protein binds to novel inverted perfect or imperfect repeats of GCACCC separated by 2 bp. We show that Roaz is capable of binding to a canonical consensus recognition sequence with high affinity (Kd = 3 nM). Analysis of the structural requirement for protein dimerization and DNA binding by Roaz reveals the role of specific zinc finger motifs in the Roaz protein for homodimerization and heterodimerization with the Olf-1/EBF transcription factor. The DNA-binding domain of Roaz is mapped to the N-terminal 277 amino acids, containing the first seven zinc finger motifs, which confers weak monomeric binding to a single half site and a stronger dimeric binding to the inverted repeat in a binding-site-dependent manner. Full-length protein can form dimers on both the inverted repeat and direct repeat but not on a single half site. These findings support the role of the TFIIIA-type Zn fingers in both protein-protein interaction and protein-DNA interaction and suggest distinct functions for specific motifs in proteins with a large number of zinc finger structures.

scholarly journals The Role of Zinc Finger Linkers in Zinc Finger Protein Binding to DNA

2020 ◽  
Author(s):  
Mazen Hamed ◽  
Reema Siam ◽  
Roza Zaid
Keyword(s):  
Amino Acid ◽  
Dna Binding ◽  
Zinc Finger ◽  
Zinc Finger Protein ◽  
Md Simulations ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Finger Protein ◽  
The Right

Zinc finger proteins (ZFP) play important roles in cellular processes. The DNA binding region of ZFP consists of 3 zinc finger DNA binding domains connected by amino acid linkers, the sequence TGQKP connects ZF1 and ZF2, and TGEKP connects ZF2 with ZF3. Linkers act to tune the zinc finger protein in the right position to bind its DNA target, the type of amino acid residues and length of linkers reflect on ZF1-ZF2-ZF3 interactions and contribute to the search and recognition process of ZF protein to its DNA target. Linker mutations and the affinity of the resulting mutants to specific and nonspecific DNA targets were studied by MD simulations and MM_GB(PB)SA. The affinity of mutants to DNA varied with type and position of amino acid residue. Mutation of K in TGQKP resulted in loss in affinity due to the loss of positive K interaction with phosphates, mutation of G showed loss in affinity to DNA, WT protein and all linker mutants showed loss in affinity to a nonspecific DNA target, this finding confirms previous reports which interpreted this loss in affinity as due to ZF1 having an anchoring role, and ZF3 playing an explorer role in the binding mechanism. The change in ZFP-DNA affinity with linker mutations is discussed in view of protein structure and role of linker residues in binding.

The role of the DNA-binding One Zinc Finger (DOF) transcription factor family in plants

Plant Science ◽  
2013 ◽  
Vol 209 ◽  
pp. 32-45 ◽  
Author(s):  
Mélanie Noguero ◽  
Rana Muhammad Atif ◽  
Sergio Ochatt ◽  
Richard D. Thompson
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Zinc Finger ◽  
Transcription Factor Family ◽  
Dof Transcription Factor

scholarly journals Structural Insights into c-Myc-interacting Zinc Finger Protein-1 (Miz-1) Delineate Domains Required for DNA Scanning and Sequence-specific Binding

2016 ◽  
Vol 292 (8) ◽  
pp. 3323-3340 ◽  
Author(s):  
Mikaël Bédard ◽  
Vincent Roy ◽  
Martin Montagne ◽  
Pierre Lavigne
Keyword(s):  
Dna Binding ◽  
Zinc Finger ◽  
Dna Sequences ◽  
Zinc Finger Protein ◽  
Specific Binding ◽  
Consensus Sequence ◽  
Compact Structure ◽  
General Role ◽  
Finger Protein

c-Myc-interacting zinc finger protein-1 (Miz-1) is a poly-Cys2His2 zinc finger (ZF) transcriptional regulator of many cell cycle genes. A Miz-1 DNA sequence consensus has recently been identified and has also unveiled Miz-1 functions in other cellular processes, underscoring its importance in the cell. Miz-1 contains 13 ZFs, but it is unknown why Miz-1 has so many ZFs and whether they recognize and bind DNA sequences in a typical fashion. Here, we used NMR to deduce the role of Miz-1 ZFs 1–4 in detecting the Miz-1 consensus sequence and preventing nonspecific DNA binding. In the construct containing the first 4 ZFs, we observed that ZFs 3 and 4 form an unusual compact and stable structure that restricts their motions. Disruption of this compact structure by an electrostatically mismatched A86K mutation profoundly affected the DNA binding properties of the WT construct. On the one hand, Miz1–4WT was found to bind the Miz-1 DNA consensus sequence weakly and through ZFs 1–3 only. On the other hand, the four ZFs in the structurally destabilized Miz1–4A86K mutant bound to the DNA consensus with a 30-fold increase in affinity (100 nm). The formation of such a thermodynamically stable but nonspecific complex is expected to slow down the rate of DNA scanning by Miz-1 during the search for its consensus sequence. Interestingly, we found that the motif stabilizing the compact structure between ZFs 3 and 4 is conserved and enriched in other long poly-ZF proteins. As discussed in detail, our findings support a general role of compact inter-ZF structures in minimizing the formation of off-target DNA complexes.

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