scholarly journals Toward rules relating zinc finger protein sequences and DNA binding site preferences.

1992 ◽  
Vol 89 (16) ◽  
pp. 7345-7349 ◽  
Author(s):  
J. R. Desjarlais ◽  
J. M. Berg
Keyword(s):  
Dna Binding ◽  
Binding Site ◽  
Zinc Finger ◽  
Zinc Finger Protein ◽  
Protein Sequences ◽  
Site Preferences ◽  
Finger Protein ◽  
Dna Binding Site

Influence of TFIIIA-type linker at the N- or C-terminal of nine-zinc finger protein on DNA-binding site

2003 ◽  
Vol 300 (1) ◽  
pp. 87-92 ◽  
Author(s):  
Wataru Nomura ◽  
Makoto Nagaoka ◽  
Yasuhisa Shiraishi ◽  
Yukio Sugiura
Keyword(s):  
Dna Binding ◽  
Binding Site ◽  
Zinc Finger ◽  
Zinc Finger Protein ◽  
Finger Protein ◽  
Dna Binding Site

scholarly journals Identification of DNA binding-site preferences for nuclear factor I-A

FEBS Letters ◽  
1996 ◽  
Vol 390 (1) ◽  
pp. 44-46 ◽  
Author(s):  
Shigehiro Osada ◽  
Shoko Daimon ◽  
Tsutomu Nishihara ◽  
Masayoshi Imagawa
Keyword(s):  
Dna Binding ◽  
Binding Site ◽  
Nuclear Factor ◽  
Factor I ◽  
Site Preferences ◽  
Dna Binding Site ◽  
Nuclear Factor I

scholarly journals Single amino acid exchanges in separate domains of the Drosophila serendipity delta zinc finger protein cause embryonic and sex biased lethality.

Genetics ◽  
1992 ◽  
Vol 131 (4) ◽  
pp. 905-916 ◽  
Author(s):  
M Crozatier ◽  
K Kongsuwan ◽  
P Ferrer ◽  
J R Merriam ◽  
J A Lengyel ◽  
...  
Keyword(s):  
Amino Acid ◽  
Dna Binding ◽  
Zinc Finger ◽  
Zinc Finger Protein ◽  
Essential Gene ◽  
Larval Instar ◽  
Single Amino Acid ◽  
Isolation And Characterization ◽  
Finger Protein

Abstract The Drosophila serendipity (sry) delta (delta) zinc finger protein is a sequence-specific DNA binding protein, maternally inherited by the embryo and present in nuclei of transcriptionally active cells throughout fly development. We report here the isolation and characterization of four ethyl methanesulfate-induced zygotic lethal mutations of different strengths in the sry delta gene. For the stronger allele, all of the lethality occurs during late embryogenesis or the first larval instar. In the cases of the three weaker alleles, most of the lethality occurs during pupation; moreover, those adult escapers that emerge are sterile males lacking partially or completely in spermatozoa bundles. Genetic analysis of sry delta thus indicates that it is an essential gene, whose continued expression throughout the life cycle, notably during embryogenesis and pupal stage, is required for viability. Phenotypic analysis of sry delta hemizygote escaper males further suggests that sry delta may be involved in regulation of two different sets of genes: genes required for viability and genes involved in gonadal development. All four sry delta alleles are fully rescued by a wild-type copy of sry delta, but not by an additional copy of the sry beta gene, reinforcing the view that, although structurally related, these two genes exert distinct functions. Molecular characterization of the four sry delta mutations revealed that these mutations correspond to single amino acid replacements in the sry delta protein. Three of these replacements map to the same (third out of seven) zinc finger in the carboxy-terminal DNA binding domain; interestingly, none affects the zinc finger consensus residues. The fourth mutation is located in the NH2-proximal part of the protein, in a domain proposed to be involved in specific protein-protein interactions.

scholarly journals Overcharging of the Zinc Ion in the Structure of the Zinc-Finger Protein Is Needed for DNA Binding Stability

Biochemistry ◽  
2020 ◽  
Vol 59 (13) ◽  
pp. 1378-1390 ◽  
Author(s):  
Ly H. Nguyen ◽  
Tuyen T. Tran ◽  
Lien Thi Ngoc Truong ◽  
Hanh Hong Mai ◽  
Toan T. Nguyen
Keyword(s):  
Dna Binding ◽  
Zinc Finger ◽  
Zinc Finger Protein ◽  
Zinc Ion ◽  
Finger Protein

scholarly journals On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF

2020 ◽  
Vol 2 (3) ◽  
Author(s):  
Alberto Meseguer ◽  
Filip Årman ◽  
Oriol Fornes ◽  
Ruben Molina-Fernández ◽  
Jaume Bonet ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Binding Site ◽  
Zinc Finger ◽  
Zinc Finger Protein ◽  
Computational Method ◽  
Chromatin Binding ◽  
Input Structure ◽  
Binding Factor ◽  
Potential Binding

Abstract Cis2-His2 zinc finger (C2H2-ZF) proteins are the largest family of transcription factors in human and higher metazoans. To date, the DNA-binding preferences of many members of this family remain unknown. We have developed a computational method to predict their DNA-binding preferences. We have computed theoretical position weight matrices (PWMs) of proteins composed by C2H2-ZF domains, with the only requirement of an input structure. We have predicted more than two-third of a single zinc-finger domain binding site for about 70% variants of Zif268, a classical member of this family. We have successfully matched between 60 and 90% of the binding-site motif of examples of proteins composed by three C2H2-ZF domains in JASPAR, a standard database of PWMs. The tests are used as a proof of the capacity to scan a DNA fragment and find the potential binding sites of transcription-factors formed by C2H2-ZF domains. As an example, we have tested the approach to predict the DNA-binding preferences of the human chromatin binding factor CTCF. We offer a server to model the structure of a zinc-finger protein and predict its PWM.

scholarly journals Identification, nuclear localization, and DNA-binding activity of the zinc finger protein encoded by the Evi-1 myeloid transforming gene.

1990 ◽  
Vol 10 (3) ◽  
pp. 1259-1264 ◽  
Author(s):  
T Matsugi ◽  
K Morishita ◽  
J N Ihle
Keyword(s):  
Dna Binding ◽  
Zinc Finger ◽  
Nuclear Protein ◽  
Zinc Finger Protein ◽  
Binding Activity ◽  
Dna Binding Activity ◽  
Double Stranded Dna ◽  
Finger Protein ◽  
Myeloid Leukemias ◽  
Transforming Gene

Activation of the Evi-1 zinc finger gene is a common event associated with transformation of murine myeloid leukemias. To characterize the gene product, we developed antisera against various protein domains. These antisera primarily detected a 145-kilodalton nuclear protein that bound double-stranded DNA. Binding was inhibited by chelating agents and partially restored by zinc ions.

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