Finger-Positional Change in Three Zinc Finger Protein Sp1:  Influence of Terminal Finger in DNA Recognition

Uno, Yumiko; Matsushita, K; Nagaoka, Makoto

doi:10.1021/bi0023596

“…In fact, it is now accepted that the best residues for DNA recognition can depend on the position of a finger in the protein and/or the effect of neighboring fingers so that each zinc finger is not completely independent. 42,44,45,47,63,71 This lack of quantitative modularity is compounded by end effects, as distal hydrogen bonds have been proposed not to be as highly constrained or shielded from the solvent as the more central ones. 65 Support for this hypothesis can be gained from inspection of the results for EGR1-f3 from our molecular dynamics simulation, which shows the largest standard deviation for the Arg6-G1 interaction (Table 2).…”

mentioning

confidence: 99%

Assessment by Molecular Dynamics Simulations of the Structural Determinants of DNA-binding Specificity for Transcription Factor Sp1

Marco

¹

,

Garcı́a-Nieto

²

,

Gago

³

2003

Journal of Molecular Biology

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The DNA-binding domain (DBD) of the ubiquituous transcription factor Sp1 consists of three consecutive zinc fingers that recognize a number of nucleotide sequences different from, but related to and sometimes overlapping, those recognized by the structurally better characterized early growth response protein 1 (EGR1, also known as Zif268, Krox-24, and NGFI-A). The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG ( ¼ CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter. Since no 3D structure of the whole DBD of Sp1 is available, either alone or in complex with DNA, a homology-based model was built and its interaction with two DNA 14-mers was studied using nanosecond molecular dynamics simulations in the presence of explicit water molecules. These oligonucleotides represent Sp1 target sites that are present in the promoters of the mdr1 and wt1 genes. For comparative purposes and validation of the protocol, the complex between the DBD of EGR1 and its DNA target site within the proximal mdr1 promoter was simulated under the same conditions. Some water molecules were seen to play an important role in recognition and stabilization of the protein-DNA complexes. Our results, which are supported by the available experimental evidence, suggest that the accuracy in the prediction of putative Sp1-binding sites can be improved by interpreting a set of rules, which are a blend of both stringency and tolerance, for the juxtaposed triplet subsites to which each zinc finger binds. Our approach can be extrapolated to WT1 and other related natural or artificial zinc-finger-containing DNA-binding proteins and may aid in the assignment of particular DNA stretches as allowed or disallowed-binding sites.

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“…To determine whether such a change in structure or interactions could occur in the shorter form of ZNF358, we modelled the tertiary structure of the variant isoform. In some DNA binding zinc finger proteins, such as Sp1, the C-terminal zinc finger domains are more active in base recognition than N-terminal domains and mutation of these can significantly disrupt protein conformation and DNA binding [44]. The polymorphic polyalanine tract in ZNF358 separates the zinc finger domains from the prolinerich domain at the C-terminus (Figure 3).…”

Section: Discussionmentioning

confidence: 99%

Structural variation in a novel zinc finger protein and investigation of its role in Hirschsprung disease

Andrew¹,

Kuiper²,

Wride³

et al. 2002

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Zinc finger transcription factors play essential roles in neural crest cell development. Even subtle disruptions of the function of these genes could contribute significantly to complex developmental phenotypes such as the multigenic disorder Hirschsprung disease (HSCR), a congenital failure of enteric neurogenesis. Although germline mutations in the RET proto‐oncogene are the most common cause of familial disease, at least 8 genes including transcription factors have been implicated in sporadic HSCR to date. Thus, a further group of candidate genes are those involved in regulating expression of known HSCR genes. In this study, we have characterized the ZNF358 zinc finger gene, a human orthologue of the mouse gene zfend, which is expressed in early developmental stages in the gut and in the neural folds at the time of neural crest differentiation. ZNF358 represents a putative transcription factor with DNA binding activity confered by 9 Cys2His2 zinc fingers. Although we did not detect disease associated mutations in a panel of HSCR patients, we did identify a novel variable sequence within the coding region of ZNF358 that would result in a deletion of nine amino acids from a polyalanine domain. Our molecular model suggests that this variant could alter protein tertiary structure and the ability of ZNF358 to regulate transcription. Together, our data suggest that, while ZNF358 may be involved in the regulation of genes such as those necessary for development or differentiation of neural crest cells, it does not play an obvious role in HSCR.

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“…As a result, the proline-rich domain may interfere with the DNA binding ability of zinc fingers in Domain III (Figure 3). In some DNA binding zinc finger proteins, such as Sp1, the C-terminal zinc finger domains are more active in base recognition than N-terminal domains and mutation of these can significantly disrupt protein conformation and DNA binding [44]. The polyalanine deletion in ZNF358 could similarly compromise the secondary structure of the protein and the ability of these domains, and the protein as a whole, to bind DNA or other transcriptional regulatory proteins.…”

Section: Discussionmentioning

confidence: 99%

Structural variation in a novel zinc finger protein and investigation of its role in Hirschsprung disease

Andrew¹,

Kuiper

²

,

Wride

³

et al. 2002

Gene Function & Disease

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Zinc finger transcription factors play essential roles in neural crest cell development. Even subtle disruptions of the function of these genes could contribute significantly to complex developmental phenotypes such as the multigenic disorder Hirschsprung disease (HSCR), a congenital failure of enteric neurogenesis. Although germline mutations in the RET proto‐oncogene are the most common cause of familial disease, at least 8 genes including transcription factors have been implicated in sporadic HSCR to date. Thus, a further group of candidate genes are those involved in regulating expression of known HSCR genes. In this study, we have characterized the ZNF358 zinc finger gene, a human orthologue of the mouse gene zfend, which is expressed in early developmental stages in the gut and in the neural folds at the time of neural crest differentiation. ZNF358 represents a putative transcription factor with DNA binding activity confered by 9 Cys2His2 zinc fingers. Although we did not detect disease associated mutations in a panel of HSCR patients, we did identify a novel variable sequence within the coding region of ZNF358 that would result in a deletion of nine amino acids from a polyalanine domain. Our molecular model suggests that this variant could alter protein tertiary structure and the ability of ZNF358 to regulate transcription. Together, our data suggest that, while ZNF358 may be involved in the regulation of genes such as those necessary for development or differentiation of neural crest cells, it does not play an obvious role in HSCR.

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Finger-Positional Change in Three Zinc Finger Protein Sp1: Influence of Terminal Finger in DNA Recognition

Cited by 22 publications

References 36 publications

Assessment by Molecular Dynamics Simulations of the Structural Determinants of DNA-binding Specificity for Transcription Factor Sp1

Assessment by Molecular Dynamics Simulations of the Structural Determinants of DNA-binding Specificity for Transcription Factor Sp1

Structural variation in a novel zinc finger protein and investigation of its role in Hirschsprung disease

Structural variation in a novel zinc finger protein and investigation of its role in Hirschsprung disease

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