scholarly journals Molecular dynamics studies on the DNA-binding process of ERG

2016 ◽  
Vol 12 (12) ◽  
pp. 3600-3610 ◽  
Author(s):  
Matthias G. Beuerle ◽  
Neil P. Dufton ◽  
Anna M. Randi ◽  
Ian R. Gould
Keyword(s):  
Molecular Dynamics ◽  
Transcription Factor ◽  
Dna Binding ◽  
Sequence Specificity ◽  
Dna Interactions ◽  
Binding Process ◽  
Protein Dna Interactions

Molecular dynamics study elucidating the mechanistic background of the DNA-binding process and the sequence specificity of the transcription factor ERG. Along with the biological findings the capabilities of unbiased DNA-binding simulations in combination with various means of analysis in the field of protein DNA-interactions are shown.

scholarly journals Assembly of the Hap2p/Hap3p/Hap4p/Hap5p-DNA Complex in Saccharomyces cerevisiae

2005 ◽  
Vol 4 (11) ◽  
pp. 1829-1839 ◽  
Author(s):  
David S. McNabb ◽  
Inés Pinto
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Factor ◽  
Dna Binding ◽  
Transcriptional Activation ◽  
Target Genes ◽  
Dna Interactions ◽  
Activation Domain ◽  
Binding Factor ◽  
Protein Dna Interactions ◽  
Dna Complex

ABSTRACT The CCAAT-binding factor (CBF) is an evolutionarily conserved multimeric transcriptional activator in eukaryotes. In Saccharomyces cerevisiae, the CCAAT-binding factor is composed of four subunits, termed Hap2p, Hap3p, Hap4p, and Hap5p. The Hap2p/Hap3p/Hap5p heterotrimer is the DNA-binding component of the complex that binds to the consensus 5′-CCAAT-3′ sequence in the promoter of target genes. The Hap4p subunit contains the transcriptional activation domain necessary for stimulating transcription after interacting with Hap2p/Hap3p/Hap5p. In this report, we demonstrate that Hap2p, Hap3p, and Hap5p assemble via a one-step pathway requiring all three subunits simultaneously, as opposed to the mammalian CCAAT-binding factor which has been shown to assemble via a two-step pathway with CBF-A (Hap3p homolog) and CBF-C (Hap5p homolog) forming a stable dimer before CBF-B (Hap2p homolog) can interact. We have also found that the interaction of Hap4p with Hap2p/Hap3p/Hap5p requires DNA binding as a prerequisite. To further understand the protein-protein and protein-DNA interactions of this transcription factor, we identified the minimal domain of Hap4p necessary for interaction with the Hap2p/Hap3p/Hap5p-DNA complex, and we demonstrate that this domain is sufficient to complement the respiratory deficiency of a hap4Δ mutant and activate transcription when fused with the VP16 activation domain. These studies provide a further understanding of the assembly of the yeast CCAAT-binding factor at target promoters and raise a number of questions concerning the protein-protein and protein-DNA interactions of this multisubunit transcription factor.

scholarly journals Protein–DNA Interactions: The Story so Far and a New Method for Prediction

2003 ◽  
Vol 4 (4) ◽  
pp. 428-431 ◽  
Author(s):  
Susan Jones ◽  
Janet M. Thornton
Keyword(s):  
Dna Binding ◽  
Protein Structures ◽  
Accessible Surface Area ◽  
New Method ◽  
Dna Interactions ◽  
Binding Function ◽  
Protein Dna Interactions ◽  
Template Library ◽  
Accessible Surface ◽  
Complete Protein

This review describes methods for the prediction of DNA binding function, and specifically summarizes a new method using 3D structural templates. The new method features the HTH motif that is found in approximately one-third of DNAbinding protein families. A library of 3D structural templates of HTH motifs was derived from proteins in the PDB. Templates were scanned against complete protein structures and the optimal superposition of a template on a structure calculated. Significance thresholds in terms of a minimum root mean squared deviation (rmsd) of an optimal superposition, and a minimum motif accessible surface area (ASA), have been calculated. In this way, it is possible to scan the template library against proteins of unknown function to make predictions about DNA-binding functionality.

scholarly journals Overlapping and CpG methylation-sensitive protein-DNA interactions at the histone H4 transcriptional cell cycle domain: distinctions between two human H4 gene promoters.

1992 ◽  
Vol 12 (7) ◽  
pp. 3273-3287 ◽  
Author(s):  
A J van Wijnen ◽  
F M van den Ent ◽  
J B Lian ◽  
J L Stein ◽  
G S Stein
Keyword(s):  
Cell Cycle ◽  
Transcriptional Regulation ◽  
Dna Binding ◽  
Consensus Sequence ◽  
Proximal Promoter ◽  
Gene Promoters ◽  
Histone H4 ◽  
Dna Interactions ◽  
Protein Dna Interactions ◽  
Diploid Cells

Transcriptional regulation of vertebrate histone genes during the cell cycle is mediated by several factors interacting with a series of cis-acting elements located in the 5' regions of these genes. The arrangement of these promoter elements is different for each gene. However, most histone H4 gene promoters contain a highly conserved sequence immediately upstream of the TATA box (H4 subtype consensus sequence), and this region in the human H4 gene FO108 is involved in cell cycle control. The sequence-specific interaction of nuclear factor HiNF-D with this key proximal promoter element of the H4-FO108 gene is cell cycle regulated in normal diploid cells (J. Holthuis, T.A. Owen, A.J. van Wijnen, K.L. Wright, A. Ramsey-Ewing, M.B. Kennedy, R. Carter, S.C. Cosenza, K.J. Soprano, J.B. Lian, J.L. Stein, and G.S. Stein, Science, 247:1454-1457, 1990). Here, we show that this region of the H4-FO108 gene represents a composite protein-DNA interaction domain for several distinct sequence-specific DNA-binding activities, including HiNF-D, HiNF-M, and HiNF-P. Factor HiNF-P is similar to H4TF-2, a DNA-binding activity that is not cell cycle regulated and that interacts with the analogous region of the H4 gene H4.A (F. LaBella and N. Heintz, Mol. Cell. Biol. 11:5825-5831, 1991). The H4.A gene fails to interact with factors HiNF-M and HiNF-D owing to two independent sets of specific nucleotide variants, indicating differences in protein-DNA interactions between these H4 genes. Cytosine methylation of a highly conserved CpG dinucleotide interferes with binding of HiNF-P/H4TF-2 to both the H4-FO108 and H4.A promoters, but no effect is observed for either HiNF-M or HiNF-D binding to the H4-FO108 gene. Thus, strong evolutionary conservation of the H4 consensus sequence may be related to combinatorial interactions involving overlapping and interdigitated recognition nucleotides for several proteins, whose activities are regulated independently. Our results also suggest molecular complexity in the transcriptional regulation of distinct human H4 genes.

scholarly journals Overlapping and CpG methylation-sensitive protein-DNA interactions at the histone H4 transcriptional cell cycle domain: distinctions between two human H4 gene promoters

1992 ◽  
Vol 12 (7) ◽  
pp. 3273-3287
Author(s):  
A J van Wijnen ◽  
F M van den Ent ◽  
J B Lian ◽  
J L Stein ◽  
G S Stein
Keyword(s):  
Cell Cycle ◽  
Transcriptional Regulation ◽  
Dna Binding ◽  
Consensus Sequence ◽  
Proximal Promoter ◽  
Gene Promoters ◽  
Histone H4 ◽  
Dna Interactions ◽  
Protein Dna Interactions ◽  
Diploid Cells

Transcriptional regulation of vertebrate histone genes during the cell cycle is mediated by several factors interacting with a series of cis-acting elements located in the 5' regions of these genes. The arrangement of these promoter elements is different for each gene. However, most histone H4 gene promoters contain a highly conserved sequence immediately upstream of the TATA box (H4 subtype consensus sequence), and this region in the human H4 gene FO108 is involved in cell cycle control. The sequence-specific interaction of nuclear factor HiNF-D with this key proximal promoter element of the H4-FO108 gene is cell cycle regulated in normal diploid cells (J. Holthuis, T.A. Owen, A.J. van Wijnen, K.L. Wright, A. Ramsey-Ewing, M.B. Kennedy, R. Carter, S.C. Cosenza, K.J. Soprano, J.B. Lian, J.L. Stein, and G.S. Stein, Science, 247:1454-1457, 1990). Here, we show that this region of the H4-FO108 gene represents a composite protein-DNA interaction domain for several distinct sequence-specific DNA-binding activities, including HiNF-D, HiNF-M, and HiNF-P. Factor HiNF-P is similar to H4TF-2, a DNA-binding activity that is not cell cycle regulated and that interacts with the analogous region of the H4 gene H4.A (F. LaBella and N. Heintz, Mol. Cell. Biol. 11:5825-5831, 1991). The H4.A gene fails to interact with factors HiNF-M and HiNF-D owing to two independent sets of specific nucleotide variants, indicating differences in protein-DNA interactions between these H4 genes. Cytosine methylation of a highly conserved CpG dinucleotide interferes with binding of HiNF-P/H4TF-2 to both the H4-FO108 and H4.A promoters, but no effect is observed for either HiNF-M or HiNF-D binding to the H4-FO108 gene. Thus, strong evolutionary conservation of the H4 consensus sequence may be related to combinatorial interactions involving overlapping and interdigitated recognition nucleotides for several proteins, whose activities are regulated independently. Our results also suggest molecular complexity in the transcriptional regulation of distinct human H4 genes.

scholarly journals The geometric influence on the Cys2His2 zinc finger domain and functional plasticity

2020 ◽  
Vol 48 (11) ◽  
pp. 6382-6402
Author(s):  
April L Mueller ◽  
Carles Corbi-Verge ◽  
David O Giganti ◽  
David M Ichikawa ◽  
Jeffrey M Spencer ◽  
...  
Keyword(s):  
Dna Binding ◽  
Zinc Finger ◽  
Zinc Fingers ◽  
Binding Specificity ◽  
Synthetic Approach ◽  
Dna Interactions ◽  
Dna Binding Specificity ◽  
Mechanistic Insight ◽  
Natural Geometry ◽  
Protein Dna Interactions

Abstract The Cys2His2 zinc finger is the most common DNA-binding domain expanding in metazoans since the fungi human split. A proposed catalyst for this expansion is an arms race to silence transposable elements yet it remains poorly understood how this domain is able to evolve the required specificities. Likewise, models of its DNA binding specificity remain error prone due to a lack of understanding of how adjacent fingers influence each other's binding specificity. Here, we use a synthetic approach to exhaustively investigate binding geometry, one of the dominant influences on adjacent finger function. By screening over 28 billion protein–DNA interactions in various geometric contexts we find the plasticity of the most common natural geometry enables more functional amino acid combinations across all targets. Further, residues that define this geometry are enriched in genomes where zinc fingers are prevalent and specificity transitions would be limited in alternative geometries. Finally, these results demonstrate an exhaustive synthetic screen can produce an accurate model of domain function while providing mechanistic insight that may have assisted in the domains expansion.

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