The DNA binding domain and bending angle of E. coli CAP protein

Liu-Johnson, Huei-Nin; Gartenberg, Marc R.; Crothers, Donald M.

doi:10.1016/0092-8674(86)90814-7

Cited by 330 publications

(205 citation statements)

References 21 publications

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“…The enhanced DNase I sensitivity of certain bases upon protein binding in complex B1 suggests that the DNA helix structure becomes distorted by the interaction with factor Bi. Such bending has been observed with other DNA-protein interactions (28,32,37,43,49). The stored energy of an induced bend could be used in a regulatory manner, such as opening the DNA helix for transcription.…”

Section: Resultsmentioning

confidence: 95%

Detection of two tissue-specific DNA-binding proteins with affinity for sites in the mouse beta-globin intervening sequence 2.

Galson¹,

Housman²

1988

Mol. Cell. Biol.

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To identify proteins from uninduced murine erythroleukemia nuclear extracts which specifically bind to sequences from the DNase I-hypersensitive region within the mouse I-globin intervening sequence 2 (IVS2), a gel electrophoretic mobility shift assay was used. Two distinct sequence-specific binding proteins were detected. The specific binding sites for these factors were delineated by both DNase I protection footprinting and methylation interference. Factor Bl bound specifically to two homologous sites, B1-A and B1-B, approximately 100 base pairs apart within the IVS2 and on opposite strands. These two regions could interact with factor B1 independently. Factor B1 was limited to cells of hematopoietic lineages. Factor B2 bound to a site approximately 5 base pairs away from the B1-A site and was limited to cells of the erythroid lineage. The limited tissue distribution of these factors and the locations of their binding sites suggest that one or both of these factors may be involved in the formation of the tissue-specific DNase I-hypersensitive site in the IVS2 of the mouse I-globin gene.

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Section: Resultsmentioning

confidence: 95%

Detection of two tissue-specific DNA-binding proteins with affinity for sites in the mouse beta-globin intervening sequence 2.

Galson¹,

Housman²

1988

Mol. Cell. Biol.

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“…5B), assuming that all peptide molecules were able to bind DNA. A similar value for the K d was obtained using an alternative experimental protocol and algorithm (Liu-Johnson et al 1986) which, in addition, allowed us to determine the "active" fraction of total peptide as 20-50%, depending on the preparation (data not shown). To estimate the specificity of DNA binding of the LEF-HMG domain, we determined the K a of its nonspecific interaction with DNA.…”

Section: Sequence-specific Dna Binding Of the Lef-hmg Domainmentioning

confidence: 88%

DNA-binding properties of the HMG domain of the lymphoid-specific transcriptional regulator LEF-1.

Giese¹,

Amsterdam²,

Grosschedl³

1991

Genes & Development

262

238

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Lymphoid enhancer-binding factor 1 (LEF-11 is a pre-B and T lymphocyte-specific nuclear protein that participates in the regulation of the T-cell antigen receptor (TCR) a enhancer by binding to the nucleotide sequence 5'-CCTTTGAA. LEF-1 protein shares with the nonhistone high mobility group protein 1 (HMG-1) and several transcriptional regulators a single region of amino acid homology, termed the HMG box, which has been implicated in DNA binding. Here, we report the biochemical analysis of the interaction of this novel structural motif with DNA. First, amino-or carboxy-terminal truncations of the LEF-1 polypeptide delineated the HMG box as the DNA-binding domain. We purified to homogeneity a LEF-HMG domain peptide expressed in Escherichia coli and determined the equilibrium constant for specific binding to DNA as 1 x 10 -9 M. Second, cotranslation of wild-type and various truncated LEF-1 polypeptides did not generate any DNA-binding heterodimers, suggesting that LEF-1 can bind DNA as a monomer. Third, methylation interference analysis indicated that the HMG domain specifically contacts DNA on one side of the double helix. Finally, changes of amino acids that are conserved among various members of the family of HMG-box proteins decreased the affinity of DNA binding by one to three orders of magnitude. Together, these data define the characteristics of specific DNA-binding by the HMG domain of LEF-1.

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“…They bind to operator DNA as a dimer or tetramer in two adjacent helical turns of the major groove along one face of the double helix. In some cases, additional protein-DNA interactions are involved, resulting in bending of the DNA, such as in E. coli CAP protein-DNA interactions (17). In these cases, the bending of DNA is usually detected as hypersensitive sites in footprinting experiments.…”

Section: Resultsmentioning

confidence: 99%

The Bacillus subtilis sin gene, a regulator of alternate developmental processes, codes for a DNA-binding protein

Gaur¹,

Oppenheim²,

Smith³

1991

J Bacteriol

109

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The sin gene of Bacillus subtilis encodes a dual-function regulatory protein, Sin, which is a negative as well as a positive regulator of alternate developmental processes that are induced at the end of vegetative growth in response to nutrient depletion. Sin has been purified to homogeneity by using a simple two-step procedure. It was found to bind to the developmentally regulated aprE (alkaline protease) gene at two sites in vitro. The stronger Sin-binding site (SBS-1) is located more than 200 bp upstream from the transcription start site. It is required for Sin repression of aprE expression in vivo, as strains bearing SBS-1 deletions were not affected by the sin gene. The second, weaker Sin-binding site lies on a DNA fragment that contains the aprE promoter. Results of DNase I, exonuclease III, and dimethyl sulfate footprinting analysis of SBS-1 suggested that Sin binding involves two adjacent binding sites which appear to contain two different partial dyad symmetries. An analysis of the predicted amino acid sequence of Sin revealed a potential leucine zipper protein dimerization motif which is flanked by two helix-turn-helix motifs that could be involved in recognizing two different dyad symmetries.

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The DNA binding domain and bending angle of E. coli CAP protein

Cited by 330 publications

References 21 publications

Detection of two tissue-specific DNA-binding proteins with affinity for sites in the mouse beta-globin intervening sequence 2.

Detection of two tissue-specific DNA-binding proteins with affinity for sites in the mouse beta-globin intervening sequence 2.

DNA-binding properties of the HMG domain of the lymphoid-specific transcriptional regulator LEF-1.

The Bacillus subtilis sin gene, a regulator of alternate developmental processes, codes for a DNA-binding protein

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