Updating structure-function relationships in the bZip family of transcription factors

Pathak, Dushyant; Sigler, Paul B.

doi:10.1016/0959-440x(92)90186-b

Cited by 31 publications

(14 citation statements)

References 33 publications

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“…The activated terpyridyl disulfide used in the preparation of [G29TL]2Fe has been described (21 [G29Ts]2Fe is not due to an overall diminished affinity that permits binding to only the more symmetric CRE site. The two nonspecific DNAs display strikingly different peptide [4] affinities. OL1 binds with dissociation constants in the micromolar range, whereas SCR binds with dissociation constants in the nanomolar range.…”

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confidence: 99%

“…The bZIP class of DNA binding proteins represents an excellent system in which to study and apply those factors that control sequence specificity (4). The domain responsible for DNA recognition is small-50 amino acids-and consists of two discrete domains: a DNA contact domain defined by conserved basic and hydrophobic residues (basic domain), and a dimerization domain identified by a heptad repeat of leucine residues (zipper domain) (5).…”

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Design of a metallo-bZIP protein that discriminates between CRE and AP1 target sites: selection against AP1.

Cuenoud

Schepartz

1993

Proc. Natl. Acad. Sci. U.S.A.

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The bZIP class of dimeric DNA binding proteins is characterized by a motif containing two discrete domains: a DNA contact domain defined by conserved basic and hydrophobic residues (basic domain), and a dimerization domain identified by a heptad repeat of leucine residues (zipper domain). Molecules are constructed in which the GCN4 dimerization domain is replaced by a series of stereochemically defined metal ion complexes that alter systematically the relative orientation of the basic domain peptides. Both the affinity and the specificity of DNA binding are modulated by seemingly small changes in metal complex stereochemistry. Although GCN4 binds CRE (ATGACGTCAT) and AP1 (ATGACTCAT) target sites with comparable affinity, one metallo-bZIP peptide ([G29TshFe) prefers the CRE by 4 kcal mol'1 (1 cal = 4.184 J).Competition experiments performed with several DNAs demonstrate that discrimination between CRE and AP1 is dominated by selection against the AP1 site.

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Design of a metallo-bZIP protein that discriminates between CRE and AP1 target sites: selection against AP1.

Cuenoud

Schepartz

1993

Proc. Natl. Acad. Sci. U.S.A.

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“…These proteins are characterized by the presence of the basic region, a subdomain of -20 residues rich in basic amino acids that mediates DNA binding. Immediately adjacent to the basic region is the leucine zipper, a dimerization motif defined by a 4-3 repeat of typically four or five leucine residues interspersed with other hydrophobic amino acids, which align in parallel to form a coiled.coil, with the leucine and additional hydrophobic residues forming a hydrophobic interface (14)(15)(16)(17)(18).A well-documented example of the intricate interactions between members of a family of related bZIP proteins is illustrated with the products ofthefos andjun oncogenes (12,13,19). There are three Jun-related proteins, each of which is capable ofbinding DNA as a homodimer, as well as forming heterodimers with each of the other Jun proteins via dimerization ofthe compatible leucine zippers.…”

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confidence: 99%

“…A well-documented example of the intricate interactions between members of a family of related bZIP proteins is illustrated with the products ofthefos andjun oncogenes (12,13,19). There are three Jun-related proteins, each of which is capable ofbinding DNA as a homodimer, as well as forming heterodimers with each of the other Jun proteins via dimerization ofthe compatible leucine zippers.…”

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Isolation and characterization of a fourth Arabidopsis thaliana G-box-binding factor, which has similarities to Fos oncoprotein.

Menkens

Cashmore

1994

Proc. Natl. Acad. Sci. U.S.A.

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A fourth member of the Aralopm G-boxb ing factor (GBF) family of bZIP proteins, GBF4, has been solated and characterized. In a manner remst of the Fos-related oncoproteins of mam n systems, GBF4 cannot bind to DNA as a ho er, although it coins a basic region cpable of spc fi g the G-box and G-boxlike elements. However, GBF4 can interact with GBF2 and GBF3 to bind DNA as hetrdmers. Mutagenesis ofthe leuine zipper of GBF4 indiates that the mutation of a single amino add coanfs upon the protein the ability to r ize the G-box as a hodimer, apparently by altering the charge distribution within the leucne zipper.The mechanisms of regulated eukaryotic gene expression are topics of intense examination. These regulatory pathways require the coordination of highly specific DNA-protein and protein-protein interactions, many of which are not fully understood. One goal is to understand the individual contribution of seemingly similar DNA elements to regulated gene expression when these conserved elements are present in promoters responding to diverse regulatory controls. In plant systems, one example of this complexity is illustrated by the hexameric G-box (5'-CACGTG-3') and those DNA elements that contain small variations on this palindromic sequence, which we refer to collectively as G-box-like elements. In some cases these elements have been identified as targets for nuclear DNA-binding factors, examples of which include the light-regulated genes of ribulose-1,5-bisphosphate carboxylase/oxygenase (1), chlorophyll a/b binding proteins (2), and chalcone synthase (3), genes regulated by abscisic acid such as the Em gene of wheat (4) and the rabl6A gene of rice (5), as well as the stress-induced Adh gene of maize and Arabidopsis (6, 7). The identification of these nuclear factors has prompted the isolation and characterization of 10 DNAbinding proteins specific for the G-box and G-box-like elements from four different plant species (4,(8)(9)(10)(11).To understand how a seemingly ubiquitous element can be involved in such diverse regulatory pathways, it is essential to understand the individual contributions made by each of the relevant DNA-binding proteins. To date, all of the plant DNA-binding proteins that recognize the G-box belong to the bZIP family of transcription factors (12, 13). These proteins are characterized by the presence of the basic region, a subdomain of -20 residues rich in basic amino acids that mediates DNA binding. Immediately adjacent to the basic region is the leucine zipper, a dimerization motif defined by a 4-3 repeat of typically four or five leucine residues interspersed with other hydrophobic amino acids, which align in parallel to form a coiled.coil, with the leucine and additional hydrophobic residues forming a hydrophobic interface (14)(15)(16)(17)(18).A well-documented example of the intricate interactions between members of a family of related bZIP proteins is illustrated with the products ofthefos andjun oncogenes (12,13,19). There are three Jun-related proteins, each of which is capa...

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Successful prediction of the coiled coil geometry of the GCN4 leucine zipper domain by simulated annealing: Comparison to the X‐ray structure

Nilges

Brünger

1993

Proteins

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The recently solved X-ray structure of the dimerization region ("leucine zipper") of the yeast transcriptional activator GCN4 (O'Shea, E.K., Klemm, J.D., Kim, P.S., Alber, T. Science 254:539-544, 1991) is compared to previously predicted models which had been obtained by a conformational search procedure employing simulated annealing without any knowledge of the crystal coordinates (Nilges, M., Brünger, A.T. Protein Eng. 4:649-659, 1991). During the course of the simulated annealing procedure, the models converged towards the X-ray structure. The averaged root mean square difference between the models and the X-ray structure is 1.26 and 1.75 A for backbone atoms and all nonhydrogen atoms at the dimerization interface, respectively. The local helix-helix crossing angle of the X-ray structure falls within the range predicted by the models; a slight unwinding of the coiled coil toward the N-terminal DNA-binding end of the dimerization region has been correctly predicted. Distance maps between the helices are largely identical. The region around asparagine 20 is asymmetric in the X-structure and in the models. Surface side chain dihedrals showed a large variation in the models although the chi 1, chi 2, chi 3, chi 4 3-fold dihedrals were correctly predicted in 69, 42, 43, and 44% of the cases, respectively. Phenomenological free energies of dimerization of the models show little correlation with the root mean square difference between the models and the X-ray structure.

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Updating structure-function relationships in the bZip family of transcription factors

Cited by 31 publications

References 33 publications

Design of a metallo-bZIP protein that discriminates between CRE and AP1 target sites: selection against AP1.

Design of a metallo-bZIP protein that discriminates between CRE and AP1 target sites: selection against AP1.

Isolation and characterization of a fourth Arabidopsis thaliana G-box-binding factor, which has similarities to Fos oncoprotein.

Successful prediction of the coiled coil geometry of the GCN4 leucine zipper domain by simulated annealing: Comparison to the X‐ray structure

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