Structural aspects of protein-DNA recognition

Freemont, Paul S.; Lane, Andrew N.; Sanderson, Mark

doi:10.1042/bj2780001

Cited by 91 publications

(54 citation statements)

References 161 publications

(169 reference statements)

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“…Remarkably, the CXC domain uses a single arginine to directly read out dinucleotide sequences from the minor groove of DNA, distinct from other DNA-binding domains that commonly recognize DNA sequence from the major groove with large secondary structure elements (Freemont et al 1991). Arginine has been documented to interact with the minor groove but, in most cases, indirectly reads out DNA sequences by binding narrow minor grooves adopted by AT-rich sequences (Rohs et al 2009).…”

Section: Discussionmentioning

confidence: 99%

Structural basis of X chromosome DNA recognition by the MSL2 CXC domain during Drosophila dosage compensation

et al. 2014

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The male-specific lethal dosage compensation complex (MSL-DCC) selectively assembles on the X chromosome in Drosophila males and activates gene transcription by twofold through histone acetylation. An MSL recognition element (MRE) sequence motif nucleates the initial MSL association, but how it is recognized remains unknown. Here, we identified the CXC domain of MSL2 specifically recognizing the MRE motif and determined its crystal structure bound to specific and nonspecific DNAs. The CXC domain primarily contacts one strand of DNA duplex and employs a single arginine to directly read out dinucleotide sequences from the minor groove. The arginine is flexible when bound to nonspecific sequences. The core region of the MRE motif harbors two binding sites on opposite strands that can cooperatively recruit a CXC dimer. Specific DNA-binding mutants of MSL2 are impaired in MRE binding and X chromosome localization in vivo. Our results reveal multiple dynamic DNA-binding modes of the CXC domain that target the MSL-DCC to X chromosomes.

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Section: Discussionmentioning

confidence: 99%

Structural basis of X chromosome DNA recognition by the MSL2 CXC domain during Drosophila dosage compensation

et al. 2014

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“…Each monomer is comprised of six a-helices (Zhang et al, 1987; see Kinemage l), of which three from each monomer (A, B, C, A', B', and C') are intertwined at the dimer interface to form the interior core of the protein. Helices D and E from each monomer make up the "helix-turn-helix" DNA-binding motif common to many prokaryotic and phage DNA binding proteins (for reviews see Steitz [1990] and Freemont et al [1991]). The last helix, F, packs against the core to form part of the second subunit interface region (see Fig.…”

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confidence: 99%

Tryptophan replacements in the trp aporepressor from escherichia coli: Probing the equilibrium and kinetic folding models

1993

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Mutants of the dimeric Escherichia coli trp aporepressor are constructed by replacement of the two tryptophan residues in each subunit in order to assess the effects on equilibrium and kinetic fluorescence properties of the folding reaction. The three kinetic phases detected by intrinsic tryptophan fluorescence in refolding of the wildtype aporepressor are also observed in folding of both Trp 19 to Phe and Trp 99 to Phe single mutants, demonstrating that these phases correspond to global rather than local conformational changes. The equilibrium results can be interpreted in terms of enhancement in the population of a monomeric folding intermediate in which the lone tryptophan residue is highly exposed to solvent, but in which substantial secondary structure is retained. The location of both mutations at the interface between the two subunits (Zhang, R.G., et al., 1987, Nature 327, 591-597) provides a simple explanation for this phenomenon.Keywords: cooperativity; folding intermediate; folding mechanism; protein stability; tryptophan fluorescence; tryptophan mutations Fluorescence spectroscopy is a sensitive and potentially informative method of monitoring both equilibrium and kinetic properties of protein-folding reactions. The hydrophobic character of aromatic residues (i.e., tryptophan, tyrosine, and phenylalanine) often leads to their being sequestered in the interior of the native conformation. Therefore, the intensity, emission maximum, and distribution of various lifetime components of these residues can differ from those exposed to solvent (Beechem & Brand, 1985). Disruption of noncovalent interactions that define the native form and exposure of these aromatic side chains to solvent during a global unfolding reaction can lead to changes that are observed readily in these static and dynamic properties (see, for example, the accompanying paper by Royer et al. [1993] A challenge for kinetic studies of folding reactions has been to obtain specific assignments and structural interpretations for observed changes in fluorescence properties. Garvey et al. (1989) solved this problem in dihydrofolate reductase from Escherichia coli by using site-directed mutagenesis to replace several of the tryptophan residues individually. These workers found that one of the kinetic phases detected in the refolding of wild-type reductase was eliminated selectively in the mutant, in which Trp 74 was replaced by Phe. This effect was attributed to the burying of Trp 74 in a hydrophobic cluster early in the folding process. Later studies demonstrated that Trp 74 packs against Trp 47 in a native-like fashion in a transient folding intermediate (Kuwajima et al., 1991).With this precedent, a set of mutations in the tryptophan aporepressor from E. coli were constructed with the goal of determining the assignments of the three kinetic phases detected previously by tryptophan fluorescence during refolding of this dimeric protein (Gittelman

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“…The interaction between a DNA-binding protein and its specific binding site on the DNA molecule is crucial in gene regulation, and this is closely related to the question of how these proteins find their binding sites (Freemont et al, 1991;Halford & Marko, 2004). Some regulatory proteins recognize multiple specific binding sites, which in most cases have a similar but not identical sequence.…”

Section: Introductionmentioning

confidence: 99%