How Proteins Recognize the TATA Box

Juo, Z. Sean; Chiu, Thang Kien; Leiberman, Paul M.; Baikalov, Igor; Berk, Arnold; Dickerson, Richard E.

doi:10.1006/jmbi.1996.0456

Cited by 304 publications

(293 citation statements)

References 41 publications

(54 reference statements)

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“…Such proteins would stabilize DNA structures that are naturally present in DNA as a consequence of translocase activity rather than simply inducing such structures. For example, like the HMG domain, TBP intercalates aminoacids between base-pairs and stabilizes untwisted DNA (Kim et al 1993a, b;Juo et al 1996). This structural preference for untwisted DNA is emphasized by its potentiation by flanking untwisted cis-platin lesions (Cohen et al 2000b).…”

Section: Gradients Of Superhelicity and Protein Bindingmentioning

confidence: 99%

The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity

Muskhelishvili

Travers

2016

Biophys Rev

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We argue that dynamic changes in DNA supercoiling in vivo determine both how DNA is packaged and how it is accessed for transcription and for other manipulations such as recombination. In both bacteria and eukaryotes, the principal generators of DNA superhelicity are DNA translocases, supplemented in bacteria by DNA gyrase. By generating gradients of superhelicity upstream and downstream of their site of activity, translocases enable the differential binding of proteins which preferentially interact with respectively more untwisted or more writhed DNA. Such preferences enable, in principle, the sequential binding of different classes of protein and so constitute an essential driver of chromatin organization.Keywords DNA supercoiling . DNA translocases . Chromatin organization . Superhelicity gradients . DNA untwisting . DNAwrithing Dynamic changes of DNA supercoiling act as a driving force behind the alterations of genetic activity and DNA compaction both in eukaryotes and prokaryotes. Both these processes involve formation of spatially organized nucleoprotein structures by DNA architectural proteins. Whereas in eukaryotes the paradigmal example is the histone octamer, in prokaryotes a similar function is attributed to a small class of highly abundant nucleoid-associated proteins. We argue that, depending on the primary sequence organization, the changes of superhelicity elicit various alterations of local DNA geometry, while these, in turn, facilitate the assembly of distinct nucleoprotein structures pertinent to genetic function. Genome-wide conversion of the superhelical energy into various three-dimensional DNA structures thus acts as an analogue code coordinating the energy supply with the genetic expression of the chromosome.Recent studies make it increasingly clear that the DNA double helix carries at least two types of encoded information and that these include the well-known genetic code and the structural information determining the form and physical properties of the double helix itself. Since both these information types are inscribed in the same DNA sequence, and yet one is discrete whereas the other is continuous, they have been respectively dubbed the digital and analog DNA codes (Marr et al. 2008;Travers et al. 2012;Muskhelishvili and Travers 2013). The potential of the DNA to adopt distinct configurations is strongly modulated by DNA supercoiling, which is increasingly recognized as one of the major forces coordinating the cellular DNA transactions in both prokaryotes (including Archaea) and eukaryotes.DNA supercoiling can be generated by the simple application of torque to the double helix (Strick et al. 1998) but, importantly, because the DNA molecule itself possesses chirality-it is, after all, a right-handed double helix-the local structures stabilized by changes in superhelical density depend on both the sign and strength of the applied torque. For example, both positive and negative torque (respectively overand underwinding of the double helix) can change the intrinsic coiling of ...

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Section: Gradients Of Superhelicity and Protein Bindingmentioning

confidence: 99%

The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity

Muskhelishvili

Travers

2016

Biophys Rev

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“…In contrast, when wild-type and V52 variant proteins were assayed with the O disC operator, high affinity operator binding was observed for multiple variants ( Figure 6 and (Figure 7 and Table 4), though V52C-red has been shown to be compromised (perhaps due to a residual amount of disulfide formation (36)). The generally higher affinity for O disC compared to O disB for V52 LacI variants may result from enhanced flexibility of central C-G step and its ability to adopt greater positive rolls in O disC (36,57,58) …”

Section: O Disb and O Disc Binding Of V52 Mutantsmentioning

confidence: 99%

Extrinsic Interactions Dominate Helical Propensity in Coupled Binding and Folding of the Lactose Repressor Protein Hinge Helix

2006

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A significant number of eukaryotic regulatory proteins are predicted to have disordered regions. Many of these proteins bind DNA, which may serve as a template for protein folding. Similar behavior is seen in the prokaryotic LacI/GalR family of proteins that couple hinge-helix folding with DNA binding. These hinge regions form short α-helices when bound to DNA, but appear to be disordered in other states. An intriguing question is whether and to what degree intrinsic helix propensity contributes to the function of these proteins. In addition to its interaction with operator DNA, the LacI hinge helix interacts with the hinge helix of the homodimer partner as well as to the surface of the inducer-binding domain. To explore the hierarchy of these interactions, we made a series of substitutions in the LacI hinge helix at position 52, the only site in the helix that does not interact with DNA and/or the inducer-binding domain. The substitutions at V52 have significant effects on operator binding affinity and specificity, and several substitutions also impair functional communication with the inducer-binding domain. Results suggest that helical propensity of amino acids in the hinge region alone does not dominate function; helix-helix packing interactions appear to also contribute. Further, the data demonstrate that variation in operator sequence can overcome side chain effects on hinge helix folding and/or hinge•hinge interactions. Thus, this system provides a direct example whereby an extrinsic interaction (DNA binding) guides internal events that influence folding and functionality. KeywordsLacI; helical propensity; allostery; DNA binding Protein folding has long been a fundamental issue in biological sciences. Beyond the general question of how a polypeptide sequence adopts a three-dimensional structure, coupled folding and binding have been identified as a key feature of partially unstructured proteins in multiple regulatory processes (e.g., transcription regulation, signal transduction, membrane transport and signaling (6-9)). Indeed, more and more intrinsically disordered proteins are found to fold upon binding to their target partners, ligands, or even small ions (10-13). In the case of transcription regulation, mutual cooperative folding of both protein and DNA has been † This work was supported by NIH Grant GM22441 and Robert A. Welch Grant C-576 to Kathleen Shive Matthews. Liskin Swint-Kruse is supported by NIH Grant P20 RR17708 from the Institutional Development Award program of the National Center for Research Resources.*To whom correspondence should be addressed. Telephone: 713−348−4871; Fax: 713−348−6149; Email: E-mail: ksm@bioc.rice.edu.. observed (6,11,14,15). In this paper, coupled folding is explored in greater detail for the hinge helix of the lactose repressor protein (LacI) 1 . NIH Public AccessLacI is a premier model for the regulation of gene expression and allosteric transition in biological systems (2) 2 . This 150-kDa homotetramer is a dimer of functionally independent dimers, with ...

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“…[4][5][6][7] Crystal structures of TBP bound to TATA DNA have shown that the C-terminal DNA binding domain of TBP looks like a saddle with stirrups hanging from each end. [8][9][10][11] Each stirrup contains phenylalanine residues, which insert into the minor groove on each side of a 6 bp stretch of DNA, centered in the middle of the 8 bp TATA box. Insertion of the phenylalanine residues disrupts the base stacking interactions and allows TBP to bend the DNA.…”

Section: Introductionmentioning

confidence: 99%

“…Insertion of the phenylalanine residues disrupts the base stacking interactions and allows TBP to bend the DNA. [8][9][10][11] TBP causes minor grove widening and changes the roll, rise, and twist of the TATA DNA.…”

Section: Introductionmentioning

confidence: 99%

TFIIA Changes the Conformation of the DNA in TBP/TATA Complexes and Increases their Kinetic Stability

Hieb

Halsey

Betterton

et al. 2007

Journal of Molecular Biology

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How Proteins Recognize the TATA Box

Cited by 304 publications

References 41 publications

The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity

The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity

Extrinsic Interactions Dominate Helical Propensity in Coupled Binding and Folding of the Lactose Repressor Protein Hinge Helix

TFIIA Changes the Conformation of the DNA in TBP/TATA Complexes and Increases their Kinetic Stability

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