(Q36557529)

14 August 2017

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title

Indirect readout of DNA sequence by proteins: the roles of DNA sequence-dependent intrinsic and extrinsic forces (English)

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14 August 2017

Gerald B Koudelka

1

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14 August 2017

Steven A Mauro

series ordinal

2

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14 August 2017

Mihai Ciubotaru

series ordinal

3

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14 August 2017

publication date

1 January 2006

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Progress in Molecular Biology and Translational Science

14 August 2017

published in

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14 August 2017

volume

81

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14 August 2017

page(s)

143-177

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Crystal structure of a yeast TBP/TATA-box complex

14 August 2017

cites work

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The three-dimensional structure of trp repressor.

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7 January 2021

Crystal structure at 1.7 A of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target

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7 January 2021

The interaction of E. coli IHF protein with its specific binding sites.

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7 January 2021

Crystal structure of the met repressor-operator complex at 2.8 A resolution reveals DNA recognition by beta-strands

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7 January 2021

Specific DNA binding by c-Myb: evidence for a double helix-turn-helix-related motif

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7 January 2021

Structure and dynamics of MarA-DNA complexes: an NMR investigation

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7 January 2021

The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements

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7 January 2021

Pausing of the restriction endonuclease EcoRI during linear diffusion on DNA.

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7 January 2021

Crystal structure of the E2 DNA-binding domain from human papillomavirus type 16: implications for its DNA binding-site selection mechanism

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7 January 2021

The complex between phage 434 repressor DNA-binding domain and operator site OR3: structural differences between consensus and non-consensus half-sites

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7 January 2021

Identification and characterization of genomic nucleosome-positioning sequences

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7 January 2021

Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences.

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7 January 2021

Nucleosome structural features and intrinsic properties of the TATAAACGCC repeat sequence

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7 January 2021

DNA sequence determinants of CAP-induced bending and protein binding affinity.

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7 January 2021

E. coli integration host factor binds to specific sites in DNA

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7 January 2021

Deformation of DNA during site-specific recombination of bacteriophage lambda: replacement of IHF protein by HU protein or sequence-directed bends

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7 January 2021

Architectural elements in nucleoprotein complexes: interchangeability of specific and non-specific DNA binding proteins.

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7 January 2021

Increased nuclear factor 1 binding to its nucleosomal site mediated by sequence-dependent DNA structure

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7 January 2021

How NF-κB can be attracted by its cognate DNA

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7 January 2021

DNA deformability as a recognition feature in the reverb response element

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7 January 2021

Autonomous DNA binding domains of lambda integrase recognize two different sequence families

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7 January 2021

Flexibility in DNA recombination: structure of the lambda integrase catalytic core

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7 January 2021

Specific binding of lac repressor to linear versus circular polyoperator molecules.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Symmetric lac operator derivatives: effects of half-operator sequence and spacing on repressor affinity

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

DNA structure and flexibility in the sequence-specific binding of papillomavirus E2 proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

DNA binding specificity studies of four ETS proteins support an indirect read-out mechanism of protein-DNA recognition.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

A new pattern for helix-turn-helix recognition revealed by the PU.1 ETS-domain-DNA complex

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

The structure of GABPalpha/beta: an ETS domain- ankyrin repeat heterodimer bound to DNA

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Structures of SAP-1 Bound to DNA Targets from the E74 and c-fos Promoters

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Structure of the elk-1-DNA complex reveals how DNA-distal residues affect ETS domain recognition of DNA

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Signals for TBP/TATA box recognition

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Energy transfer analysis of Fos-Jun dimerization and DNA binding

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Analysis of the DNA-binding affinity, sequence specificity and context dependence of the glucocorticoid receptor zinc finger region

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Influence of a steroid receptor DNA-binding domain on transcriptional regulatory functions

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Allosteric effects of DNA on transcriptional regulators

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Mutations in the glucocorticoid receptor DNA-binding domain mimic an allosteric effect of DNA 1 1Edited by P. E. Wright

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https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

DNA structure determines protein binding and transcriptional efficiency of the proenkephalin cAMP-responsive enhancer

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Refinement of the structure of B-DNA and implications for the analysis of X-ray diffraction data from fibers of biopolymers

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

THE MOLECULAR CONFIGURATION OF DEOXYRIBONUCLEIC ACID. IV. X-RAY DIFFRACTION STUDY OF THE A FORM

1 reference

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7 January 2021

Stereochemistry of nucleic acids and their constituents. X. Solid-state base-stacking patterns in nucleic acid constituents and polynucleotides

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Crystal structure analysis of a complete turn of B-DNA

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Structure of a B-DNA dodecamer: conformation and dynamics

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Absence of minor groove monovalent cations in the crosslinked dodecamer C-G-C-G-A-A-T-T-C-G-C-G

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

The B-DNA dodecamer at high resolution reveals a spine of water on sodium

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Mechanics of sequence-dependent stacking of bases in B-DNA

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Sequence-dependent DNA structure: tetranucleotide conformational maps

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https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Sequence-dependent DNA structure: dinucleotide conformational maps

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Bending and torsional flexibility of G/C-rich sequences as determined by cyclization assays

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

The effects of sequence context on DNA curvature.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Unconventional helical phasing of repetitive DNA motifs reveals their relative bending contributions

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

The structure of an oligo(dA).oligo(dT) tract and its biological implications

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

The assessment of the geometry of dinucleotide steps in double-helical DNA; a new local calculation scheme.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Use of a 3D structure data base for understanding sequence-dependent conformational aspects of DNA.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

DNA structure: cations in charge?

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

DNA bending by small, mobile multivalent cations

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Force-induced melting of the DNA double helix. 2. Effect of solution conditions

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Double helix at atomic resolution

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Structural analysis of spermine and magnesium ion binding to yeast phenylalanine transfer RNA

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Locating monovalent cations in the grooves of B-DNA

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Atomic-resolution crystal structures of B-DNA reveal specific influences of divalent metal ions on conformation and packing

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

DNA-cation interactions: The major and minor grooves are flexible ionophores.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

DNA-dependent divalent cation binding in the nucleosome core particle

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Homology among DNA-binding proteins suggests use of a conserved super-secondary structure

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Repression of transcription initiation at 434 P(R) by 434 repressor: effects on transition of a closed to an open promoter complex

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Design of a "minimAl" homeodomain: the N-terminal arm modulates DNA binding affinity and stabilizes homeodomain structure

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Repressor structure and the mechanism of positive control

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

DNA sequence requirements for the activation of 434 P(RM) transcription by 434 repressor

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

RNA polymerase bound to the PR promoter of bacteriophage lambda inhibits open complex formation at the divergently transcribed PRM promoter. Implications for an indirect mechanism of transcriptional activation by lambda repressor

1 reference

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7 January 2021

Mutually exclusive utilization of P(R) and P(RM) promoters in bacteriophage 434 O(R)

1 reference

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7 January 2021

Genetic regulatory mechanisms in the synthesis of proteins

1 reference

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7 January 2021

The bacteriophage 434 right operator. Roles of O(R)1, O(R)2 and O(R)3.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

RNA polymerase idling and clearance in gal promoters: use of supercoiled minicircle DNA template made in vivo

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

The lambda repressor contains two domains

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Recognition of a DNA operator by the repressor of phage 434: a view at high resolution

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Structure of the amino-terminal domain of phage 434 repressor at 2.0 A resolution

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

A comparative study of the immunity region of lambdoid phages including Shiga-toxin-converting phages: molecular basis for cross immunity

1 reference

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7 January 2021

A structural taxonomy of DNA-binding domains

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Interactions between DNA-bound repressors govern regulation by the λ phage repressor

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Crystal structure of LexA: a conformational switch for regulation of self-cleavage

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Carboxyl-terminal domain dimer interface mutant 434 repressors have altered dimerization and DNA binding specificities

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

DNA-induced conformational changes in bacteriophage 434 repressor

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and Cro

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Structure of the repressor-operator complex of bacteriophage 434.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

DNA twisting and the effects of non-contacted bases on affinity of 434 operator for 434 represser

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

The phage 434 OR2/R1-69 complex at 2.5 A resolution

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Theory of twisting and bending of chain macromolecules; analysis of the fluorescence depolarization of DNA

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Bending of synthetic bacteriophage 434 operators by bacteriophage 434 proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Recognition of DNA structure by 434 repressor

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Dependence of the torsional rigidity of DNA on base composition

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Dimerization specificity of P22 and 434 repressors is determined by multiple polypeptide segments

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

The role of the minor groove substituents in indirect readout of DNA sequence by 434 repressor

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

DNA twisting and the affinity of bacteriophage 434 operator for bacteriophage 434 repressor

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

How 434 repressor discriminates between OR1 and OR3. The influence of contacted and noncontacted base pairs

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Operator sequence context influences amino acid-base-pair interactions in 434 repressor-operator complexes.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Sequence specificity of bacteriophage 434 repressor-operator complexation

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

A physiological role for DNA supercoiling in the osmotic regulation of gene expression in S. typhimurium and E. coli

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

The downstream regulatory element of the proU operon of Salmonella typhimurium inhibits open complex formation by RNA polymerase at a distance.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Role of DNA supercoiling and rpoS sigma factor in the osmotic and growth phase-dependent induction of the gene osmE of Escherichia coli K12

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Osmotic regulation of porin expression: a role for DNA supercoiling.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Responses of E. coli to osmotic stress: large changes in amounts of cytoplasmic solutes and water

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Biophysical compensation mechanisms buffering E. coli protein-nucleic acid interactions against changing environments

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Monovalent cations regulate DNA sequence recognition by 434 repressor

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

The Lambda and P22 Phage Repressors

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

Structural mechanics of bent DNA

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2806%2981004-4

7 January 2021

10.1016/S0079-6603(06)81004-4

Identifiers

DOI

1 reference

14 August 2017

1 reference