Mean DNA bend angle and distribution of DNA bend angles in the CAP-DNA complex in solution

Journal of Molecular Biology

Volumn 312, Issue 3, 2001, Pages 453-468

  Kapanidis, Achillefs N ^a   Ebright, Yon W ^a   Ludescher, Richard D ^b   Chan, Shirley ^c   Ebright, Richard H ^a  

^a RUTGERS UNIVERSITY   (United States)

^b RUTGERS UNIVERSITY   (United States)

^c PRINCETON UNIVERSITY   (United States)

Author keywords

cAMP receptor protein (CRP); Catabolite activator protein (CAP); Fluorescence resonance energy transfer; Protein induced DNA bending; Transcriptional activation

Indexed keywords

CHELATE; CURVED DNA; CYCLIC AMP BINDING PROTEIN; LANTHANIDE;

ANISOTROPY; ARTICLE; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; DNA PROTEIN COMPLEX; DNA STRUCTURE; ENERGY TRANSFER; ESCHERICHIA COLI; FLUORESCENCE; NONHUMAN; PRIORITY JOURNAL; TRANSCRIPTION INITIATION;

EID: 0035929295     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.4976     Document Type: Article

References (76)

1. Transcriptional regulation by cAMP and its receptor protein
2. Transcription activation by catabolite activator protein (CAP)
3. Consensus DNA site for the Escherichia coli catabolite gene activator protein (CAP): CAP exhibits a 450-fold higher affinity for the consensus DNA site than for the E. coli lac DNA site
4. Structure of a complex of catabolite gene activator protein and cAMP refined to 2.5 Å resolution
5. Structure of the CAP-DNA complex at 2.5 Å resolution: A complete picture of the protein-DNA interface
6. Crystal structure of a CAP-DNA complex: The DNA is bent by 90°
7. Aromatic hydrogen bond in sequence-specific protein DNA recogrution
8. The structure of a CAP-DNA complex having two cAMP molecules bound to each other
9. The helix-turn-helix DNA binding motif
10. Transcriptional activation by Escherichia coli CAP protein
11. DNA sequence determinants of CAP-induced bending and protein binding affinity
12. The locus of sequence-directed and protein-induced DNA bending
13. The DNA binding domain and bending angle of E. coli CAP protein
14. Empirical estimation of protein-induced DNA bending angles: Applications to λ site-specific recombination complexes
15. Comparative gel electrophoresis measurement of the DNA bend angle induced by the catabolite activator protein
16. Catabolite activator protein-induced DNA bending in transcription initiation
17. Identification of the activating region of catabolite gene activator protein (CAP): Isolation and characterization of mutants of CAP specifically defective in transcription activation
18. The change of DNA structure by specific binding of the cAMP receptor protein from rotation diffusion and dichroism measurements
19. Turn of promotor DNA by cAMP receptor protein characterized by bead model simulation of rotational diffusion
20. The cyclic AMP receptor promoter DNA complex: A comparison of crystal and solution structure by quantitative molecular electrooptics
21. Variations of intramolecular ligation rates allow the detection of protein-induced bends in DNA
22. Protein-induced bending and DNA cyclization
23. Measurement of the DNA bend angle induced by the catabolite activator protein using Monte Carlo simulation of cyclization kinetics
24. Topological measurement of protein-induced DNA bend angles
25. Solution studies of the structure of bent DNA in the cAMP receptor protein-lac DNA complex
26. Fluorescence energy transfer analysis of DNA structures containing several bulges and their interaction with CAP
27. Recent advances in FRET: Distance determination in protein-DNA complexes
28. DNA sequence determinants for binding of the Escherichia coli catabolite gene activator protein
29. The renaissance of fluorescence resonance energy transfer
30. Fluorescence resonance energy transfer as a structural tool for nucleic acids
31. Luminescence resonance energy transfer
32. Simultaneous binding and bending of promoter DNA by the TATA binding protein: Real-time kinetic measurements
33. Detection of DNA bending in a DNA-PAP1 protein complex by fluorescence resonance energy transfer
34. Structural and kinetic studies of a cisplatin-modified DNA icosamer binding to HMG1 domain B
35. DNA bending induced by high mobility group proteins studied by fluorescence resonance energy transfer
36. Global structure similarities of intact and nicked DNA complexed with IHF measured in solution by fluorescence resonance energy transfer
37. Bends in TATA-binding protein-TATA complexes in solution are DNA sequence-dependent
38. DNA sequence-dependent differences in TATA-binding protein-induced DNA bending in solution are highly sensitive to osmolytes
39. Conformational transitions in the calcium adenosinotriphosphatase studied by time-resolved fluorescence resonance energy transfer
40. Design and characterization of a multisite fluorescence energy-transfer system for protein folding studies: A steady-state and time-resolved study of yeast phosphoglycerate kinase
41. Electrostatic calculations and model-building suggest that DNA bound to CAP is sharply bent
42. Sequence-dependent contribution of distal binding domains to CAP protein-DNA binding affinity
43. Evaluation of the distribution of distances between energy donors and acceptors by fluorescence decay
44. Distributions of fluorescence decay times for parinaric acids in phospbolipid membranes
45. Environmental modulation of M13 coat protein tryptophan fluorescence dynamics
46. Luminescent energy transfer using a terbium chelate: Improvements on fluorescence energy transfer
47. Thiol-reactive, luminescent europium chelates: Luminescent probes for resonance energy transfer distance measurements in biomolecules
48. Collective protein dynamics in relation to function
49. Molecular dynamics simulation of nucleic acids
50. Diffusion-enhanced fluorescence energy transfer
51. Core RNA polymerase from E. coli induces a major change in the domain arrangement of the sigma70 subunit
52. CAP interacts with RNA polymerase in solution in the absence of promoter DNA
53. The estimation of distances between specific backbone-labelled sites in DNA using fluorescence resonance energy transfer
54. Random mutagenesis of gene-sized DNA molecules by use of PCR with Taq DNA polymerase
55. Efficient site-directed mutagenesis using uracil-containing DNA
56. Derivatives of CAP having no solvent-accessible cysteine residues, or having a unique solvent-accessible cysteine residue at amino acid 2 of the helix-turn-helix motif
57. Stroboscopic optical boxcar technique for the determination of fluorescence lifetimes
58. A review of photon-counting and phase-modulation measurements of fluorescence decay kinetics
59. Fluorescence polarization: Measurement with ultraviolet-polarizing filters in a spectrophotofluorometer
60. Synthesis and characterization of two fluorescent sulfhydryl reagents
61. Analysis of time-resolved fluorescence anisotropy decays
62. A theory of fluorescence polarization decay in membranes
63. The orientational freedom of molecular probes
64. Effect of the orientation of donor and acceptor on the probability of energy transfer involving electronic transitions of mixed polarization
65. Dynamics and conformational energetics of a peptide hormone: Vasopressin
66. Molecular dynamics simulations in biology
67. A new force field for molecular mechanical simulation of nucleic acids and proteins
68. RATTLE: A "velocity" version of the SHAKE algorithm for molecular dynamics calculations
69. Computer simulation of the conformational properties of oligopeptides. Comparison of theoretical methods and analysis of experimental results
70. Structure and energetics of ligand binding to proteins: Escherichia coli dihydrofolate reductase-trimethoprim, a drug-receptor system
71. Molecular dynamics of the anti-fluorescein 4-4-20 antigen-binding fragment. 1. Computer simulations
72. Computer experiments on classical fluids. I. Thermodynamic properties of Lennard-Jones molecules
73. Atomic level simulations on a million particles: The cell multipole method for Coulomb and London nonbond interactions
74. The orientation of transition moments of dye molecules used in fluorescence studies of muscle systems
75. Quantum efficiency of luminescent lanthanide chelates and far-red dyes measured by diffusion-enhanced energy transfer