Protein surface salt bridges and paths for DNA wrapping

Current Opinion in Structural Biology

Volumn 12, Issue 3, 2002, Pages 311-319

  Saecker, Ruth M ^a   Record Jr, M Thomas ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATION; CELL DNA; DNA TOPOISOMERASE (ATP HYDROLYSING); INTEGRATION HOST FACTOR; PROTEIN; PROTEIN IHF; PROTEIN UVRB; RNA POLYMERASE; SINGLE STRANDED DNA BINDING PROTEIN; SODIUM CHLORIDE; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; DNA; DNA BINDING PROTEIN; DNA DIRECTED RNA POLYMERASE; ESCHERICHIA COLI PROTEIN; HELICASE; INORGANIC SALT; LACI PROTEIN, BACTERIA; REPRESSOR PROTEIN; UVRB PROTEIN, E COLI;

BINDING AFFINITY; CHROMOSOME; CONCENTRATION (PARAMETERS); DNA BINDING; DNA PACKAGING; DNA RECOMBINATION; DNA REPAIR; DNA REPLICATION; DNA STRUCTURE; DNA TRANSCRIPTION; ENTHALPY; ENTROPY; HEAT; LACTOSE OPERON; NONHUMAN; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DNA BINDING; PROTEIN STRUCTURE; REVIEW; THERMODYNAMICS; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; PROTEIN BINDING; PROTEIN TERTIARY STRUCTURE;

BACTERIAL PROTEINS; DNA; DNA GYRASE; DNA HELICASES; DNA-BINDING PROTEINS; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI PROTEINS; INTEGRATION HOST FACTORS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; REPRESSOR PROTEINS; SALTS; THERMODYNAMICS;

EID: 0036600872     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(02)00326-3     Document Type: Review

References (64)

1. Recognition of specific DNA sequences
2. The Protein Data Bank and the challenge of structural genomics
3. An overview of the structures of protein-DNA complexes
4. Structural features of protein-nucleic acid recognition sites
5. Geometric analysis and comparison of protein-DNA interfaces: Why is there no simple code for recognition?
6. Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level
7. Coupling of local folding to site-specific binding of proteins to DNA
8. Specific and non-specific interactions of integration host factor with DNA: Thermodynamic evidence for disruption of multiple IHF surface salt-bridges coupled to DNA binding
9. Thermodynamic origins of specificity in the lac repressor-operator interaction. Adaptability in the recognition of mutant operator sites
10. Intrinsically unstructured proteins: Re-assessing the protein structure-function paradigm
11. If the loop fits
12. Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: Interpretation in terms of coupled processes of formation and association of single-stranded helices
13. A highly salt-dependent enthalpy change for Escherichia coli SSB protein-nucleic acid binding due to ion-protein interactions
14. Calorimetric studies of E. coli SSB protein-single-stranded DNA interactions. Effects of monovalent salts on binding enthalpy
15. Adenine base unstacking dominates the observed enthalpy and heat capacity changes for the Escherichia coli SSB tetramer binding to single-stranded oligoadenylates
16. Large contributions of coupled protonation equilibria to the observed enthalpy and heat capacity changes for ssDNA binding to Escherichia coli SSB protein
17. Multiple DNA-protein interactions governing high-precision DNA transactions
18. Nucleoprotein structures initiating DNA replication, transcription, and site-specific recombination
19. Crystal structure of the nucleosome core particle at 2.8 Å resolution
20. Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions
21. Structure of the DNA binding domain of E. coli SSB bound to ssDNA
22. Crystal structure of an IHF-DNA complex: A protein-induced DNA U-turn
23. Wrapping of flanking non-operator DNA in lac repressor-operator complexes: Implications for DNA looping
24. A model for the mechanism of strand passage by DNA gyrase
25. Electron microscopic study of (A)BC excinuclease DNA is sharply bent in the UvrB-DNA complex
26. Architecture of nucleotide excision repair complexes: DNA is wrapped by UvrB before and after damage recognition
27. Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: A practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts
28. Some thermodynamic principles of nonspecific and site-specific protein-DNA interactions
29. Thermodynamic extent of counterion release upon binding oligolysines to single-stranded nucleic acids
30. Thermodynamics of single-stranded RNA binding to oligolysines containing tryptophan
31. Thermodynamics of oligoarginines binding to RNA and DNA
32. Interaction of an N-methylated polyamine analogue, hexamethonium(2+), with NaDNA: Quantitative 14N and 23Na NMR relaxation rate studies of the cation-exchange process
33. NMR studies of cation-binding environments on nucleic acids
34. + concentrations on lac repressor-lac operator binding: In vitro thermodynamic analysis and in vivo relevance
35. Ion concentration and temperature dependence of DNA binding: Comparison of PurR and LacI repressor proteins
36. 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
37. Equilibrium DNA-binding of AraC protein compensation for displaced ions
38. Energetics and affinity of the histone octamer for defined DNA sequences
39. R promoter by salt concentration
40. Micrococus luteus DNA gyrase: Active components and a model for its supercoiling of DNA
41. Mapping the topography of DNA wrapped around gyrase by nucleolytic and chemical probing of complexes of unique DNA sequences
42. Conversion of DNA gyrase into a conventional type II topoisomerase
43. Crystal structure of the breakage-reunion domain of DNA gyrase
44. Crystal structure of an N-terminal fragment of the DNA gyrase B protein
45. Dimerization of Escherichia coli DNA-gyrase B provides a structural mechanism for activating the ATPase catalytic center
46. Structure and mechanism of DNA topoisomerase II
47. sym operators to a LacI tetramer: Evidence for contributions of non-operator DNA binding by wrapping and looping
48. Crystal structure of lac repressor core tetramer and its implications for DNA looping
49. Crystal structure of the lactose operon repressor and its complexes with DNA and inducer
50. DNA supercoiling changes the spacing requirement of two lac operators for DNA loop formation with lac repressor
51. In vivo thermodynamic analysis of repression with and without looping in lac constructs. Estimates of free and local lac repressor concentrations and of physical properties of a region of supercoiled plasmid DNA in vivo
52. Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator
53. Designed hyperstable lac repressor-DNA loop topologies suggest alternative loop geometries
54. Thermodynamics of the interactions of lac repressor with variants of the symmetric lac operator: Effects of converting a consensus site to a non-specific site
55. A closer view of the conformation of the lac repressor bound to operator
56. Wrapping of DNA around the E. coli RNA polymerase open promoter complex
57. Structural basis for H-NS mediated trapping of RNA polymerase in the open initiation complex at the rrnB P1
58. 2+ binding and its structural consequences at the transcription start site
59. Three-dimensional structure of E. coli core RNA polymerase: Promoter binding and elongation conformations of the enzyme
60. DNA bending and wrapping around RNA polymerase: A 'revolutionary' model describing transcriptional mechanisms
61. Structure of UvrABC exinuclease-UV-damaged DNA complexes studied by flow linear dichroism. DNA curved by UvrB and UvrC
62. Crystal structure of the DNA nucleotide excision repair enzyme UvrB from Thermus thermophilus
63. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
64. Raster3D: Photorealistic molecular graphics