Crossref journal-article
Elsevier BV
Journal of Molecular Biology (78)
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Mandel-Gutfreund, Y., Margalit, H., Jernigan, R. L., & Zhurkin, V. B. (1998). A role for CH…O interactions in protein-DNA recognition. Journal of Molecular Biology, 277(5), 1129–1140.

Authors 4
  1. Yael Mandel-Gutfreund (first)
  2. Hanah Margalit (additional)
  3. Robert L Jernigan (additional)
  4. Victor B Zhurkin (additional)
References 70 Referenced 159
  1. 10.1126/science.3187531 / Science / Recognition of a DNA operator by the repressor of phage 434 by Aggarwal (1988)
  2. 10.1006/jmbi.1996.0758 / J. Mol. Biol. / Inter-residue potential in globular proteins and the dominance of highly specific hydrophilic interaction at close separation by Bahar (1997)
  3. 10.1016/0022-2836(92)90690-L / J. Mol. Biol. / Refined 1. 8 Å crystal structure of the lambda repressor-operator complex by Beamer (1992)
  4. 10.1006/jmbi.1996.0673 / J. Mol. Biol. / Crystallographic evidence for Cα-H…O  C hydrogen bonds in a collagen triple helix by Bella (1996)
  5. 10.1073/pnas.93.22.12116 / Proc. Natl Acad. Sci. USA / Inter-strand C-H…O hydrogen bonds stabilizing four-stranded intercalated molecules by Berger (1996)
  6. 10.1016/S0006-3495(92)81649-1 / Biophys. J. / The nucleic acid database by Berman (1992)
  7. 10.1002/j.1460-2075.1994.tb06708.x / EMBO J. / Structure of PvuII endonuclease with cognate DNA by Cheng (1994)
  8. 10.1126/science.8023157 / Science / Crystal structure of a p53 tumor suppressor-DNA complex by Cho (1994)
  9. 10.1073/pnas.91.23.11168 / Proc. Natl Acad. Sci. USA / Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions by Choo (1994)
  10. 10.1038/364412a0 / Nature / Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5 by Clark (1993)
  11. 10.1021/ja00124a002 / J. Am. Chem. Soc. / A second generation force field for the simulation of proteins, nucleic acids and organic molecules by Cornell (1995)
  12. 10.1006/jmbi.1995.0492 / J. Mol. Biol. / The occurrence of C-H…O hydrogen bonds in proteins by Derewenda (1995)
  13. 10.1021/ar00010a002 / Acc. Chem. Res. / The C-H…O hydrogen bonds in crystals by Desiraju (1991)
  14. 10.1101/gad.8.8.970 / Genes Dev. / Crystal structure of transcription factor E47 by Ellenberger (1994)
  15. 10.1016/S0092-8674(05)80070-4 / Cell / The GCN4 basic region leucine zipper binds DNA as a dimer of uninterupted α helices by Ellenberger (1997)
  16. 10.1016/S0969-2126(96)00125-6 / Structure / Zif268 protein-DNA complex refined at 1.6 Å by Elrod-Erickson (1996)
  17. 10.1038/366483a0 / Nature / The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition by Fairall (1993)
  18. 10.1126/science.8278807 / Science / Hin recombinase bound to DNA by Feng (1994)
  19. 10.1038/363038a0 / Nature / Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain by Ferré-D’ Amaré (1993)
  20. 10.1002/j.1460-2075.1994.tb06247.x / EMBO J / Structure and function of the b/HLH/Z domain of USF by Ferré-D’ Amaré (1994)
  21. 10.1038/373257a0 / Nature / Crystal structure of the heterodimeric bZIP transcription factor c-Fos-c-Jun bound to DNA by Glover (1995)
  22. 10.1038/359505a0 / Nature / Crystal structure at 1.7 Å of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target by Hegde (1992)
  23. 10.1002/j.1460-2075.1995.tb00318.x / EMBO J. / Structure of the Even-skipped homeodomain complexed to AT-rich DNA by Hirsch (1995)
  24. 10.1006/jmbi.1993.1217 / J. Mol. Biol. / Sequence-dependent DNA structure. The role of base stacking interactions by Hunter (1993)
  25. {'key': '10.1006/jmbi.1998.1660_BIB25', 'series-title': 'Hydrogen Bonding in Biological Structures', 'first-page': '111', 'author': 'Jeffrey', 'year': '1991'} / Hydrogen Bonding in Biological Structures by Jeffrey (1991)
  26. 10.1038/nsb0994-638 / Nature Struct. Biol. / 1.9 Å resolution refined structure of TBP recognizing the minor groove of TATAAAAG by Kim (1994)
  27. 10.1126/science.2399465 / Science / Refinement of EcoRI endonuclease crystal structure by Kim (1990)
  28. 10.1038/365512a0 / Nature / Crystal structure of a yeast TBP/TATA-box complex by Kim (1993)
  29. 10.1016/0092-8674(90)90453-L / Cell / Crystal structure of an engrailed homeodomain-DNA complex at 2. 8 Å resolution by Kissinger (1990)
  30. 10.1016/0092-8674(94)90231-3 / Cell / Crystal structure of the Oct-1 POU domain bound to an octamer site by Klemm (1994)
  31. 10.1006/jmbi.1993.1490 / J. Mol. Biol. / The X-ray structure of the GCN4-bZIP bound to ATF/CREB site DNA shows the complex depends on DNA flexibility by Konig (1993)
  32. 10.1021/bi00002a036 / Biochemistry / Mg2+ binding to the active site of EcoRV endonuclease by Kostrewa (1995)
  33. 10.1038/366178a0 / Nature / Tandem binding in crystals of a trp repressor/operator half-site complex by Lawson (1993)
  34. 10.1126/science.270.5234.262 / Science / Crystal structure of the MATa1/MAT α2 homeodomain heterodimer bound to DNA by Li (1995)
  35. 10.1038/352497a0 / Nature / Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA by Luisi (1991)
  36. 10.1093/nar/23.22.4707 / Nucl. Acids Res. / Consistencies of individual DNA base-amino acid interactions in structures and sequences by Lustig (1995)
  37. 10.1016/0092-8674(94)90159-7 / Cell / Crystal structure of MyoD bHLH domain-DNA complex by Ma (1994)
  38. 10.1006/jmbi.1995.0559 / J. Mol. Biol. / Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes by Mandel-Gutfreund (1995)
  39. 10.1038/356408a0 / Nature / DNA recognition by GAL4 by Marmorstein (1992)
  40. 10.1101/gad.8.20.2504 / Genes Dev. / Crystal structure of a PPR1-DNA complex by Marmorstein (1994)
  41. 10.1021/j100589a006 / J. Phys. Chem. / Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occuring amino acids by Momany (1975)
  42. 10.1016/0022-2836(91)90568-Q / J. Mol. Biol. / The phage 434 Cro/Or1 complex at 2. 5 Å resolution by Mondragon (1991)
  43. 10.1038/373311a0 / Nature / Structure of the NF-κb p50 homodimer bound to DNA by Muller (1995)
  44. 10.1073/pnas.93.10.4862 / Proc. Natl Acad. Sci. USA / Crystal structure of a human TATA box-binding protein/TATA element complex by Nikolov (1996)
  45. 10.1080/07391102.1997.10508169 / J. Biomol. Struct. Dynam. / Ab Initio quantum mechanics analysis of imidazole C-H…O water hydrogen bonding and a molecular mechanics forcefield correction by Ornstein (1997)
  46. 10.1038/335321a0 / Nature / Crystal structure of trp repressor/operator complex at atomic resolution by Otwinowski (1988)
  47. 10.1006/jmbi.1996.0409 / J. Mol. Biol. / Structure of the CAP-DNA complex at 2.5 Å resolution by Parkinson (1996)
  48. {'key': '10.1006/jmbi.1998.1660_BIB48', 'series-title': 'The Nature of the Chemical Bond', 'author': 'Pauling', 'year': '1960'} / The Nature of the Chemical Bond by Pauling (1960)
  49. 10.1126/science.8378770 / Science / Crystal structure of a five-finger GLI-DNA complex by Pavletich (1993)
  50. 10.1016/0022-2836(90)90019-I / J. Mol. Biol. / Atomic charges for DNA constituents derived from single-crystal X-ray diffraction data by Pearlman (1990)
  51. 10.1073/pnas.91.13.6161 / Proc. Natl Acad. Sci. USA / Formation of base triplets by non-Watson-Crick bonds mediates homologous recognition in RecA recombination filaments by Rao (1994)
  52. 10.1038/367754a0 / Nature / DNA recognition by beta-sheets in the Arc repressor-operator crystal structure by Raumann (1994)
  53. 10.1002/bip.360100707 / Biopolymers / Stereochemistry of nucleic acids and polynucleotides. III. Elecronic charge distribution by Renugopalakrishnan (1971)
  54. 10.1016/0969-2126(93)90012-6 / Structure / The complex between phage 434 repressor DNA-binding domain and operator site OR3 by Rodgers (1993)
  55. 10.1126/science.7973627 / Science / Crystal structure of LacI member, PurR, bound to DNA by Schumacher (1994)
  56. 10.1016/0092-8674(93)90390-C / Cell / The crystal structure of the estrogen receptor DNA-binding domain bound to DNA by Schwabe (1993)
  57. 10.1073/pnas.73.3.804 / Proc. Natl Acad. Sci. USA / Sequence-specific recognition of double helical nucleic acids by proteins by Seeman (1976)
  58. 10.1006/jmbi.1993.1434 / J. Mol. Biol. / The phage 434 OR2/R1-69 complex at 2.5 Å resolution by Shimon (1993)
  59. 10.1038/359387a0 / Nature / Crystal structure of the met repressor-operator complex at 2.8 Å resolution reveals DNA recognition by beta-strands by Somers (1992)
  60. 10.1080/07391102.1996.10508935 / J. Biomol. Struct. Dynam. / Hydrogen bonding and stacking of DNA bases by Sponer (1996)
  61. 10.1016/0141-8130(94)90003-5 / Int. J. Biol. Macromol. / Close mutual contacts of the amino groups in DNA by Sponer (1994)
  62. 10.1038/195068a0 / Nature / The C-H…O hydrogen bond in crystals by Sutor (1962)
  63. 10.1016/S0969-2126(00)00033-2 / Structure / A framework for the DNA-protein recognition code of the probe helix in transcription factors by Suzuki (1994)
  64. 10.1021/ja00383a012 / J. Am. Chem. Soc. / Crystallographic evidence for the existence of C-H…O, C-H… N, and C-H…Cl hydrogen bonds by Taylor (1982)
  65. 10.1038/nsb0196-24 / Nature Struct. Biol. / The structure of r(UUCGCG) has a 5′-UU-overhang exhibiting Hoogsteen-like trans U. U base pairs by Wahl (1996)
  66. {'key': '10.1006/jmbi.1998.1660_BIB66', 'first-page': '97', 'article-title': 'C-H…O hydrogen bonding in biology', 'volume': '22', 'author': 'Wahl', 'year': '1997', 'journal-title': 'TIBS'} / TIBS / C-H…O hydrogen bonding in biology by Wahl (1997)
  67. 10.1016/0092-8674(95)90468-9 / Cell / High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA by Wilson (1995)
  68. 10.1016/0092-8674(91)90526-5 / Cell / Crystal structure of a MAT α2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions by Wolberger (1991)
  69. 10.1016/0092-8674(95)90518-9 / Cell / Crystal structure of a paired domain-DNA complex at 2.5 Å resolution reveals structural basis for Pax developmental mutations by Xu (1995)
  70. 10.1006/jmbi.1994.1362 / J. Mol. Biol. / A parallel DNA triplex as a model for the intermediate in homologous recombination by Zhurkin (1994)
Dates
Type When
Created 22 years, 11 months ago (Sept. 18, 2002, 3:24 p.m.)
Deposited 5 years, 8 months ago (Dec. 16, 2019, 12:49 a.m.)
Indexed 1 week, 6 days ago (Aug. 20, 2025, 8:25 a.m.)
Issued 27 years, 5 months ago (April 1, 1998)
Published 27 years, 5 months ago (April 1, 1998)
Published Print 27 years, 5 months ago (April 1, 1998)
Funders 0

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@article{Mandel_Gutfreund_1998, title={A role for CH…O interactions in protein-DNA recognition}, volume={277}, ISSN={0022-2836}, url={http://dx.doi.org/10.1006/jmbi.1998.1660}, DOI={10.1006/jmbi.1998.1660}, number={5}, journal={Journal of Molecular Biology}, publisher={Elsevier BV}, author={Mandel-Gutfreund, Yael and Margalit, Hanah and Jernigan, Robert L and Zhurkin, Victor B}, year={1998}, month=apr, pages={1129–1140} }