A role for CH···O interactions in Protein-DNA recognition

Journal of Molecular Biology

Volumn 277, Issue 5, 1998, Pages 1129-1140

  Mandel Gutfreund, Yael ^a   Margalit, Hanah ^a   Jernigan, Robert L ^b   Zhurkin, Victor B ^b  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^b 12 South Drive 20892 5677   (United States)

Author keywords

CH O interactions; Electrostatics; Hydrogen bonds; Protein DNA recognition

Indexed keywords

CYTOSINE; METHYL GROUP; THYMINE; DNA; DNA BINDING PROTEIN; PROTEIN;

ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA PROTEIN COMPLEX; HYDROGEN BOND; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; STEREOCHEMISTRY; CHEMICAL STRUCTURE; CHEMISTRY; DNA BASE COMPOSITION; ELECTRICITY; X RAY CRYSTALLOGRAPHY;

BASE COMPOSITION; CRYSTALLOGRAPHY, X-RAY; DNA; DNA-BINDING PROTEINS; ELECTROSTATICS; HYDROGEN BONDING; MODELS, MOLECULAR; PROTEINS;

EID: 0032540011     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1660     Document Type: Article

References (70)

1. Aggarwal A.K., Rodgers D.W., Drottar M., Ptashne M., Harrison S.C. Recognition of a DNA operator by the repressor of phage 434 a view of high resolution. Science. 242:1988;899-907
2. Bahar I., Jernigan R.L. Inter-residue potential in globular proteins and the dominance of highly specific hydrophilic interaction at close separation. J. Mol. Biol. 266:1997;195-214
3. Beamer L.J., Pabo C.O. Refined 1. 8 Å crystal structure of the lambda repressor-operator complex. J. Mol. Biol. 227:1992;177-196
4. Bella J., Berman H.M. Crystallographic evidence for Cα-H...O C hydrogen bonds in a collagen triple helix. J. Mol. Biol. 264:1996;734-742
5. Berger I., Egli M., Rich A. Inter-strand C-H...O hydrogen bonds stabilizing four-stranded intercalated molecules stereoelectronic effects of O4′ in cytosine-rich DNA. Proc. Natl Acad. Sci. USA. 93:1996;12116-12121
6. Berman H.M., Olson W.K., Beveridge D.L., Westbrook J., Gelbin A., Demeny T., Hsieh S.-H., Srinivasan A.R., Schneider B. The nucleic acid database a comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63:1992;751-759
7. Cheng X., Balendiran K., Schildkraut I., Anderson J.E. Structure of PvuII endonuclease with cognate DNA. EMBO J. 13:1994;3927-3935
8. Cho Y., Gorina S., Jeffrey P.D., Pavletich N.P. Crystal structure of a p53 tumor suppressor-DNA complex understanding tumorigenic mutations. Science. 265:1994;346-355
9. Choo Y., Klug A. Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions. Proc. Natl Acad. Sci. USA. 91:1994;11168-11172
10. Clark K.L., Halay E.D., Lai E., Burley S.K. Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5. Nature. 364:1993;412-420
11. Cornell W.D., Cieplak P., Bayly I.B., Gould I.R., Merz K.M., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., Kollman P.A. A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J. Am. Chem. Soc. 117:1995;5179-5197
12. Derewenda Z.S., Lee L., Derewenda U. The occurrence of C-H...O hydrogen bonds in proteins. J. Mol. Biol. 252:1995;248-262
13. Desiraju G.R. The C-H...O hydrogen bonds in crystals what is it? Acc. Chem. Res. 24:1991;290-296
14. Ellenberger T., Fass D., Arnaud M., Harrison S.C. Crystal structure of transcription factor E47 E-box recognition by a basic region helix-loop-helix dimer. Genes Dev. 8:1994;970-980
15. Ellenberger T.E., Brandl C.J., Struhl K., Harrison S.C. The GCN4 basic region leucine zipper binds DNA as a dimer of uninterupted α helices crystal structure of the protein-DNA complex. Cell. 71:1997;1223-1237
16. Elrod-Erickson M., Rould M.A., Nekludova L., Pabo C.O. Zif268 protein-DNA complex refined at 1.6 Å a model system for understanding zinc finger-DNA interactions. Structure. 4:1996;1171-1180
17. Fairall L., Schwabe J.W., Chapman L., Finch J.T., Rhodes D. The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition. Nature. 366:1993;483-487
18. Feng J.A., Johnson R.C., Dickerson R.E. Hin recombinase bound to DNA the origin of specificity in major and minor groove interactions. Science. 263:1994;348-355
19. Ferré-D' Amaré R., Prendergast G.C., Ziff E.B., Burley S.K. Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain. Nature. 363:1993;38-45
20. Ferré-D' Amaré R., Pognonec P., Roeder R.G., Burley S.K. Structure and function of the b/HLH/Z domain of USF. EMBO J. 13:1994;180-189
21. Glover J.N., Harrison S.C. Crystal structure of the heterodimeric bZIP transcription factor c-Fos-c-Jun bound to DNA. Nature. 373:1995;257-261
22. Hegde R.S., Grossman S.R., Laimins L.A., Sigler P.B. Crystal structure at 1.7 Å of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target. Nature. 359:1992;505-512
23. Hirsch J.A., Aggarwal A.K. Structure of the Even-skipped homeodomain complexed to AT-rich DNA new perspectives on homeodomain specificity. EMBO J. 14:1995;6280-6291
24. Hunter C.A. Sequence-dependent DNA structure. The role of base stacking interactions. J. Mol. Biol. 230:1993;1025-1054
25. Jeffrey G.A., Saenger W. Hydrogen Bonding in Biological Structures. 1991;111-135 Springer, Berlin
26. Kim J.L., Burley S.K. 1.9 Å resolution refined structure of TBP recognizing the minor groove of TATAAAAG. Nature Struct. Biol. 1:1994;638-653
27. Kim Y.C., Grable J.C., Love R., Greene P.J., Rosenberg J.M. Refinement of EcoRI endonuclease crystal structure a revised protein chain tracing. Science. 249:1990;1307-1309
28. Kim Y., Geiger J.H., Hahn S., Sigler P.B. Crystal structure of a yeast TBP/TATA-box complex. Nature. 365:1993;512-520
29. Kissinger C.R., Liu B., Martin-Blanco E., Kornberg T.B., Pabo C.O. Crystal structure of an engrailed homeodomain-DNA complex at 2. 8 Å resolution a framework for understanding homeodomain-DNA interactions. Cell. 63:1990;579-590
30. Klemm J.D., Rould M.A., Aurora R., Herr W., Pabo C.O. Crystal structure of the Oct-1 POU domain bound to an octamer site DNA recognition with tethered DNA-binding modules. Cell. 77:1994;21-32
31. Konig P., Richmond T.J. The X-ray structure of the GCN4-bZIP bound to ATF/CREB site DNA shows the complex depends on DNA flexibility. J. Mol. Biol. 233:1993;139-154
32. Kostrewa D., Winkler F.K. Mg2+ binding to the active site of EcoRV endonuclease a crystallographic study of complexes with substrate and product DNA at 2 Å resolution. Biochemistry. 34:1995;683-696
33. Lawson C.L., Carey J. Tandem binding in crystals of a trp repressor/operator half-site complex. Nature. 366:1993;178-182
34. Li T., Stark M.R., Johnson A.D., Wolberger C. Crystal structure of the MATa1/MAT α2 homeodomain heterodimer bound to DNA. Science. 270:1995;262-269
35. Luisi B.F., Xu W., Otwinowski Z., Freedman L.P., Yamamoto K.R., Sigler P.B. Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA. Nature. 352:1991;497-505
36. Lustig B., Jernigan R.L. Consistencies of individual DNA base-amino acid interactions in structures and sequences. Nucl. Acids Res. 23:1995;4707-4711
37. Ma P.C., Rould M.A., Weintraub H., Pabo C.O. Crystal structure of MyoD bHLH domain-DNA complex perspectives on DNA recognition and implications for transcriptional activation. Cell. 77:1994;451-459
38. Mandel-Gutfreund Y., Schueler O., Margalit H. Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes in search of common principles. J. Mol. Biol. 253:1995;370-382
39. Marmorstein R., Carey M., Ptashne M., Harrison S.C. DNA recognition by GAL4 structure of a protein-DNA complex. Nature. 356:1992;408-414
40. Marmorstein R., Harrison S.C. Crystal structure of a PPR1-DNA complex DNA recognition by proteins containing a Zn2Cys6 binuclear cluster. Genes Dev. 8:1994;2504-2512
41. Momany F.A., McGuire R.F., Burgess A.W., Scheraga H.A. 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. J. Phys. Chem. 79:1975;2361-2381
42. Mondragon A., Harrison S.C. The phage 434 Cro/Or1 complex at 2. 5 Å resolution. J. Mol. Biol. 219:1991;321-334
43. Muller C.W., Rey F.A., Sodeoka M., Verdine G.L., Harrison S.C. Structure of the NF-κb p50 homodimer bound to DNA. Nature. 373:1995;311-317
44. Nikolov D.B., Chen H., Halay E.D., Hoffman A., Roeder R.G., Burley S.K. Crystal structure of a human TATA box-binding protein/TATA element complex. Proc. Natl Acad. Sci. USA. 93:1996;4862-4867
45. Ornstein R.L., Zheng Y. Ab Initio quantum mechanics analysis of imidazole C-H...O water hydrogen bonding and a molecular mechanics forcefield correction. J. Biomol. Struct. Dynam. 14:1997;657-665
46. Otwinowski Z., Schevitz R.W., Zhang R.G., Lawson C.L., Joachimiak A., Marmorstein R.Q., Luisi B.F., Sigler P.B. Crystal structure of trp repressor/operator complex at atomic resolution. Nature. 335:1988;321-329
47. Parkinson G., Wilson C., Gunasekera A., Ebright Y.W., Ebright R.E., Berman H.M. Structure of the CAP-DNA complex at 2.5 Å resolution a complete picture of the protein-DNA interface. J. Mol. Biol. 260:1996;395-408
48. Pauling L. The Nature of the Chemical Bond. 3rd edit.:1960;Cornell University Press, Ithaca
49. Pavletich N.P., Pabo C.O. Crystal structure of a five-finger GLI-DNA complex new perspectives on zinc fingers. Science. 261:1993;1701-1707
50. Pearlman D.A., Kim S. Atomic charges for DNA constituents derived from single-crystal X-ray diffraction data. J. Mol. Biol. 211:1990;171-187
51. Rao B.J., Radding C.M. Formation of base triplets by non-Watson-Crick bonds mediates homologous recognition in RecA recombination filaments. Proc. Natl Acad. Sci. USA. 91:1994;6161-6165
52. Raumann B.E., Rould M.A., Pabo C.O., Sauer R.T. DNA recognition by beta-sheets in the Arc repressor-operator crystal structure. Nature. 367:1994;754-757
53. Renugopalakrishnan V., Lakshminarayanan A.V., Sasisekharan V. Stereochemistry of nucleic acids and polynucleotides. III. Elecronic charge distribution. Biopolymers. 10:1971;1159-1167
54. Rodgers D.W., Harrison S.C. The complex between phage 434 repressor DNA-binding domain and operator site OR3 structural differences between consensus and non-consensus half-sites. Structure. 1:1993;227-240
55. Schumacher M.A., Choi K.Y., Zalkin H., Brennan R.G. Crystal structure of LacI member, PurR, bound to DNA minor groove binding by alpha helices. Science. 266:1994;763-770
56. Schwabe J.W., Chapman L., Finch J.T., Rhodes D. The crystal structure of the estrogen receptor DNA-binding domain bound to DNA how receptors discriminate between their response elements. Cell. 75:1993;567-578
57. Seeman N.C., Rosenberg J.M., Rich A. Sequence-specific recognition of double helical nucleic acids by proteins. Proc. Natl Acad. Sci. USA. 73:1976;804-808
58. Shimon L.J., Harrison S.C. The phage 434 OR2/R1-69 complex at 2.5 Å resolution. J. Mol. Biol. 232:1993;826-838
59. Somers W.S., Phillips S.E. Crystal structure of the met repressor-operator complex at 2.8 Å resolution reveals DNA recognition by beta-strands. Nature. 359:1992;387-393
60. Sponer J., Leszczynski J., Hobza P. Hydrogen bonding and stacking of DNA bases a review of quantum-chemical ab initio studies. J. Biomol. Struct. Dynam. 14:1996;117-135
61. Sponer J., Kypr J. Close mutual contacts of the amino groups in DNA. Int. J. Biol. Macromol. 16:1994;3-6
62. Sutor D.J. The C-H...O hydrogen bond in crystals. Nature. 195:1962;68-69
63. Suzuki M. A framework for the DNA-protein recognition code of the probe helix in transcription factors the chemical and stereochemical rules. Structure. 2:1994;317-326
64. Taylor R., Kennard O. Crystallographic evidence for the existence of C-H...O, C-H... N, and C-H...Cl hydrogen bonds. J. Am. Chem. Soc. 104:1982;5063-5070
65. Wahl M.C., Rao S.T., Sundaralingam M. The structure of r(UUCGCG) has a 5′-UU-overhang exhibiting Hoogsteen-like trans U. U base pairs. Nature Struct. Biol. 3:1996;24-31
66. Wahl M.C., Sundaralingam M. C-H...O hydrogen bonding in biology. TIBS. 22:1997;97-102
67. Wilson D.S., Guenther B., Desplan C., Kuriyan J. High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA. Cell. 82:1995;709-719
68. Wolberger C., Vershon A.K., Liu B., Johnson A.D., Pabo C.O. Crystal structure of a MAT α2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions. Cell. 67:1991;517-528
69. Xu W., Rould M.A., Jun S., Desplan C., Pabo C.O. Crystal structure of a paired domain-DNA complex at 2.5 Å resolution reveals structural basis for Pax developmental mutations. Cell. 80:1995;639-650
70. Zhurkin V.B., Raghunathan G., Ulyanov N.B., Camerini Otero R.D., Jernigan R.L. A parallel DNA triplex as a model for the intermediate in homologous recombination. J. Mol. Biol. 239:1994;181-200