Характеристика взаимодействия ДНК-узнающего участка белка и ДНК по большой бороздке тема диссертации и автореферата по ВАК РФ 03.00.03, кандидат биологических наук Васильев, Сергей Александрович

• Васильев, Сергей Александрович
• кандидат биологических наук
• 1999

Оглавление диссертации кандидат биологических наук Васильев, Сергей Александрович

Список принятых сокращений.

1. Введение.

2. Цель и задачи работы.

3. Научная новизна.

4 . Обзор литературы.

4.1. Принципы узнавания ДНК белком.

4.2. Особенности структуры ДНК.

4.3. Роль а-спирали и ^-структуры в образовании ДНК-белковых комплексов.

4.4. Строение ДНК-узнающих областей белка.

4.5. Роль конформационных изменений ДНК в образовании ДНК-белковых комплексов.

4.6. ДНК-узнающий домены.

4.6.1. ДНК-узнающий домен НТН.

4.6.2. Цинк содержащие ДНК-узнающие домены.

4.7. Код ДНК-белкового взаимодействия.

4.8. Базы данных, содержащие информацию о пространственной структуре ДНК-белковых комплексов.

5. Материалы и методы.

6. Определения основных объектов.

7 . Результаты.

7.1. Формализованное описание зоны контакта.

7.2. Распределение ДНК-узнающих белковых участков по кластерам.

7.3. Классификация ДНК-узнающих участков по вторичной структуре.

7.4. Распределение показателя водородных связей.

7.5. Распределение показателя гидрофобного взаимодействия.

7.6. Анализ вклада оснований ДНК в образование гидрофобного взаимодействия.

7.7. Роль коротких ДНК-узнающих участков.

7.8. Вариабельность показателей для

ДНК-узнающих участков.

7.9. Показатели у белков с малой специфичностью узнавания ДНК.

7.10. Распределение показателей по типам ДНК-узнающих доменов.

7.11. Сравнение двух показателей.

7.12. Построение таблиц физико-химических взаимодействий.

7.13. Расчет модели ДНК-белкового взаимодействия.

8. Обсуждение результатов.

8.1. Организация информации.

8.2. Выбор критерия отбора ДНК-узнающего участка фильтр 6М45).

8.3. Роли цитозина и гуанина в гидрофобном взаимодействии

8.4. Показатели взаимодействия белка с большой бороздкой ДНК.

8.5. Значение показателей у одинаковых зон контакта.

8.6. Соотношение показателей у разных

ДНК-узнающих доменов.

8.7. Построение таблиц физико-химических взаимодействий.

9. Выводы.

10. Литература.

Заключение диссертации по теме «Молекулярная биология», Васильев, Сергей Александрович

9. Выводы.

1. Полученная в результате применения теоретических правил модель ДНК-белкового взаимодействия адекватно описывает специфические контакты, образующиеся при взаимодействии с промоторной областью собственного гена ДНК-метилтрансферазы SsoII, что свидетельствует о возможности применения теоретических правил для предсказания ДНК-белковых контактов.

2. Разработана оригинальная объектно-ориентированная реляционная база данных ДНК-белковых взаимодействий DNA-Protein Interaction Data Base (DPIDB) с адекватной организацией информации о трехмерных расшифровках ДНК-белковых комплексов.

3. Впервые разработано и алгоритмически реализовано формализованное описание зоны ДНК-белкового контакта, что позволяет эффективно осуществлять компьютерный сравнительный анализ зон контакта в любом объеме данных.

4. Впервые предложены нецелочисленные показатели водородных связей и гидрофобного взаимодействия, рассчитанные на основе метода извлечения потенциала взаимодействия из статистических данных о трехмерной структуре ДНК-белковых комплексов с учетом всех известных на сегодняшний день комплексов. Эти показатели численно отражают взаимодействие ДНК-узнающего участка белка с большой бороздкой ДНК.

5. Впервые показано, что для корректного расчета гидрофобного взаимодействия в зоне ДНК-белкового контакта необходимо учитывать, что в образовании гидрофобных взаимодействий между большой бороздкой ДНК и белком примерно в 45% случаев участвуют С5М и С б атомы тимина. Кроме того, атомы С5 и С б цитозина, и атомы С5 и С8 гуанина в сумме образуют примерно то же количество гидрофобных контактов.

6. Соотношение показателей водородных связей и парного гидрофобного взаимодействия и сами значения этих показателей у различных типов ДНК-узнающих доменов существенно различны.

Список литературы диссертационного исследования кандидат биологических наук Васильев, Сергей Александрович, 1999 год

1. Молекулярное взаимодействие. // М., Мир, 198 4

2. Васильев С.А., Севастьянова Г.А. Структурные аспекты ДНК-белкового взаимодействия на примере фермента 5-метилцитозин-метилтрансферазы. // М., МПГУ, 1997.

3. Васильев С.А., Алексеевский А.В., Спирин С.А., Ташлицкий В.Н., Тихонова Т.В., Карягина А. С. Оценка взаимодействия узнающей области белка с большой бороздкой ДНК. // Биофизика, 1999, 12 (в печати).

4. Зенгер В. Принципы структурной организации нуклеиновых кислот. // М., Мир, 1987.

5. Кантор Ч., Шиммел П. Биофизическая химия, в 3-х томах. // М., Мир, 1984.

6. Лыоин Б. Гены. // М., Мир, 1987.

7. Пташне М. Переключение генов. Регуляция генной активности и фаг X. // М., Мир, 1988.

8. PDB newsletter. // PDB, 1999.

9. Protein Data Bank Contents Guide: atomic coordinate entry format description, version 2.1 (draft). // PDB, 1996.

10. Abóla E.E., Sussman J.L., Prilusky J., Manning N.O. Protein Data Bank archives of three-dimensional macromolecu-lar structures. // Methods Enzymol., 1997, v. 277, p. 556571.

11. Abóla E.E., Manning N.O., Prilusky J., Stampf D.R., Sussman J.L. The Protein Data Bank: current status and future challenges. // J.Res.Natl.Inst.Stand.Technol., 1996, v. 101, p. 231-241.

12. Aggarwal A.K., Wah D.A. Novel site-specific DNA endonu-cleases. // Curr.Opin.Struct.Biol., 1998, v. 8, p. 19-25.

13. Albright R.A., Matthews B.W. Crystal structure of a-Cro bounding to a consensus operator at 3.0 A resolution. // J.Mol.Biol., 1998 , v. 280, p. 137-151.

14. Allen M.D., Yamasaki K., Ohme-Takagi M., Tateno M., Suzuki M. A novel mode of DNA recognition by a fJ-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA. // EMBO J., 1998, v. 17, p. 5484-5496.

15. Anderson J.E., Ptashne M., Harrison S.C. Structure of the repressor-operator complex of bacteriophage 434. // Nature, 1987, v. 326 , p. 846-852.

16. Apaya R.P., Bondi M., Price S.L. The orientation of N-H.0=C and N-H.N hydrogen bonds in biological systems:

17. How good is a point charge as a model for a hydrogen binding atom? // J.Comput.-Aided Mol.Desighn, 1997, v. 11, p. 479-490.

18. Auffinger P., Westhof E. Simulation of the molecular dynamics of nucleic acids. // Curr . Opin.Struct.Biol. , 1998, v. 8, p. 227-236.

19. Balaeff A., Churchill M.E.A., Schulten K. Structural prediction of a complex between the chromosomal protein HMG-D and DNA. // Proteins Struct.Funct.Genet., 1998, v. 30, p. 113-135.

20. Barrett T., Savva R., Panayotou G., Barlow T., Brown T., Jiricny J., Pearl L.H. Crystal structure of a G:T/U mismatch-specific DNA glycosylase: mismatch recognition by complementary-strand interactions. // Cell, 1998, v. 92, p. 117129.

21. Bastia D. Structural aspects of protein-DNA interactions as revealed by conversion of the interacting protein into a sequence-specific cross-linking agent or a chemical nuclease. // Structure, 1996, v. 4, p. 661-664.

22. Berg J.M. DNA binding specificity of steroid receptors. // Cell, 1989, v. 57, p. 1065-1068.

23. Berg J.M. Proposed structure for the zinc-binding domains from transcription factor IIIA and related proteins. // Proc.Natl.Acad.Sci.U.S.A, 1988, v. 85, p. 99-102.

24. Berger C., Piubelli L., Haditsch U., Bosshard H.R. Diffu-siom-controlled DNA recognition by an unfolded, monomeric bZIP transcription factor. // FEBS Lett., 1998, v. 425, p. 14-18.

25. Berger J.M. Type II topoisomerases. // Curr.Opin.Struct. Biol., 1998, v. 8, p. 26-32.

26. Berger J.M., Gamblin S.J., Harrison S.C., Wang J.C. Structure and mechanism of DNA topoisomerase II. // Nature, 1996, v. 379, p. 225-232.

27. Bernstein F.C., Koetzle T.F., Williams G.J., Meyer E.E. Jr., Brice M.D., Rodgers J.R., Kennard 0., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. // J.Mol.Biol., 1977, v. 112, p. 535-542.

28. Billeter M., Qian Y.Q., Otting G., Muller M., Gehring W., Wuthrich K. Determination of the nuclear magnetic resonance solution structure of an antennapedia homeodomain-DNA complex. // J.Mol.Biol., 1993, v. 234, p. 1084-1097.

29. Bird L.E., Subramanya H.S., Wigley D.B. Helicases: a unifying structural theme? // Curr.Opin.Struct.Biol., 1998, v. 8, p. 14-18.

30. Bochkarev A., Barwell J.A., Pfuetzner R.A., Bochkareva E., Frappier L., Edwards A.M. Crystal structure of the DNA-binding domain of the Epstein-Barr virus origin-binding protein, EBNA1, bound to DNA. // Cell, 1996, v. 84, p. 791800.

31. Bochkarev A., Barwell J.A., Pfuetzner R.A., Furey W., Edwards A.M., Frappier L. Crystal structure of the DNA-bind-ing domain of the Epstein-Barr virus origin-binding protein EBNA1. // Cell, 1995, v. 83, p. 39-46.

32. Bornberg-Bauer E., Rivals E., Vingron M. Computational approach to identify leucine zippers. // Nucleic Acids Res., 1998, v. 26, p. 2740-2746.

33. Brautigam C.A., Steitz T.A. Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes. // Curr.Opin. Struct. Biol., 1998, v. 8, p. 63.

34. Brennan R.G. DNA recognition by the helix-turn-helix motif. // Curr.Opin.Struct.Biol. , 1992, v. 2, p. 100-108.

35. Brennan R.G. Interaction of the helix-turn-helix binding domain. // Curr.Opin.Struct.Biol., 1991, v. 1, p. 80-88.

36. Brennan R.G., Matthews B.W. Structural basis of DNA-protein recognition. // Trends Biochem.Sei., 1989, v. 14, p. 286-290.

37. Buning H., Gatner U., von Schack D., Baeuerle P.A., Zorbas H. The histidine tail of a recombination DNA binding proteins may influence the quality of interaxtion with DNA. // Anal.Biochem. , 1996, v. 234, p. 227-230.

38. Burley S.K. The TATA box binding protein. // Curr.Opin. Struct.Biol., 1996, v. 6, p. 69-75.

39. Chen J., Pongor S., Simoncsits A. Recognition of DNA by single-chain derivatives of the phage 434 repressor: high affinity binding depends on both the contacted and non-contacted base pairs. // Nucleic Acids Res., 1997, v. 25, p. 2047-2054.

40. Cho Y., Gorina S., Jeffrey P.D., Pavletich N.P. Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations. // Science, 1994, v. 265, p. 346-355.

41. Choo Y. End effects in DNA recognition by zinc finger arrays. // Nucleic Acids Res., 1998, v. 26, p. 554-557.

42. 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, 1993, v. 364, p. 412-420.

43. Crothers D.M. DNA curvature and deformation in protein-DNA complexes: a step in the right direction. // Proc.Natl.Acad. Sci.USA, 1998, v. 95, p. 15163-15165.

44. Damante G., Pellizzari L., Esposito G., Fogolari F., Viglino P., Fabbro D., Tell G., Formisano S., Lauro R.D. A molecular code dictates sequence-specific DNA recognition by ho-meodomains. // EMBO J., 1996, v. 15 , p. 4992-5000.

45. Deng Q.L., Ishii S., Sarai A. Binding site analysis of c-Myb: screening of potentional binding sites by using the mutation matrix derived from systematic binding affinity measurements. // Nucleic Acids Res., 1996, v. 24, p. 766774 .

46. Desjarlais J.R., Berg J.M. Use of a zinc-finger consensus sequence framework and specificity rules to design specific DNA binding proteins. // Proc.Natl.Acad.Sci.USA, 1993, v. 90, p. 2256-2260.

47. Dickerson R.E. DNA bending: the prevalence of kinkiness and the virtues of normality. // Nucleic Acids Res., 1998, v. 26, p. 1906-1926.

48. Dickerson R.E. Definition and nomenclature of nucleic acid structure parameters. // J.Biomol.Struct.Dyn., 1989, v. 4, p. 627-634.

49. Dodd I.B., Egan J.B. Improved detection of helix-turn-helix DNA-binding motifs in protein sequences. // Nucleic Acids Res., 1990, v. 18, p. 5019-5026.

50. Doherty A.J., Serpell L.C., Ponting C.P. The helix-hairpin-helix DNA-binding motif: a structural basis for non-sequence-specific recognition of DNA. // Nucleic Acids Res., 1996, v. 24, p. 2488-2497.

51. Duong T.H., Zakrzewska K. Sequence specificity of bacte-riphage 434 repressor-operator complexation. // J.Mol.Biol., 1998, v. 280, p. 31-39.

52. Edwards A.M., Bochkarev A., Frappier L. Origin DNA-binding proteins. // Curr.Opin.Struct.Biol., 1998, v. 8, p. 49-53.

53. Ellenberger T.E., Brandl C.J., Struhl K., Harrison S.C. The GCN4 basic region leucine zipper binds DNA as a dinner of uninterrupted a helices: crystal structure of the protein-DNA complex. // Cell, 1992, v. 71, p. 1223-1237.

54. Elrod-Erickson M., Benson T.E., Pabo C.O. High-resolution structures of variant Zif268-DNA complexes: implication for understanding zinc finger-DNA recognition. // Structure, 1998, v. 6, p. 451-464.

55. Elrod-Erickson M., Rould M.A., Nekludova L., Pabo C.O. Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interaction. // Structure, 1996, v. 4, p. 1171-1180.

56. Ezaz-Nikpay K., Verdine G.L. The effects of N7-methylgua-nine on duplex DNA structure. // Chem.Biol., 1994, v. 1, p. 235-240.

57. 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, 1993, v. 366, p. 483-487.

58. Feng D.F., Johnson M.S., Doolittle R.F. Aligning amino acid sequences: comparison of commonly used methods. // J.Mol.Evol., 1985, v. 21, p. 112-125.

59. 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, 1994, v. 263, p. 348-355.

60. Ferre-D'Amare A.R., Pognonec P., Roeder R.G., Burley S.K. Structure and function of the b/HLH/Z domain of USF. // EMBO J., 1994, v. 13, p. 180-189.

61. Fields D.S., Stormo G.D. Quantatative DNA sequencing to determine the relative protein-DNA binding constants to multiple DNA sequences. // Anal.Biochem., 1994, v. 219, p. 230239.

62. Fogh R.H., Ottleben G., Ruterjans H., Schnarr M., Boelens R., Kaptein R. Solution structure of the LexA repressor

63. DNA binding domain determined by 1H NMR spectroscopy. // EMBO J., 1994, v. 13, p. 3936-3944.

64. Fraenkel E., Pabo C.O. Comparison of X-ray and NMR structures for the Antennapedia homeodomain-DNA complex. // Nat.Struct.Biol., 1998, v. 5, p. 692-697.

65. Fraenkel E., Rould M.A., Chambers K.A., Pabo C.O. Engrailed homeodomain-DNA complex at 2.2 A resolution: a detailed view of the interface and comparison with other engrailed structures. // J.Mol.Biol. , 1998, v. 284, p. 351361.

66. Frankel A.D., Bredt D.S., Pabo C.O. Tat protein from human immunodeficiency virus forms a metal-linked dimer. // Science, 1988, v. 240, p. 70-73.

67. Freedman L.P., Luisi B.F., Korszun Z.R., Basavappa R., Si-gler P.B., Yamamoto K.R. The function and structure of the metal coordination sites within the glucocorticoid receptor DNA binding domain. // Nature, 1988, v. 334, p. 543546.

68. Giffin W., Torrance H., Rodda D.J., Prefontaine G.G., Pope L., Hache R.J.G. Sequence-specific DNA binding by Ku autoantigen and its effect on transcription. // Nature, 1996, v. 380, p. 265-268.

69. Gilis D., Rooman M.J. Stability changes upon mutation of solvent-accessible residues in proteins evaluted by database-derived potentials. // J.Mol.Biol., 1996, v. 257, p. 1112-1126.

70. Gorin A.A., Zhurkin V.B., Olson W.K. B-DNA twisting correlates with base-pare morphology. // J.Mol.Biol., 1995, v. 247, p. 34-48.

71. Gromiha M.M., Munteanu M.G., Simon I., Pongor S. The role of DNA bending in Cro protein-DNA interaction. // Biophys.Chem. , 1997, v. 69, p. 153-160.

72. Harrison S.C. A structural taxonomy of DNA-binding domains. // Nature, 1991, v. 353, p. 715-719.

73. Harrison S.C., Aggarwal A.K. DNA recognition by proteins with the helix-turn-helix motif. // Annu.Rev.Biochem., 1990, v. 59, p. 933-969.

74. Hegde R.S., Grossman S.R., Laimins L.A., Sigler P.B. Crystal structure at 1.7 Â of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target. // Nature, 1992, v. 359, p. 505-512.

75. Jacobs G., Michaels G. Zinc finger gene database. // New Biol., 1990, v. 2, p. 583.

76. Janin J. Quantifuing biological specificity: the statistical mechanics of molecular recognition. // Proteins Struct.Funct. Genet., 1996, v. 25, p. 438-445.

77. Jansen C., Gronenborn A.M., Clore G.M. The binding of the cyclic AMP receptor protein to synthetic DNA sites containing permutations in the consensus sequence TGTGA. // Biochem.J., 1987, v. 246, p. 227-232.

78. Jeon C., Yoon H., Agarwal K. The transcription factor TFI-IS zinc ribbon dipeptide Asp-Glu is critical for stimulation of elongation and RNA cleavage by RNA polymerase II. // Proc.Natl.Acad.Sci.U.S .A, 1994, v. 91, p. 9106-9110.

79. Jin C., Marsden I., Chen X., Liao X. Dynamic DNA contacts observed in the NMR structure of winged helix protein-DNA complex. // J.Mol.Biol., 1999, v. 289, p. 683-690.

80. Jones S., van Heyningen P., Berman H.M., Thronton J.M. Protein-DNA interactions: a structural analysis. // J.Mol.Biol., 1999, v. 287, p. 877-896.

81. Jordan S.R., Pabo C.O. Structure of the lambda complex at 2.5 A resolution: details of the repressor-operator interactions. // Science, 1988, v. 242, p. 893-899.

82. Kabsch W. , Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. // Biopolymers, 1983, v. 22, p. 2577-2637.

83. Kaptein R., Zuiderweg E.R., Scheek R.M., Boelens R., van Gunsteren D. A protein structure from nuclear magnetic resonance data Lac repressor headpiece. // J.Mol.Biol., 1985, v. 182, p. 179-182.

84. Karlin S., Brendel V. Chance and statistical significance in protein and DNA sequence analysis. // Science, 1992, v. 257, p. 39-49.

85. Keller W., Konig P., Richmond T.J. Crystal structure of a bZip/DNA complex at 2.2 Â: determinants of DNA specificrecognition. // J.Mol.Biol., 1995, v. 254, p. 657-667.

86. Kim J.L., Nikolov D.B., Burley S.K. Co-crystal structure of TBP recognizing the minor groove of a TATA element. // Nature, 1993, v. 365, p. 520-527.

87. Kim Y., Geiger J.H., Hahn S., Sigler P.B. Crystal structure of a yeast TBP/TATA-box complex. // Nature, 1993, v. 365, p. 512-527.

88. Kissinger C.R., Liu B.S., Martin-Blanco E., Kornberg T.B., Pabo C.O. Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: a framework for understanding homeodomain-DNA interactions. // Cell, 1990, v. 63, p. 579-590.

89. 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, 1994, v. 77, p. 21-32.

90. Klug A., Rhodes D. Zinc fingers: a novel protein fold for nucleic acid recognition. // Cold Spring Harb.Symp. Quant.Biol., 1987, v. 52, p. 473-482.

91. Kodandapani R., Pio F., Ni C., Piccialli G., Klemsz M., McKercher S., Maki R.A., Ely K.R. A new pattern for helix-turn-helix recognition revealed by the PU.l ETS-domain-DNA complex. // Nature, 1996, v. 380, p. 456-460.

92. Kohn W.D., Mant C.T., Hodges R.S. a-helical protein assembly motifs. // J.Biol.Chem. , 1997, v. 272, p. 2583-2586.

93. Konig P., Girado R., Chapman L., Rhodes D. The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA. // Cell, 1996, v. 85, p. 125-136.

94. Kostrewa D., Winkler F.K. Mg-+ binding to the active site of EcoRV endonuclease: a cristallographic study of complexes with substrate and product DNA at 2 A resolution. // Biochemistry, 1995, v. 34, p. 683-696.

95. Kostrewa D., Granzin J., Stock D., Choe H.W., Labahn J., Saenger W. Crystal structure of the factor for inversion stimulation FIS at 2.0 A resolution. // J.Mol.Biol., 1992, v. 226, p. 209-226.

96. Koudelka G.B. Recognition of DNA structure by 434 repressor. // Nucleic Acids Res., 1998, v. 26, p. 669-675.

97. Leplae R. , Hubbard T., Tramontane» A. GLASS: a tool to visualize protein structure prediction data in three dimensions and evaluate their consistency. // Proteins Struct.Funct. Genet., 1998, v. 30, p. 339-351.

98. Lesser D.R., Kurpiewski M.R., Waters T., Connolly B.A., Jen-Jacobson L. Facilitated distortion of the DNA site enhances EcoRI endonuclease-DNA recognition. // Proc.Natl.Acad. Sci.U.S.A, 1993, v. 90, p. 7548-7552.

99. Lindauer K., Bendic C., Suhnel J. HBexplore a new tool for identifying and analysing hydrogen bonding patterns in biological macromolecules. // CABIOS communication, 1996, v. 12 (4), p. 281-289.

100. Lipanov A., Kopka M.L., Kaczor-Grzeskowiak M., Quintana J., Dickerson R.E. Structure of the B-DNA decamer C-C-A-A-C-I-T-T-G-G in two different space groups: conformation flexibility of B-DNA. // Biochemistry, 1993, v. 32, p. 13731389.

101. Louse-May S., Auffinger P., Westhof E. Calculation of nucleic acid conformation. // Curr.Opin.Struct.Biol., 1996, v. 6, p. 289-298.

102. Luger K., Richmond T.J. DNA binding within the nucleosome core. // Curr.Opin.Struct.Biol., 1998, v. 8, p. 33-40.

103. Luger K., Rechsteiner T.J., Flaus A.J., Waye M.M., Richmond T.J. Characterization of nucleosome core particles containing histone proteins made in bacteria. // J.Mol.Biol., 1997, v. 272, p. 301-311.

104. Luisi B.F., Xu W.X., Otwinowski Z., Freedman L.P., Yamamo-to K.R., Sigler P.B. Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA. // Nature, 1991, v. 352, p. 497-505.

105. Luscombe N.M., Laskowski R.A., Thronton J.M. NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions. // Nucleic Acids Res., 1997, v. 25, p. 4940-4945.

106. Ma P.C.M., 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, 1994, v. 77, p. 451-459.

107. Mandel-Gutfreund Y., Margalit H., Jernigan R.L., Zhurkin V.B. A role for CH.0 interactions in protein-DNA recognition. // J.Mol.Biol., 1998, v. 277, p. 1129-1140.

108. Mandel-Gutfreund Y., Margalit H. Quantitave parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites. // Nucleic Acids Res., 1998, v. 26, p. 2306-2312.

109. Mandel-Gutfreund Y., Schueler 0., Margalit H. Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: insearch of common principles. // J.Mol.Biol., 1995, v. 253, p. 370-382.

110. Marmorstein R.Q., Carey M., Ptashne M., Harrison S.C. DNA recognition by GAL4: structure of a protein-DNA complex. // Nature, 1992, v. 356, p. 408-414.

111. Matsuo H., Shirakawa M., Kyogoku Y. Three-dimentional dimer structure of the X-Cro repressor in solution as determined by heteronuclear multidimensional NMR. // J.Mol.Biol., 1995, v. 254, p. 668-680.

112. Matthews B.W. Protein-DNA interaction. No code for recognition. // Nature, 1988, v. 335, p. 294-295.

113. McCammon J.A. Theory of biomolecular recognition. // Curr.Opin.Struct.Biol., 1998, v. 8, p. 245-249.

114. Misra V.K., Sharp K.A., Friedman R.A., Honig B. Salt effects on ligand-DNA binding minor groove binding antibiotics. // J.Mol.Biol., 1994, v. 238, p. 245-263.

115. Misra V.K., Hecht J.L., Sharp K.A., Friedman R.A., Honig B. Salt effects on protein-DNA interactions. The A-cI repressor and -EcoRI endonuclease. // J.Mol.Biol., 1994, v. 238, p. 264-280.

116. Mondragon A., Subbiah S., Almo S.C., Drottar M., Harrison S.C. Structure of the amino-terminal domain of phage 434 repressor at 2.0 A resolution. // J.Mol.Biol., 1989, v. 205, p. 189-200.

117. Mueser T.C., Nossal N.G., Hyde C.C. Structure of bacteriophage T4 RNase H, a 5' to 3' RNA-DNA and DNA-DNA Exonu-clease with sequence similarity to the RAD2 family of eu-karyotic proteins. // Cell, 1996, v. 85, p. 1101-1112.

118. Nardelli J., Gibson T.J., Vesque C., Charnay P. Base sequence discrimination by zinc-finger DNA-binding domains. // Nature, 1991, v. 349, p. 175-178.

119. Nekludova L., Pabo C.O. Distinctive DNA conformation with enlarged major groove is found in Zn-finger-DNA and other protein-DNA complexes. // Proc.Natl.Acad.Sci.U.S.A, 1994, v. 91, p. 6948-6952.

120. Nelson H.C.M. Structure and function of DNA-binding proteins. // Curr.Opin.Genet.& Dev., 1995, v. 5, p. 180-189.

121. Newman M., Lunnen K., Wilson G., Greci J., Schildkraut I., Phillips S.E.V. Crystal structure of restriction endonu-clease Bgl I bound to its interrupted recognition sequence. // EMBO J., 1998, v. 17, p. 5466-5476.

122. Oelgeschlager T., Chiang C., Roeder R.G. Topology and reorganization of a human TFIID-promoter complex. // Nature,1996, v. 382, p. 735-738.

123. Ogata K., Morikawa S., Nakamura H., Sekikawa A., Inoue T., Kanai H., Sarai A., Ishii S., Nishimura Y. Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices. // Cell, 1994, v. 79, p. 639-648.

124. Olson W.K., Gorkin A.A. , Lu X., Hock L.M., Zhurkin V.B. DNA sequence-dependent deformability deduced from proteinDNA crystal complexes. // Proc.Natl.Acad.Sci.USA, 1998, v. 95, p. 11163-11168.

125. 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, 1988, v. 335, p. 321-329.

126. Pabo C.O., Aggarwal A.K., Jordan S.R., Beamer L.J., Obey-sekare U.R., Harrison S.C. Conserved residues make similar contacts in two repressor-operator complexes. // Science, 1990, v. 247, p. 1210-1213.

127. Pabo C.O. New generation databases for molecular biology. // Nature, 1987, v. 327, p. 467.136137138139140141142143144145146147148149

128. Pabo C.O., Suchanek E.G. Computer-aided model-building strategies for protein design. // Biochemistry, 1986, v. 25, p. 5987-5991.

129. Pabo C.O., Sauer R.T. Protein-DNA recognition. // Annu.Rev.Biochem. , 1984 , v. 53, p. 293-321. Pabo C.O., Lewis M. The operator-binding domain of X repressor: structure and DNA recognition. // Nature, 1982, v. 298, p. 443-447.

130. Pabo C.O., Sauer R.T., Sturtevant J.M., Ptashne M. The X repressor contains two domains. // Proc.Natl .Acad.Sci.U.S.A, 1979, v. 76, p. 1608-1612.

131. Packer M.J., Hunter C.A. Sequence-dependent DNA structure: the role of the sugar-phosphate backbone. // J.Mol.Biol., 1998, v. 280, p. 407-420.

132. Pan T., Coleman J.E. GAL4 transcription factor is not a wzinc finger" but forms a Zn(II)2Cys6 binuclear cluster. // Proc.Natl.Acad.Sci.U.S.A, 1990, v. 87, p. 2077-2081 .

133. Pavletich N.P., Pabo C.O. Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers. // Science, 1993, v. 261, p. 1701-1707.

134. Pavletich N.P., Pabo C.O. Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A. // Science, 1991, v. 252, p. 809-817.

135. Pettitt M., Makarov V.A., Andrews B.K. Protein hydration density: theory, simulations and crystallography. // Curr.Opin.Struct.Biol. , 1998, v. 8, p. 218-221.

136. Phillips S.E.V. Specific p-sheet interaction. // Curr.Opin.Struct.Biol., 1991, v. 1, p. 89-98.

137. Pomerantz J.L., Pabo C.O., Sharp P.A. Analysis of home-odomain function by structure-based design of a transcription factor. // Proc.Natl.Acad.Sci.USA, 1995, v. 92, p. 97529756.

138. Povey J.F., Diakun G.P., Garner C.D., Wilson S.P., Laue E.D. Metal ion co-ordination in the DNA binding domain of the yeast transcriptional activator GAL4. // FEBS Lett.,1501511521531541551561571581591601611621631990, v. 266, p. 142-146.

139. Preibner R., Goede A., Fruromel C. Dictionary of interfaces in proteins (DIP) . Data bank of complementary molecular surface patches. // J.Mol.Biol., 1998, v. 280, p. 535-550.

140. Ptashne M., Jeffrey A., Johnson A.D., Maurer R., Meyer B.J., Pabo C.O., Roberts T.M., Sauer R.T. How the X repressor and cro work. // Cell, 1980, v. 19, p. 1-11.

141. Raumann B.E., Rould M.A., Pabo C.O., Sauer R.T. DNA recognition by ß-sheets in the Arc repressor-operator crystal structure. // Nature, 1994, v. 367, p. 754-757.

142. Rice P.A., Yang S., Mizuuchi K. , Nash H.A. Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. // Cell, 1996, v. 87, p. 1295-1306.

143. Ringe D. What makes a binding site a binding site? // Curr.Opin.Struct.Biol. , 1995, v. 5, p. 825-829.

144. Robinson H., Gao Y., McCrary B.S., Edmondson S.P., Shriver J.W., Wang A.H.J. Thehyperthermophile chromosomal protein Sac7d sharply kinks DNA. // Nature, 1998, v. 392, p. 202205.

145. Rozenberg H., Rabinovich D., Frolow F., Hegde R.S., Shakked Z. Structural code for DNA recognition revealed in crystal structures of papillomavirus E2-DNA targets. // Proc.Natl.Acad.Sei.USA, 1998, v. 95, p. 15194-15199.

146. Sandmann C., Cordes F., Saenger W. Structure model of a complex between the factor for inversion stimulation (FIS) and DNA: modeling protein-DNA complexes with dyad symmetry and known protein structures. // Proteins, 1996, v. 25, p. 486-500.

147. Saroff H.A. Energetics of protein-DNA interactions: an exact calculation for binding of ligands to a lattice of overlapping sites. // Biopolymers, 1994, v. 36, p. 121134 .

148. Sauer R.T. Lac repressor at last. // Structure, 1996, v. 4, p. 219-222.

149. Sayle R. RasMol user manual. 1992.

150. Scheif R. DNA binding by proteins. // Science, 1988, v. 241, p. 1182-1187.

151. Schildbach J.F., Karzai A.W., Raumann B.E., Sauer R.T. Origins of DNA-binding specificity: role of protein contacts with the DNA backbone. // Proc .Natl .Acad. Sei . USA, 1999, v. 96, p. 811-817.

152. Schneider R., Daruvar A., Sander C. The HSSP database of protein structure-sequence aliment. // Nucleic Acids Res.,1997, v. 25, p. 226-230.

153. Schneider T.D. Sequence walker: a graphical method to display how binding proteins interact with DNA or RNA sequences. // Nucleic Acids Res., 1997, v. 25, p. 4408-4415.

154. Schreiber J., Enderich J., Wegner M. Structural requirement for DNA binding of GCM proteins. // Nucleic Acids Res., 1998, v. 26, p. 2337-2343.

155. Schultz S.C., Shields G.C., Steitz T.A. Crystal structure of a CAP-DNA complex: the DNA is bent by 90. // Science, 1991, v. 253, p. 1001-1007.

156. 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, 1994, v. 266, p. 763-770.

157. Schwabe J.W.R., Chapman L., Flinch J.T. The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements. // Cell, 1993, v. 75, p. 567-578.

158. Shilov I., Tashlitskii V., Khodoun M., Vasil'ev S., Alek-seev Y., Kuzubov A., Kubareva E.A., Karyagina A.S. DNA-methyltransferase SsoII interaction with own promotor region binding site. // Nucleic Acids Res., 1998, v. 26, p. 2659-2664.

159. Shimofurutani N., Kisu Y., Suzuki M., Esaka M. Functional analyses of the Dof domain, a zinc finger DNA-binding domain, in a pumpking DNA-protein AOBP. // FEBS Lett., 1998, v. 430, p. 251-256.

160. Simoncsits A., Chen J., Percipalle P., Wang S., Toro I., Pongor S. Single-chain repressors containing engineered DNA-binding domains of the phage 434 repressor recognize symmetric or asymmetric DNA operators. // J.Mol.Biol., 1997, v. 267, p. 118-131.

161. Sippl M.J., Jaritz M. Prediction power of mean force pair potentials. // n/a, 1996, p. 113-134.

162. Sippl M.J., Ortner M., Jaritz M., Lackner P., Flockner H. Helmholtz free energies of atom pair interactions in proteins. // Fold.Des., 1996, v. 1, p. 289-298.

163. Sippl M.J. Helmholtz free energy of peptide hydrogen bonds in proteins. // J.Mol.Biol., 1996, v. 260, p. 644-648.

164. Somers W.S., Phillips S.E.V. Crystal structure of the met repressor-operator complex at 2.8 A resolution reveals DNA recognition by b-strands. // Nature, 1992, v. 359, p. 387393.176177178179180181182183184185186187188189

165. Steitz T.A. Structural studies of protein-nucleic acid interaction: the sources of sequence-specific binding. // Q.Rev.Biophys. , 1990, v. 23, p. 205-280.

166. Sternberg M.J.E., Gabb H.A., Jackson R.M. Predictive docking of protein-protein and protein-DNA complexes. // Curr.Opin.Struct.Biol., 1998, v. 8, p. 250-256.

167. Stormo G.D., Fields D.S. Specifity, free energy and information contents in protein-DNA interaction. // TIBS, 1998, v. 23, p. 109-113.

168. Suzuki M., Amano N., Kakinuma J., Tateno M. Use a 3D structure data base for understanding sequence-dependent conformational aspects of DNA. // J.Mol.Biol., 1997, v. 274, p. 421-435.

169. Suzuki M., Yagi N. An in-the-groove view of DNA structures in complexes with proteins. // J.Mol.Biol., 1996, v. 255, p. 677-687.

170. Suzuki M., Yagi N., Finch J.T. Role of base-backbone and base-base interactions in alternating DNA conformations. / / FEBS Lett., 1996, v. 379, p. 148-152.

171. Suzuki M., Brenner S.E., Gerstein M., Yagi N. DNA recognition code of transcription factors. // Protein Eng., 1995, v. 8, p. 319-328.

172. Suzuki M., Yagi N., Gerstein M. DNA recognition and superstructural formation by helix-turn-helix proteins. // Protein Eng., 1995, v. 8, p. 329-338.

173. Suzuki M., Gerstein M., Yagi N. Stereochemical basis of DNA recognition by Zn finger. // Nucleic Acids Res., 1994, v. 22, p. 3397-3405.

174. Suzuki M., Yagi N. DNA recognition rules for steroid hormone receptors and GATA1: specificity of the rules. // Proc.Japan Acad., 1994, v. 70B, p. 62-66.

175. Suzuki M., Yagi N. DNA recognition rules for steroid hormone receptors and GATA1: chemical and stereochemical rules. // Proc.Japan Acad., 1994, v. 70B, p. 58-61.

176. Suzuki M. A framework for the DNA-protein recognition code of the probe helix in transcription factors: the chemical and stereochemical rules. // Structure, 1994, v. 2, p. 317326.

177. Suzuki M., Yagi N. DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families. // Proc.Natl.Acad.Sci.USA, 1994, v. 91, p. 12357-12361.

178. Tan S., Richmond T.J. Eukariotic transcription factors. // Curr.Opin.Struct.Biol., 1998, v. 8, p. 41-48.

179. Tan S., Hunziker Y., Sargent D.F., Richmond T.J. Crystal structure of a yeast TFIIA/TBP/DNA complex. // Nature, 1996, v. 381, p. 127-134.

180. Turner D.H. Thermodynamics of base pairing. // Curr.Opin. Struct.Biol., 1996, v. 6, p. 299-304.

181. Vipond I.B., Baldwin G.S., Halford S.E. Divalent metal ions at the active sites of the EcoRV and EcoRI restriction endonucleases. // Biochemistry, 1995, v. 34, p. 697-704.

182. Vuister G.W., Kim S.J., Orosz A., Marquardt J., Wu C., Bax A. Solution structure of the DNA-binding domain of Droso-phila heat shock transcription factor. // Nat.Struct.Biol., 1994, v. 1, p. 605-614.

183. Waters T.R., Connolly B.A. Interaction of the restriction endonuclease UcoRV with the deoxyguanosine and deoxycyti-dine bases in its recognition sequence. // Biochemistry, 1994, v. 33, p. 1812-1819.

184. Werner M.H., Gronenborn A.M., Clore G.M. Intercalation, DNA kinking, and control of transcription. // Science, 1996, v. 271, p. 778-784.

185. Werner M.H., Clore G.M., Fisher C.L., Fisher R.J., Trinh L., Shiloach J., Gronenborn A.M. The solution structure of the human ETS1-DNA complex reveals a novel mode of binding and true side chain intercalation. // Cell, 1995, v. 83, p. 761-771.

186. Westcott T.P., Tobias I., Olson W.K. Elasticity theory and numerical analysis of DNA supercoiling: an application to DNA looping. // J.Phys.Chem., 1995, v. 99, p. 17926-17935.

187. Wikstrum A., Berglund H., Hambraeus C., van der Berg S., Hurd T. Conformational dynamics and molecular recognition: backbone dynamics of the estrogen receptor DNA-binding domain. // J.Mol.Biol. , 1999, v. 289, p. 963-979.

188. Wilson D.S., Guenther B., Desplan C., Kuriyan J. High resolution cristal structure of a paired (Pax) class cooperative homeodomain dimer on DNA. // Cell, 1995, v. 82, p. 709719.

189. Wingenber E., Dietze P., Karas H., Knuppel R. TRANSFAC: a database on transcription factors and their DNA binding sites. // Nucleic Acids Res., 1996, v. 24, p. 238-241.

190. Wintjens R.T., Rooman M.J., Wodak S.J. Automatic classification and analysis of aa-turn motifs in proteins. // J.Mol.Biol., 1996, v. 255, p. 235-253.

191. Wintjens R.T., Rooman M.J. Structural classification of HTH DNA-binding domains and protein-DNA interaction modes. // J.Mol.Biol., 1996, v. 262, p. 294-313.

192. Wolberger C. Homeodomain interactions. // Curr.Opin. Struct.Biol., 1996, v. 6, p. 62-68.

193. Wolberger C., Vershon A.K., Liu B., Johnson A.D., Pabo C.O. Crystal structure of a MATa2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions. // Cell, 1991, v. 67, p. 517-528.

194. Wolberger C., Dong Y., Ptashne M., Harrison S.C. Structure of a phage 434 Cro/DNA complex. // Nature, 1988, v. 335, p. 789-795.

195. Wolfe S.A., Greisman H.A., Ramm E.I., Pabo C.O. Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code. // J.Mol.Biol., 1999, v. 285, p. 1917-1934.

196. Yang W., Steitz T.A. Crystal structure of the site-specific recombinase y5 resolvase complexed with a 34 bp cleavage site. // Cell, 1995, v. 82, p. 193-207.

197. Yura K., Tomoda S., Go M. Repeat of a helix-turn-helix module in DNA-binding proteins. // Protein Eng., 1993, v. 6, p. 621-628.

198. Zhang H., Zhao D., Revington M., Lee W., Jia X., Arrow-smith C., Jardetzky 0. The solution structures of the trp repressor-operator DNA complex. // J.Mol.Biol., 1994, v. 238, p. 592-614.

199. Zhang P., Tobias I., Olson W.K. Computer simulation of protein-induced structural changes in closed circular DNA. // J.Mol.Biol., 1994, v. 242, p. 271-290.

200. Zhou P., Sun L.J., Dotch V., Wagner G., Verdine G.L. Solution structure of the core NFATCl/DNA complex. // Cell, 1998, v. 92, p. 687-696.

201. Zou Q., Habermann-Rottinghaus S.M., Murphy K.P. Urea effects on protein stability: hydrogen bonding and the hydrophobic effect. // Proteins Struct.Funct.Genet., 1998, v. 31, p. 107-115.

202. Код БД-источника Kofl DPIDB БД-ис- ТОЧ-НИК Заголовок Состав Разрешение Дата (A)1 1А02 2 3 4 5 6 7

203. MOLECULE: DNA; CHAIN: D, E MOLECULE: 3-1BNK P1BNK PDB DNA REPAIR METHYLADENINE DNA GLYCOSYLASE; CHAIN: A, B, 2 . 70 29 . 07 .981. C; SYNONYM: AAG, I1BNZ P1BNZ PDB PROTEIN-DNA INTERACTION MOL ID: 1; MOLECULE: SS07D; CHAIN: NULL 2 .00 31 .07 . 98

204. CHAIN: T, P, D; ENGINEERED: YES;1BPX P1BPX PDB COMPLEX (NUCLEOTIDYL- OTHER DETAILS: GAPPED DNA IS COMPOSED OF 3 2 .40 11 . 04 .97

205. TRANSFERASE / DNA ) STRANDS TEMPLATE, PRIMER, AND DOWNSTREAM1. OLIGO SYNONYM: POL-B

206. CHAIN: T, P, D; ENGINEERED: YES;1BPY P1BPY PDB COMPLEX (NUCLEOTIDYLTRANSFERASE / DNA ) OTHER DETAILS: GAPPED DNA IS COMPOSED OF 3 STRANDS TEMPLATE, PRIMER, AND DOWNSTREAM 2 .20 15 .04 .971. OLIGO SYNONYM: POL B

207. COMPLEX (ENDONUCLEASE /DNA) CHAIN: B, C; ENGINEERED: YES MOLECULE: FOKI RESTRICTION ENDONUCLEASE; CHAIN: A; SYNONYM: 2.80 R. FOK 18.04.97

208. COMPLEX (GENE-REGULATORY PROTEIN/DNA) C-JUN PROTO-ONCOGENE (TRANSCRIPTION FACTOR AP-1) DIMERIZED WITH C-FOS AND COMPLEXED WITH 3.05 DNA 07.03.95

209. LU 1-- 1HCQ PI GLU P1HCQ PDB PDB PDB GLUCOCORTICOID RECEPTOR (DNA-BINDING DOMAIN) COMPLEX WITH DNA (FIRST SIX RESIDUES ARE CLONAL LINKERS) 2 . 90

210. COMPLEX (DNA-BINDING PROTEIN/DNA) MOL ID 1, MOLECULE: HUMAN SRY; CHAIN: A; MOL ID 2, HMP 09.05.951HRZ P1HRZ PDB COMPLEX (DNA-BINDING PROTEIN/DNA) MOL ID 1, MOLECULE: HUMAN SRY; CHAIN: A; MOL ID 2, HMP 09.05.95

211. Fl 1IGN UHF PI I Fl PDB COMPLEX (DNA-BINDING PROTEIN/DNA) S MOLECULE: INTERFERON REGULATORY FACTOR 1; CHAIN: A, B; FRAGMENT: DNA- 3 . 00 2.25 12.09.97 29.02.96

212. P1IGN PDB P1IHF PDB ■ COMPLEX (DNA-BINDING PROTEIN/DNA) ENGINEERED: YES MOLECULE: RAP1; CHAIN: A, B; FRAGMENT: DNA

213. CHAIN: A, B; ENGINEERED: YE

214. DNA POLYMERASE I (KLENOW FRAGMENT)1KLN P1KLN PDB NUCLEOTIDYLTRANSFERASE (E.C.2.7.7.7) MUTANT WITH ASP 3 55 REPLACED BY 3.20 24 . 05. 94

215. ALA (D355A) COMPLEXED WITH DNA1LAT < 1 P1LAT PDB 1 1 COMPLEX (TRANSCRIPTION REGULATION/DNA) CHAIN: C, D; SYNONYM: GRESO; ENGINEERED: YES; OTHER DETAILS: 2 GRE HALF-SITES SEPARATED BY ZERO BASE PAIRS OF SPACE 1 . 90 18 . 12 . 95

216. C REPRESSOR ("HEADPIECE") COMPLEX WITH AN1LCC P1LCC PDB GENE-REGULATING PROTEIN 11 BASE-PAIR HALF-OPERATOR CORRESPONDING TO THE LEFT HALF OF THE WILD TYPE LAC OPERATOR ÜMP 25. 03. 931. NMR, BEST STRUCTURE)

217. C REPRESSOR ("HEADPIECE") COMPLEX WITH AN1LCD 1 PlLCD GENE-REGULATING PROTEIN 11 BASE-PAIR HALF-OPERATOR CORRESPONDING TO THE LEFT HALF OF THE WILD TYPE LAC OPERATOR HMP 25. 03. 931. NMR, 3 STRUCTURES)

218. MBDA REPRESSOR MUTANT WITH VAL 3 6 REPLACED1LLI P1LLI PDB TRANSCRIPTION REGULA- BY LEU, MET 40 REPLACED BY LEU, AND VAL 47 2.10 25. 03. 94

219. TION PROTEIN/DNA REPLACED BY ILE (V36L,M4OL,V471) COMPLEXED WITH DNA OPERATOR1LMB P1LMB PDB DNA-BINDING REGULATORY PROTEIN LAMBDA REPRESSOROPERATOR COMPLEX 1.80 05. 11. 91

220. MYOD BASIC-HELIX-LOOP-HELIX (BHLH) DOMAIN1MDY P1MDY PDB TRANSCRIPTION ACTIVA- (RESIDUES 102 166) MUTANT WITH CYS 135 RE- 2 .80 09. 06. 94

221. S F 1NFK 10CT 1 PAR COMPLEX (BINDING PRO-P1MSFPDB TEIN/DNA) C-MYB DNA-BINDING DOMAIN COMPLEXED WITH DNA (NMR, 25 STRUCTURES) 24.01.95

222. P1NFK PIOCT PI PAR PDB PDB PDB COMPLEX (TRANSCRIPTION FACTOR/DNA) THE HOMODIMER IS BOUND TO A KB SITE MOLECULE: NUCLEAR FACTOR KAPPA-B; CHAIN: A, B; FRAGMENT : P50 2 .30 03.10.96

223. DNA-BINDING PROTEIN OCT-1 (POU DOMAIN) 3 . 00 2 . 60 09.05.94 22.03.94

224. COMPLEX (DNA-BINDING PROTEIN/DNA)1TRO P1TRO PDB I L > — 51TRR P1TRR PDB

225. ARE NONCODING STRAND NUCLEOTIDES + 62 +92, CHAINS C AND F ARE CODING STRAND NUCLEOTIDES + 6

226. ENGINEERED: YES MOLECULE: HUMAN TATA BINDING PROTEIN; CHAIN: A; SYNONYM: HTBP;1TSR P1TSR PDB

227. DNA-BINDING REGULATORY PROTEIN

228. DNA-BINDING REGULATORY PROTEIN

229. COMPLEX (DNA-BINDING PROTEIN/DNA)

230. TRP REPRESSOR COMPLEX WITH OPERATOR290 13 1.90 30

231. TRP REPRESSOROPERATOR HALF-SITE TANDEM COMPLEX2.401TUP P1TUP PDB1UBD P1UBD PDB1.AS P1VAS PDB i1VOL P1VOL1VPW A00191.' I '1WET A00201.I ""1XBR1YRN 1YSA1. P1XBR1. P1YRN P1YSA1. PDB1. PDB1. PDB1. PDB1. PDB PDB

232. COMPLEX (TUMOR SUP-PRESSOR/DNA)

233. COMPLEX (TRANSCRIPTION CHAIN: A, B; ENGINEERED: YES MOLECULE: YY1; REGULATION/DNA) COMPLEX (ENDONUCLEase/dna)1. COMPLEX(TRANSCRIPTIONI1. FACTOR/REGN/DNA)

234. MOL ID: 1; MOLECULE: P53 TUMOR SUPPRESSOR; CHAIN: A, B, C; ENGINEERED: YE

235. MOL ID: 1; MOLECULE: TUMOR SUPPRESSOR P53; CHAIN: A, B, C; MOL ID: 2;chain: c; fragment: zinc5'-d(tpapgpcpgpcpapapcpgpcpgpa)-3'); chain: B, c; engineered: yes chain: a; ec: 3.1.25.1;

236. MOL ID: 3; MOLECULE: 16 BASE-PAIR TATA-CONTAINING OLIGONUCLEOTIDE; CHAIN: C, D; ENGINEERED: YES FRAGMENT: RESI1. PROTEIN/DNA)

237. ENGINEERED: YES; OTHER DETAILS: BOUND TO COMPLEX (DNA-BINDING COREPRESSOR, HYPOXANTHINE, AND PURF OPERATOR.

238. NO 5' PHOSPHATE ON OLIGONUCLEOTIDE CHAIN: A; ENGINEERED: YE

239. MOL ID: 1; MOLECULE: PURINE REPRESSOR-GUANINE-PURF-OPERATOR; CHAIN: A; MOL ID: 2;

240. COMPLEX (DNA-BINDING PROTEIN/DNA)

241. COMPLEX (TRANSCRIPTION FACTOR/DNA)1. COMPLEX (TWO DNA

242. ENGINEERED: YES; OTHER DETAILS: 24-MERIC DNA DUPLEX MOLECULE: T PROTEIN; CHAIN: A, B; FRAGMENT: T DO

243. DOMAIN: HOMEODOMAIN; SYNONYM: MAT ALPHA-2;

244. BINDING PROTEINS/DNA) ENGINEERED: YES; MOL ID: 3; MOLECULE: DNA;1.UCINE ZIPPER

245. GCN4 (BASIC REGION, LEUCINE ZIPPER) COMPLEX220 2.20 2.50275 2.702 .702128 11 0408