Бесплатный автореферат и диссертация по биологии на тему

Характеристика взаимодействия ДНК-узнающего участка белка и ДНК по большой бороздке

ВАК РФ 03.00.03, Молекулярная биология

Содержание диссертации, кандидата 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 Диссертация 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.

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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