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

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-исТОЧ-НИК Заголовок Состав Разрешение Дата (A)1 1А02 2 3 4 5 6 7.

203. MOLECULE: DNACHAIN: D, E MOLECULE: 3−1BNK P1BNK PDB DNA REPAIR METHYLADENINE DNA GLYCOSYLASECHAIN: A, B, 2. 70 29. 07 .981. CSYNONYM: AAG, I1BNZ P1BNZ PDB PROTEIN-DNA INTERACTION MOL ID: 1- MOLECULE: SS07DCHAIN: NULL 2 .00 31 .07. 98.

204. CHAIN: T, P, DENGINEERED: YES-1BPX P1BPX PDB COMPLEX (NUCLEOTIDYLOTHER 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, DENGINEERED: 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, CENGINEERED: YES MOLECULE: FOKI RESTRICTION ENDONUCLEASECHAIN: ASYNONYM: 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 SRYCHAIN: AMOL ID 2, HMP 09.05.951HRZ P1HRZ PDB COMPLEX (DNA-BINDING PROTEIN/DNA) MOL ID 1, MOLECULE: HUMAN SRYCHAIN: AMOL 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, BFRAGMENT: 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, BFRAGMENT: DNA.

213. CHAIN: A, BENGINEERED: 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, DSYNONYM: GRESOENGINEERED: YESOTHER 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 UMP 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 REGULABY 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-BCHAIN: A, BFRAGMENT: 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 PROTEINCHAIN: ASYNONYM: 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, BENGINEERED: YES MOLECULE: YY1- REGULATION/DNA) COMPLEX (ENDONUCLEase/dna)1. COMPLEX (TRANSCRIPTIONI1. FACTOR/REGN/DNA).

234. MOL ID: 1- MOLECULE: P53 TUMOR SUPPRESSORCHAIN: A, B, CENGINEERED: YE.

235. MOL ID: 1- MOLECULE: TUMOR SUPPRESSOR P53- CHAIN: A, B, CMOL ID: 2-chain: cfragment: zinc5'-d (tpapgpcpgpcpapapcpgpcpgpa)-3') — chain: B, cengineered: yes chain: aec: 3.1.25.1;

236. MOL ID: 3- MOLECULE: 16 BASE-PAIR TATA-CONTAINING OLIGONUCLEOTIDECHAIN: C, DENGINEERED: YES FRAGMENT: RESI1. PROTEIN/DNA).

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

238. NO 5' PHOSPHATE ON OLIGONUCLEOTIDE CHAIN: AENGINEERED: YE.

239. MOL ID: 1- MOLECULE: PURINE REPRESSOR-GUANINE-PURF-OPERATORCHAIN: AMOL ID: 2;

240. COMPLEX (DNA-BINDING PROTEIN/DNA).

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

242. ENGINEERED: YESOTHER DETAILS: 24-MERIC DNA DUPLEX MOLECULE: T PROTEINCHAIN: A, BFRAGMENT: T DO.

243. DOMAIN: HOMEODOMAINSYNONYM: MAT ALPHA-2;

244. BINDING PROTEINS/DNA) ENGINEERED: YESMOL ID: 3- MOLECULE: DNA-1.UCINE ZIPPER.

245. GCN4 (BASIC REGION, LEUCINE ZIPPER) COMPLEX220 2.20 2.50 275 2.702 .702 128 11 0408.