mohammad tabish ahmed - eTheses Repository - University of ...

More documents

Recommendations

Info

Ellis, R. J. & S. M. Hemmingsen, (1989) Molecular chaperones: proteins essential for the biogenesis of some macromolecular structures. Trends Biochem Sci 14: 339-342. England, J., D. Lucent & V. Pande, (2008) Rattling the cage: computational models of chaperonin-mediated protein folding. Curr Opin Struct Biol 18: 163-169. Erbse, A., O. Yifrach, S. Jones & P. A. Lund, (1999) Chaperone activity of a chimeric GroEL protein that can exist in a single or double ring form. J Biol Chem 274: 20351-20357. Eyles, S. J. & L. M. Gierasch, (2010) Nature's molecular sponges: small heat shock proteins grow into their chaperone roles. Proc Natl Acad Sci U S A 107: 2727-2728. Fayet, O., T. Ziegelhoffer & C. Georgopoulos, (1989) The groES and groEL heat shock gene products of Escherichia coli are essential for bacterial growth at all temperatures. J Bacteriol 171: 1379-1385. Fenton, W. A. & A. L. Horwich, (2003) Chaperonin-mediated protein folding: fate of substrate polypeptide. Q Rev Biophys 36: 229-256. Ferbitz, L., T. Maier, H. Patzelt, B. Bukau, E. Deuerling & N. Ban, (2004) Trigger factor in complex with the ribosome forms a molecular cradle for nascent proteins. Nature 431: 590-596. Festa, R. A., F. McAllister, M. J. Pearce, J. Mintseris, K. E. Burns, S. P. Gygi & K. H. Darwin, (2010) Prokaryotic ubiquitin-like protein (Pup) proteome of Mycobacterium tuberculosis. PLoS One 5: e8589. Fink, A. L., (1999) Chaperone-mediated protein folding. Physiol Rev 79: 425-449. Flaherty, K. M., C. DeLuca-Flaherty & D. B. McKay, (1990) Three-dimensional structure of the ATPase fragment of a 70K heat-shock cognate protein. Nature 346: 623-628. Frydman, J., (2001) Folding of newly translated proteins in vivo: the role of molecular chaperones. Annu Rev Biochem 70: 603-647. 253
Fux, C. A., J. W. Costerton, P. S. Stewart & P. Stoodley, (2005) Survival strategies of infectious biofilms. Trends Microbiol 13: 34-40. Gatenby, A. A., (1984) The properties of the large subunit of maize ribulose bisphosphate carboxylase/oxygenase synthesised in Escherichia coli. European journal of biochemistry / FEBS 144: 361-366. Gay, P., D. Le Coq, M. Steinmetz, T. Berkelman & C. I. Kado, (1985) Positive selection procedure for entrapment of insertion sequence elements in gram-negative bacteria. J Bacteriol 164: 918-921. Geissler, S., K. Siegers & E. Schiebel, (1998) A novel protein complex promoting formation of functional alpha- and gamma-tubulin. Embo J 17: 952-966. Genevaux, P., C. Georgopoulos & W. L. Kelley, (2007) The Hsp70 chaperone machines of Escherichia coli: a paradigm for the repartition of chaperone functions. Mol Microbiol 66: 840-857. Genevaux, P., F. Keppel, F. Schwager, P. S. Langendijk-Genevaux, F. U. Hartl & C. Georgopoulos, (2004) In vivo analysis of the overlapping functions of DnaK and trigger factor. EMBO reports 5: 195-200. Georgopoulos, C. P., R. W. Hendrix, S. R. Casjens & A. D. Kaiser, (1973) Host participation in bacteriophage lambda head assembly. J Mol Biol 76: 45-60. Georgopoulos, C. P., R. W. Hendrix, A. D. Kaiser & W. B. Wood, (1972) Role of the host cell in bacteriophage morphogenesis: effects of a bacterial mutation on T4 head assembly. Nat New Biol 239: 38-41. Georgopoulos, C. P. & B. Hohn, (1978) Identification of a host protein necessary for bacteriophage morphogenesis (the groE gene product). Proc Natl Acad Sci U S A 75: 131- 135. Gething, M. J. & J. Sambrook, (1992) Protein folding in the cell. Nature 355: 33-45. 254
Page 1 and 2:
FUNCTIONAL AND STRUCTURAL CHARACTER
Page 3 and 4:
Abstract Proteins are involved in a
Page 5 and 6:
Dedicated to Mum, Dad, and Sharique
Page 7 and 8:
Index of contents Chapter 1: Introd
Page 9 and 10:
2.4.5: Bacteriophage P1 Transductio
Page 11 and 12:
4.1.5: Chimeras DHF & GEI 162 4.2:
Page 13 and 14:
List of illustrations Chapter 1: In
Page 15 and 16:
Fig 4.1: Schematic representation o
Page 17 and 18:
List of tables Chapter 1: Introduct
Page 19 and 20:
SDW STPKs TAE TEMED TBS Sterile dis
Page 21 and 22:
Chapter 1 1.1 Protein Folding The g
Page 23 and 24:
Chapter 1 Fig 1.1: The energy lands
Page 25 and 26:
Chapter 1 To try and escape from th
Page 27 and 28:
Chapter 1 Fig 1.2: Pathways regulat
Page 29 and 30:
Chapter 1 As protein folding in Myc
Page 31 and 32:
Chapter 1 1.4 The molecular chapero
Page 33 and 34:
Chapter 1 1.4.1 Classes of molecula
Page 35 and 36:
Chapter 1 Hsp40 DnaJ CbpA DjlA Ydj1
Page 37 and 38:
Chapter 1 obtained. These revertant
Page 39 and 40:
Chapter 1 1.4.3.1 The ribosome asso
Page 41 and 42:
Chapter 1 (A) (B) Fig 1.7: Structur
Page 43 and 44:
Chapter 1 complete the reaction cyc
Page 45 and 46:
Chapter 1 1.4.3.4 The small Hsps On
Page 47 and 48:
Chapter 1 1.4.3.5 Hsp90 family of c
Page 49 and 50:
Chapter 1 Fig 1.11: Structure of Ht
Page 51 and 52:
Chapter 1 1.4.3.6 Hsp100 family of
Page 53 and 54:
Chapter 1 Fig 1.13: The different r
Page 55 and 56:
Chapter 1 encoded by more than one
Page 57 and 58:
Chapter 1 Fig 1.15: The illustratio
Page 59 and 60:
Chapter 1 (Rommelaere et al., 1993,
Page 61 and 62:
Chapter 1 Fig 1.16: Octameric struc
Page 63 and 64:
Chapter 1 main difference between t
Page 65 and 66:
Chapter 1 1.5.3.3 Prefoldin It has
Page 67 and 68:
Chapter 1 result the substrate prot
Page 69 and 70:
Chapter 1 Fig 1.18: The structures
Page 71 and 72:
Chapter 1 6- If the released peptid
Page 73 and 74:
Chapter 1 1.5.4.3 GroEL substrates
Page 75 and 76:
Chapter 1 Recent work has suggested
Page 77 and 78:
Chapter 1 (A) cpn10 cpn60.1 cpn60.2
Page 79 and 80:
Chapter 1 1998). Cpn60.1 however ha
Page 81 and 82:
Chapter 1 1.6 Aims of the project T
Page 83 and 84:
Chapter 2 Materials and Methods: 2.
Page 85 and 86:
Chapter 2 pET-cpn10- cpn60.1 Deriva
Page 87 and 88:
Chapter 2 2.3 Primers: Below is a l
Page 89 and 90:
Chapter 2 Mut EL.3 Rev groEL 1401-1
Page 91 and 92:
Chapter 2 29R-EL-60.2 groEL 432-412
Page 93 and 94:
Chapter 2 Biofilm base media: 13.6g
Page 95 and 96:
Chapter 2 Preparation of bacterioph
Page 97 and 98:
Chapter 2 then resuspended in 200µ
Page 99 and 100:
Chapter 2 - 10X BSA (depending on t
Page 101 and 102:
Chapter 2 - Colony/culture 1μl - S
Page 103 and 104:
Chapter 2 The PCR cycling parameter
Page 105 and 106:
Chapter 2 tubes were placed on ice
Page 107 and 108:
Chapter 2 2.6 Protein analysis 2.6.
Page 109 and 110:
Chapter 2 2.6.2- Native gel Reagent
Page 111 and 112:
Chapter 2 - Diluted primary antibod
Page 113 and 114:
Chapter 2 supernatant was decanted
Page 115 and 116:
Chapter 2 2.6.6- Analytical ultrace
Page 117 and 118:
Chapter 3 Background As discussed a
Page 119 and 120:
Chapter 3 the -35 region of the trp
Page 121 and 122:
Chapter 3 20 mins 40 mins 60 mins 8
Page 123 and 124:
Chapter 3 (a) 60 mins 90 mins 120 m
Page 125 and 126:
Chapter 3 For this experiment, MGM1
Page 127 and 128:
Chapter 3 When IPTG was not include
Page 129 and 130:
Chapter 3 The results from these co
Page 131 and 132:
Chapter 3 3.2.1 The effect of chang
Page 133 and 134:
Chapter 3 3.2.2 Using pRARE plasmid
Page 135 and 136:
Chapter 3 3.3 Complementation and e
Page 137 and 138:
Chapter 3 of MGM100. The use of Tab
Page 139 and 140:
Chapter 3 3.3.1 Using pET plasmid i
Page 141 and 142:
Chapter 3 1 2 3 4 5 6 7 8 95 kDa 72
Page 143 and 144:
Chapter 3 it only digests the paren
Page 145 and 146:
Chapter 3 72 kDa 1 2 3 4 5 55 kDa 1
Page 147 and 148:
Chapter 3 30°C/26°C 37°C MGM100
Page 149 and 150:
Chapter 3 Fig 3.12: Comparison of t
Page 151 and 152:
Chapter 3 AI90/pACYC-Ptrc-GroESL-Sa
Page 153 and 154:
Chapter 3 1 2 3 4 5 6 7 1000 bp 600
Page 155 and 156:
Chapter 3 10 -1 10 -2 10 -3 10 -4 1
Page 157 and 158:
Chapter 3 this observation. The res
Page 159 and 160:
Chapter 3 expression. However, from
Page 161 and 162:
Chapter 4 Construction and analysis
Page 163 and 164:
Chapter 4 Background In the last ch
Page 165 and 166:
Chapter 4 Experimental design To ma
Page 167 and 168:
Chapter 4 Cpn60.2 7 8 9 Cpn60.1 1 2
Page 169 and 170:
Chapter 4 The full list of all the
Page 171 and 172:
Chapter 4 4.1 Imprecise domain swap
Page 173 and 174:
Chapter 4 4.1.1 Chimera AEC This is
Page 175 and 176:
Chapter 4 (a) Dilutions 10 -1 10 -2
Page 177 and 178:
Chapter 4 of GroEL (fig 4.7). This
Page 179 and 180:
Chapter 4 (a) Dilutions 10 -1 10 -2
Page 181 and 182:
Chapter 4 4.1.5 Chimeras DHF & GEI
Page 183 and 184:
Chapter 4 4.2 Precise domain swaps
Page 185 and 186:
Chapter 4 intermediate domains were
Page 187 and 188:
Chapter 4 1 2 800 kDa 480 kDa 146 k
Page 189 and 190:
Chapter 4 Dilutions 10 -2 10 -3 10
Page 191 and 192:
Chapter 4 is important to note that
Page 193 and 194:
Chapter 4 Summary the complementati
Page 195 and 196:
Chapter 4 The other aspect of this
Page 197 and 198:
Chapter 4 caused due to lack of exp
Page 199 and 200:
Chapter 4 structures were not expec
Page 201 and 202:
Chapter 4 Name Construct Blue -Cpn6
Page 203 and 204:
Chapter 5 Background As discussed i
Page 205 and 206:
Chapter 5 macromolecules at equilib
Page 207 and 208:
Chapter 5 5.1 Purification of JNL 5
Page 209 and 210:
Chapter 5 (a) 1 2 3 4 5 6 7 8 9 10
Page 211 and 212:
Chapter 5 (a) A B C D E (b) 1 2 3 4
Page 213 and 214:
Chapter 5 5.2 AUC analysis of JNL U
Page 215 and 216:
Chapter 5 (a) 1 JNL in Buffer 5 0.9
Page 217 and 218:
Chapter 5 (a) (b) 100 mM P i 75 mM
Page 219 and 220:
Chapter 5 In this experiment GroEL
Page 221 and 222: Chapter 5 1 2 3 Corrected values Av
Page 223 and 224: Chapter 5 expected, evidence of lar
Page 225 and 226: Chapter 5 In summary, based on the
Page 227 and 228: Chapter 6 In this chapter I will be
Page 229 and 230: Chapter 6 of Mscpn60.1 can indirect
Page 231 and 232: Chapter 6 can produce products with
Page 233 and 234: Chapter 6 As the group in Pittsburg
Page 235 and 236: Chapter 6 Fig 6.3: Masses of 4 day
Page 237 and 238: Chapter 6 than 7 days, so there is
Page 239 and 240: Chapter 6 are required to facilitat
Page 241 and 242: Chapter 6 Fig 6.4: Sequence alignme
Page 243 and 244: Chapter 6 To ensure that the lack o
Page 245 and 246: Chapter 6 6.2.3 Complementation ana
Page 247 and 248: Chapter 6 Discussion The double rin
Page 249 and 250: Chapter 6 Section 6.3: Testing the
Page 251 and 252: Chapter 6 Experimental design For t
Page 253 and 254: Chapter 6 EcoRV groEL (1.6kb) HindI
Page 255 and 256: Chapter 6 6.3.2 Complementation res
Page 257 and 258: Chapter 6 1 2 3 4 72 kDa 55 kDa Fig
Page 259 and 260: Chapter 6 10 -1 10 -2 10 -3 10 -4 1
Page 261 and 262: Chapter 6 Discussion The results th
Page 263 and 264: Summary The main aim of this study
Page 265 and 266: together, these results strongly su
Page 267 and 268: Basha, E., K. L. Friedrich & E. Vie
Page 269 and 270: Cehovin, A., A. R. Coates, Y. Hu, Y
Page 271: Diaz-Acosta, A., M. L. Sandoval, L.
Page 275 and 276: Gupta, P., S. Mishra & T. K. Chaudh
Page 277 and 278: Hoffmann, A., F. Merz, A. Rutkowska
Page 279 and 280: Ito, K., Y. Akiyama, T. Yura & K. S
Page 281 and 282: Krzewska, J., G. Konopa & K. Libere
Page 283 and 284: Lin, Z., D. Madan & H. S. Rye, (200
Page 285 and 286: Mogk, A. & B. Bukau, (2004) Molecul
Page 287 and 288: Patzelt, H., G. Kramer, T. Rauch, H
Page 289 and 290: Rommelaere, H., M. Van Troys, Y. Ga
Page 291 and 292: Strickland, E., B. H. Qu, L. Millen
Page 293 and 294: Tyagi, N. K., W. A. Fenton & A. L.
Page 295: Yamamori, T. & T. Yura, (1982) Gene
show all

mohammad tabish ahmed - eTheses Repository - University of ...

Create successful ePaper yourself

Delete template?

Save as template?