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Chen, S., A. M. Roseman, A. S. Hunter, S. P. Wood, S. G. Burston, N. A. Ranson, A. R. Clarke & H. R. Saibil, (1994) Location of a folding protein and shape changes in GroEL- GroES complexes imaged by cryo-electron microscopy. Nature 371: 261-264. Chuang, S. E. & F. R. Blattner, (1993) Characterization of twenty-six new heat shock genes of Escherichia coli. J Bacteriol 175: 5242-5252. Cong, Y., M. L. Baker, J. Jakana, D. Woolford, E. J. Miller, S. Reissmann, R. N. Kumar, A. M. Redding-Johanson, T. S. Batth, A. Mukhopadhyay, S. J. Ludtke, J. Frydman & W. Chiu, (2010) 4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement. Proc Natl Acad Sci U S A 107: 4967-4972. Cowing, D. W., J. C. Bardwell, E. A. Craig, C. Woolford, R. W. Hendrix & C. A. Gross, (1985) Consensus sequence for Escherichia coli heat shock gene promoters. Proc Natl Acad Sci U S A 82: 2679-2683. Coyle, J. E., F. L. Texter, A. E. Ashcroft, D. Masselos, C. V. Robinson & S. E. Radford, (1999) GroEL accelerates the refolding of hen lysozyme without changing its folding mechanism. Nat Struct Biol 6: 683-690. Cyr, D. M., (1995) Cooperation of the molecular chaperone Ydj1 with specific Hsp70 homologs to suppress protein aggregation. FEBS Lett 359: 129-132. Das Gupta, T., B. Bandyopadhyay & S. K. Das Gupta, (2008) Modulation of DNAbinding activity of Mycobacterium tuberculosis HspR by chaperones. Microbiology 154: 484-490. de Jong, W. W., G. J. Caspers & J. A. Leunissen, (1998) Genealogy of the alphacrystallin--small heat-shock protein superfamily. Int J Biol Macromol 22: 151-162. Deuerling, E., A. Schulze-Specking, T. Tomoyasu, A. Mogk & B. Bukau, (1999) Trigger factor and DnaK cooperate in folding of newly synthesized proteins. Nature 400: 693-696. 251
Diaz-Acosta, A., M. L. Sandoval, L. Delgado-Olivares & J. Membrillo-Hernandez, (2006) Effect of anaerobic and stationary phase growth conditions on the heat shock and oxidative stress responses in Escherichia coli K-12. Archives of microbiology. Ditzel, L., J. Lowe, D. Stock, K. O. Stetter, H. Huber, R. Huber & S. Steinbacher, (1998) Crystal structure of the thermosome, the archaeal chaperonin and homolog of CCT. Cell 93: 125-138. Dougan, D. A., B. G. Reid, A. L. Horwich & B. Bukau, (2002) ClpS, a substrate modulator of the ClpAP machine. Mol Cell 9: 673-683. Effantin, G., M. R. Maurizi & A. C. Steven, (2010) Binding of the ClpA unfoldase opens the axial gate of ClpP peptidase. J Biol Chem 285: 14834-14840. Ehrnsperger, M., M. Gaestel & J. Buchner, (2000) Analysis of chaperone properties of small Hsp's. Methods Mol Biol 99: 421-429. Ellis, J., (1987) Proteins as molecular chaperones. Nature 328: 378-379. Ellis, R. J., (1994) Molecular chaperones. Opening and closing the Anfinsen cage. Curr Biol 4: 633-635. Ellis, R. J., (1995) Revisiting the Anfinsen cage. Fold Des 1: R9-R15. Ellis, R. J., (1997) Molecular chaperones: avoiding the crowd. Curr Biol 7: R531-533. Ellis, R. J., (2001) Macromolecular crowding: obvious but underappreciated. Trends Biochem Sci 26: 597-604. Ellis, R. J., (2005) Chaperomics: in vivo GroEL function defined. Curr Biol 15: R661-663. Ellis, R. J., (2007) Protein misassembly: macromolecular crowding and molecular chaperones. Advances in experimental medicine and biology 594: 1-13. 252
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FUNCTIONAL AND STRUCTURAL CHARACTER
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Abstract Proteins are involved in a
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Dedicated to Mum, Dad, and Sharique
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Index of contents Chapter 1: Introd
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2.4.5: Bacteriophage P1 Transductio
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4.1.5: Chimeras DHF & GEI 162 4.2:
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List of illustrations Chapter 1: In
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Fig 4.1: Schematic representation o
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List of tables Chapter 1: Introduct
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SDW STPKs TAE TEMED TBS Sterile dis
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Chapter 1 1.1 Protein Folding The g
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Chapter 1 Fig 1.1: The energy lands
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Chapter 1 To try and escape from th
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Chapter 1 Fig 1.2: Pathways regulat
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Chapter 1 As protein folding in Myc
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Chapter 1 1.4 The molecular chapero
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Chapter 1 1.4.1 Classes of molecula
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Chapter 1 Hsp40 DnaJ CbpA DjlA Ydj1
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Chapter 1 obtained. These revertant
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Chapter 1 1.4.3.1 The ribosome asso
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Chapter 1 (A) (B) Fig 1.7: Structur
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Chapter 1 complete the reaction cyc
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Chapter 1 1.4.3.4 The small Hsps On
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Chapter 1 1.4.3.5 Hsp90 family of c
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Chapter 1 Fig 1.11: Structure of Ht
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Chapter 1 1.4.3.6 Hsp100 family of
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Chapter 1 Fig 1.13: The different r
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Chapter 1 encoded by more than one
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Chapter 1 Fig 1.15: The illustratio
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Chapter 1 (Rommelaere et al., 1993,
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Chapter 1 Fig 1.16: Octameric struc
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Chapter 1 main difference between t
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Chapter 1 1.5.3.3 Prefoldin It has
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Chapter 1 result the substrate prot
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Chapter 1 Fig 1.18: The structures
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Chapter 1 6- If the released peptid
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Chapter 1 1.5.4.3 GroEL substrates
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Chapter 1 Recent work has suggested
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Chapter 1 (A) cpn10 cpn60.1 cpn60.2
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Chapter 1 1998). Cpn60.1 however ha
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Chapter 1 1.6 Aims of the project T
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Chapter 2 Materials and Methods: 2.
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Chapter 2 pET-cpn10- cpn60.1 Deriva
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Chapter 2 2.3 Primers: Below is a l
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Chapter 2 Mut EL.3 Rev groEL 1401-1
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Chapter 2 29R-EL-60.2 groEL 432-412
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Chapter 2 Biofilm base media: 13.6g
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Chapter 2 Preparation of bacterioph
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Chapter 2 then resuspended in 200µ
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Chapter 2 - 10X BSA (depending on t
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Chapter 2 - Colony/culture 1μl - S
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Chapter 2 The PCR cycling parameter
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Chapter 2 tubes were placed on ice
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Chapter 2 2.6 Protein analysis 2.6.
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Chapter 2 2.6.2- Native gel Reagent
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Chapter 2 - Diluted primary antibod
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Chapter 2 supernatant was decanted
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Chapter 2 2.6.6- Analytical ultrace
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Chapter 3 Background As discussed a
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Chapter 3 the -35 region of the trp
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Chapter 3 20 mins 40 mins 60 mins 8
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Chapter 3 (a) 60 mins 90 mins 120 m
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Chapter 3 For this experiment, MGM1
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Chapter 3 When IPTG was not include
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Chapter 3 The results from these co
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Chapter 3 3.2.1 The effect of chang
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Chapter 3 3.2.2 Using pRARE plasmid
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Chapter 3 3.3 Complementation and e
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Chapter 3 of MGM100. The use of Tab
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Chapter 3 3.3.1 Using pET plasmid i
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Chapter 3 1 2 3 4 5 6 7 8 95 kDa 72
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Chapter 3 it only digests the paren
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Chapter 3 72 kDa 1 2 3 4 5 55 kDa 1
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Chapter 3 30°C/26°C 37°C MGM100
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Chapter 3 Fig 3.12: Comparison of t
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Chapter 3 AI90/pACYC-Ptrc-GroESL-Sa
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Chapter 3 1 2 3 4 5 6 7 1000 bp 600
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Chapter 3 10 -1 10 -2 10 -3 10 -4 1
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Chapter 3 this observation. The res
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Chapter 3 expression. However, from
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Chapter 4 Construction and analysis
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Chapter 4 Background In the last ch
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Chapter 4 Experimental design To ma
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Chapter 4 Cpn60.2 7 8 9 Cpn60.1 1 2
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Chapter 4 The full list of all the
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Chapter 4 4.1 Imprecise domain swap
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Chapter 4 4.1.1 Chimera AEC This is
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Chapter 4 (a) Dilutions 10 -1 10 -2
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Chapter 4 of GroEL (fig 4.7). This
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Chapter 4 (a) Dilutions 10 -1 10 -2
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Chapter 4 4.1.5 Chimeras DHF & GEI
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Chapter 4 4.2 Precise domain swaps
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Chapter 4 intermediate domains were
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Chapter 4 1 2 800 kDa 480 kDa 146 k
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Chapter 4 Dilutions 10 -2 10 -3 10
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Chapter 4 is important to note that
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Chapter 4 Summary the complementati
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Chapter 4 The other aspect of this
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Chapter 4 caused due to lack of exp
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Chapter 4 structures were not expec
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Chapter 4 Name Construct Blue -Cpn6
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Chapter 5 Background As discussed i
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Chapter 5 macromolecules at equilib
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Chapter 5 5.1 Purification of JNL 5
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Chapter 5 (a) 1 2 3 4 5 6 7 8 9 10
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Chapter 5 (a) A B C D E (b) 1 2 3 4
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Chapter 5 5.2 AUC analysis of JNL U
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Chapter 5 (a) 1 JNL in Buffer 5 0.9
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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: Cehovin, A., A. R. Coates, Y. Hu, Y
Page 273 and 274: Fux, C. A., J. W. Costerton, P. S.
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
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