How evolutionary pressure against protein aggregation shaped chaperone specificity

Journal of Molecular Biology

Volumn 355, Issue 5, 2006, Pages 1037-1047

  Rousseau, Frederic ^a   Serrano, Luis ^b   Schymkowitz, Joost W H ^a  

^a DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

Chaperone; Cross beta; Gatekeeper; Protein aggregation; Protein misfolding; Specificity

Indexed keywords

ARGININE; CHAPERONE; GLOBULAR PROTEIN; LYSINE; PROLINE; PROTEOME;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; HYDROPHOBICITY; MOLECULAR EVOLUTION; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN FUNCTION;

PYRONIA TITHONUS;

EID: 29444444251     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.11.035     Document Type: Article

References (42)

1. C.M. Dobson Protein-misfolding diseases: getting out of shape Nature 418 2002 729 730
2. J.C. Young, V.R. Agashe, K. Siegers, and F.U. Hartl Pathways of chaperone-mediated protein folding in the cytosol Nature Rev. Mol. Cell. Biol. 5 2004 781 791
3. A. Mogk, T. Tomoyasu, P. Goloubinoff, S. Rudiger, D. Roder, H. Langen, and B. Bukau Identification of thermolabile Escherichia coli proteins: prevention and reversion of aggregation by DnaK and ClpB EMBO J. 18 1999 6934 6949
4. J. Weibezahn, P. Tessarz, C. Schlieker, R. Zahn, Z. Maglica, and S. Lee Thermotolerance requires refolding of aggregated proteins by substrate translocation through the central pore of ClpB Cell 119 2004 653 665
5. M. Bucciantini, E. Giannoni, F. Chiti, F. Baroni, L. Formigli, and J. Zurdo Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases Nature 416 2002 507 511
6. M. Bucciantini, G. Calloni, F. Chiti, L. Formigli, D. Nosi, C.M. Dobson, and M. Stefani Pre-fibrillar amyloid protein aggregates share common features of cytotoxicity J. Biol. Chem. 279 2004 31374 31382
7. J.M. Barral, S.A. Broadley, G. Schaffar, and F.U. Hartl Roles of molecular chaperones in protein misfolding diseases Semin. Cell Dev. Biol. 15 2004 17 29
8. D.E. Otzen, S. Miron, M. Akke, and M. Oliveberg Transient aggregation and stable dimerization induced by introducing an Alzheimer sequence into a water-soluble protein Biochemistry 43 2004 12964 12978
9. D.E. Otzen, O. Kristensen, and M. Oliveberg Designed protein tetramer zipped together with a hydrophobic Alzheimer homology: a structural clue to amyloid assembly Proc. Natl Acad. Sci. USA 97 2000 9907 9912
10. J.S. Richardson, and D.C. Richardson Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation Proc. Natl Acad. Sci. USA 99 2002 2754 2759
11. A. Korepanova, C. Douglas, and T.M. Logan Glutamine 53 is a gatekeeper residue in the FK506 binding protein J. Mol. Biol. 323 2002 285 296
12. C. Parrini, N. Taddei, M. Ramazzotti, D. Degl'Innocenti, G. Ramponi, C.M. Dobson, and F. Chiti Glycine residues appear to be evolutionarily conserved for their ability to inhibit aggregation Structure (Camb) 13 2005 1143 1151
13. A. Steward, S. Adhya, and J. Clarke Sequence conservation in Ig-like domains: the role of highly conserved proline residues in the fibronectin type III superfamily J. Mol. Biol. 318 2002 935 940
14. A. Erbse, M.P. Mayer, and B. Bukau Mechanism of substrate recognition by Hsp70 chaperones Biochem. Soc. Trans. 32 2004 617 621
15. A.M. Fernandez-Escamilla, F. Rousseau, J. Schymkowitz, and L. Serrano Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins Nature Biotechnol. 22 2004 1302 1306
16. F. Chiti, M. Stefani, N. Taddei, G. Ramponi, and C.M. Dobson Rationalization of the effects of mutations on peptide and protein aggregation rates Nature 424 2003 805 808
17. M.L. de la Paz, and L. Serrano Sequence determinants of amyloid fibril formation Proc. Natl Acad. Sci. USA 101 2004 87 92
18. J.M. Chandonia, N.S. Walker, L. Lo Conte, P. Koehl, M. Levitt, and S.E. Brenner ASTRAL compendium enhancements Nucl. Acids Res. 30 2002 260 263
19. R. Linding, J. Schymkowitz, F. Rousseau, F. Diella, and L. Serrano A comparative study of the relationship between protein structure and beta-aggregation in globular and intrinsically disordered proteins J. Mol. Biol. 342 2004 345 353
20. A.K. Dunker, Z. Obradovic, P. Romero, E.C. Garner, and C.J. Brown Intrinsic protein disorder in complete genomes Genome Inform. Ser. Workshop Genome Inform. 11 2000 161 171
21. P. Tompa Intrinsically unstructured proteins Trends Biochem. Sci. 27 2002 527 533
22. S. Rudiger, J. Schneider-Mergener, and B. Bukau Its substrate specificity characterizes the DnaJ co-chaperone as a scanning factor for the DnaK chaperone EMBO J. 20 2001 1042 1050
23. S. Rudiger, L. Germeroth, J. SchneiderMergener, and B. Bukau Substrate specificity of the DnaK chaperone determined by screening cellulose-bound peptide libraries EMBO J. 16 1997 1501 1507
24. H. Patzelt, S. Rudiger, D. Brehmer, G. Kramer, S. Vorderwulbecke, and E. Schaffitzel Binding specificity of Escherichia coli trigger factor Proc. Natl Acad. Sci. USA 98 2001 14244 14249
25. N.T. Knoblauch, S. Rudiger, H.J. Schonfeld, A.J. Driessen, J. Schneider-Mergener, and B. Bukau Substrate specificity of the SecB chaperone J. Biol. Chem. 274 1999 34219 34225
26. T. Scheibel, T. Weikl, and J. Buchner Two chaperone sites in Hsp90 differing in substrate specificity and ATP dependence Proc. Natl Acad. Sci. USA 95 1998 1495 1499
27. Q. Wang, A.M. Buckle, and A.R. Fersht From minichaperone to GroEL 1: information on GroEL-polypeptide interactions from crystal packing of minichaperones J. Mol. Biol. 304 2000 873 881
28. S. Perrett, R. Zahn, G. Stenberg, and A.R. Fersht Importance of electrostatic interactions in the rapid binding of polypeptides to GroEL J. Mol. Biol. 269 1997 892 901
29. L.S. Itzhaki, D.E. Otzen, and A.R. Fersht Nature and consequences of GroEL-protein interactions Biochemistry 34 1995 14581 14587
30. J. Chatellier, F. Hill, P.A. Lund, and A.R. Fersht In vivo activities of GroEL minichaperones Proc. Natl Acad. Sci. USA 95 1998 9861 9866
31. E. Deuerling, H. Patzelt, S. Vorderwulbecke, T. Rauch, G. Kramer, and E. Schaffitzel Trigger factor and DnaK possess overlapping substrate pools and binding specificities Mol. Microbiol. 47 2003 1317 1328
32. T. Hesterkamp, S. Hauser, H. Lutcke, and B. Bukau Escherichia coli trigger factor is a prolyl isomerase that associates with nascent polypeptide chains Proc. Natl Acad. Sci. USA 93 1996 4437 4441
33. V.N. Uversky Natively unfolded proteins: a point where biology waits for physics Protein Sci. 11 2002 739 756
34. W. Li, L. Jaroszewski, and A. Godzik Tolerating some redundancy significantly speeds up clustering of large protein databases Bioinformatics 18 2002 77 82
35. E. Gasteiger, E. Jung, and A. Bairoch SWISS-PROT: connecting biomolecular knowledge via a protein database Curr. Issues Mol. Biol. 3 2001 47 55
36. L. Lo Conte, B. Ailey, T.J. Hubbard, S.E. Brenner, A.G. Murzin, and C. Chothia SCOP: a structural classification of proteins database Nucl. Acids Res. 28 2000 257 259
37. W. Kabsch, and C. Sander Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 1983 2577 2637
38. C.A. Andersen, A.G. Palmer, S. Brunak, and B. Rost Continuum secondary structure captures protein flexibility Structure (Camb) 10 2002 175 184
39. A. Matouschek, J.T. Kellis Jr, L. Serrano, and A.R. Fersht Mapping the transition state and pathway of protein folding by protein engineering Nature 340 1989 122 126
40. A. Fersht Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding 1999 W. H. Freeman New York
41. K. Nakai, and P. Horton PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization Trends Biochem. Sci. 24 1999 34 35
42. F. Chiti, N. Taddei, F. Baroni, C. Capanni, M. Stefani, G. Ramponi, and C.M. Dobson Kinetic partitioning of protein folding and aggregation Nature Struct. Biol. 9 2002 137 143