Analysis of peptides and proteins in their binding to GroEL

Journal of Peptide Science

Volumn 16, Issue 12, 2010, Pages 693-700

  Li, Yali ^a   Zheng, Zhida ^a   Ramsey, Andrew ^a   Chen, Lingling ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

GroEL; ITC; Molecular chaperon; Peptide; Substrate folding

Indexed keywords

ALPHA LACTALBUMIN; CHAPERONIN; MALATE DEHYDROGENASE; PEPTIDE; PEPTIDE SBP; POLYPEPTIDE; THIOSULFATE SULFURTRANSFERASE; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; BINDING SITE; ENZYME BINDING; HYDROPHOBIC INTERACTION CHROMATOGRAPHY; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN INTERACTION; THERMODYNAMICS;

AMINO ACID SEQUENCE; BINDING SITES; CALORIMETRY; CHAPERONIN 60; PEPTIDES; PROTEIN BINDING; PROTEINS; THERMODYNAMICS;

EID: 78649602176     PISSN: 10752617     EISSN: 10991387     Source Type: Journal    
DOI: 10.1002/psc.1288     Document Type: Article

References (51)

1. Saibil HR, Ranson NA. The chaperonin folding machine. Trends Biochem. Sci. 2002; 27(12): 627-632.
2. Thirumalai D, Lorimer GH. Chaperonin-mediated protein folding. Annu. Rev. Biophys. Biomol. Struct. 2001; 30: 245-269.
3. Horovitz A, Willison KR. Allosteric regulation of chaperonins. Curr. Opin. Struct. Biol. 2005; 15(6): 646-651.
4. Sigler PB, Xu Z, Rye HS, Burston SG, Fenton WA, Horwich AL. Structure and function in GroEL-mediated protein folding. Annu. Rev. Biochem. 1998; 67: 581-608.
5. Lin Z, Rye HS. GroEL-mediated protein folding: making the impossible, possible. Crit. Rev. Biochem. Mol. Biol. 2006; 41(4): 211-239.
6. Horwich AL, Farr GW, Fenton WA. GroEL-GroES-mediated protein folding. Chem. Rev. 2006; 106(5): 1917-1930.
7. Hartl FU, Hayer-Hartl M. Molecular chaperones in the cytosol: from nascent chain to folded protein. Science 2002; 295(5561): 1852-1858.
8. Braig K, Adams PD, Brunger AT. Conformational variability in the refined structure of the chaperonin GroEL at 2.8 A resolution. Nat. Struct. Biol. 1995; 2(12): 1083-1094.
9. Braig K, Otwinowski Z, Hegde R, Boisvert DC, Joachimiak A, Horwich AL, Sigler PB. The crystal structure of the bacterial chaperonin GroEL at 2.8 Å. Nature 1994; 371: 578-586.
10. Fenton WA, Kashi Y, Furtak K, Horwich AL. Residues in chaperonin GroEL required for polypeptide binding and release. Nature 1994; 371: 614-619.
11. Buckle AM, Zahn R, Fersht AR. A structural model for GroEL-polypeptide recognition. Proc. Natl. Acad. Sci. U.S.A. 1997; 94(8): 3571-3575.
12. Chen L, Sigler P. Crystal structure of a GroEL/peptide complex: plasticity as a basis for substrate diversity. Cell 1999; 99: 757-768.
13. Wang J, Chen L. Domain motions in GroEL upon binding of an oligopeptide. J. Mol. Biol. 2003; 334: 489-499.
14. Xu Z, Horwich AL, Sigler PB. The crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex. Nature 1997; 388(6644): 741-750.
15. Boisvert DC, Wang J, Otwinowski Z, Horwich AL, Sigler PB. The 2.4 Å crystal structure of the bacterial chaperonin GroEL complexed with ATP gamma S. Nat. Struct. Biol. 1996; 3: 170-177.
16. Roseman AM, Chen S, White H, Braig K, Saibil HR. The chaperonin ATPase cycle: mechanism of allosteric switching and movements of substrate-binding domains in GroEL. Cell 1996; 87(2): 241-251.
17. Ranson NA, Farr GW, Roseman AM, Gowen B, Fenton WA, Horwich AL, Saibil HR. ATP-bound states of GroEL captured by cryo-electron microscopy. Cell 2001; 107(7): 869-879.
18. Viitanen PV, Gatenby AA, Lorimer GH. Purified chaperonin 60 (groEL) interacts with the nonnative states of a multitude of Escherichia coli proteins. Protein Sci. 1992; 1(3): 363-369.
19. Houry WA, Frishman D, Eckerskorn C, Lottspeich F, Hartl FU. Identification of in vivo substrates of the chaperonin GroEL. Nature 1999; 402: 147-154.
20. Kerner MJ, Naylor DJ, Ishihama Y, Maier T, Chang HC, Stines AP, Georgopoulos C, Frishman D, Hayer-Hartl M, Mann M, Hartl FU. Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli. Cell 2005; 122(2): 209-220.
21. Chen S, Roseman AM, Hunter AS, Wood SP, Burston SG, Ranson NA, Clarke AR, Saibil HR. Location of a folding protein and shape changes in GroEL-GroES complexes imaged by cryo-electron microscopy. Nature 1994; 371: 261-264.
22. Thiyagarajan P, Henderson SJ, Joachimiak A. Solution structures of GroEL and its complex with rhodanese from smallangle neutron scattering. Structure 1996; 4: 79-88.
23. Falke S, Tama F, Brooks CL 3rd, Gogol EP, Fisher MT. The 13 angstroms structure of a chaperonin GroEL-protein substrate complex by cryo-electron microscopy. J. Mol. Biol. 2005; 348(1): 219-230.
24. Elad N, Farr GW, Clare DK, Orlova EV, Horwich AL, Saibil HR. Topologies of a substrate protein bound to the chaperonin GroEL. Mol. Cell 2007; 26(3): 415-426.
25. Clare DK, Bakkes PJ, van Heerikhuizen H, van der Vies SM, Saibil HR. Chaperonin complex with a newly folded protein encapsulated in the folding chamber. Nature 2009; 457(7225): 107-110.
26. Farr GW, Furtak K, Rowland MB, Ranson NA, Saibil HR, Kirchhausen T, Horwich AL. Multivalent binding of nonnative substrate proteins by the chaperonin GroEL. Cell 2000; 100(5): 561-573.
27. Kobayashi N, Freund SMV, Chatellier J, Zahn R, Fersht AR. NMR Analysis of the binding of a rhodanese peptide to a minichaperone in solution. J. Mol. Biol. 1999; 292: 181-190.
28. Shewmaker F, Maskos K, Simmerling C, Landry SJ. The disordered mobile loop of GroES folds into a defined beta-hairpin upon binding GroEL. J. Biol. Chem. 2001; 276(33): 31257-31264.
29. Ashcroft AE, Brinker A, Coyle JE, Weber F, Kaiser M, Moroder L, Parsons MR, Jager J, Hartl UF, Hayer-Hartl M, Radford SE. Structural plasticity and noncovalent substrate binding in the GroEL apical domain. A study using electrospay ionization mass spectrometry and fluorescence binding studies. J. Biol. Chem. 2002; 277(36): 33115-33126.
30. Miller DM, Kurzban GP, Mendoza JA, Chirgwin JM, Hardies SC, Horowitz PM. Recombinant bovine rhodanese: purification and comparison with bovine liver rhodanese. Biochim. Biophys. Acta 1992; 1121(3): 286-292.
31. Lanzetta PA, Alvarez LJ, Reinach PS, Candia OA. An improved assay for nanomole amounts of inorganic phosphate. Anal. Biochem. 1979; 100(1): 95-97.
32. Hayer-Hartl MK, Ewbank JJ, Creighton TE, Hartl FU. Conformational specificity of the chaperonin GroEL for the compact folding intermediates of alpha-lactalbumin. Embo. J. 1994; 13(13): 3192-3202.
33. Robinson CV, Gross M, Eyles SJ, Ewbank JJ, Mayhew M, Hartl FU, Dobson CM, Radford SE. Conformation of GroEL-bound alpha-lactalbumin probed by mass spectrometry. Nature 1994; 372(6507): 646-651.
34. Okazaki A, Ikura T, Nikaido K, Kuwajima K. The chaperonin GroEL does not recognize apo-alpha-lactalbumin in the molten globule state. Nat. Struct. Biol. 1994; 1(7): 439-446.
35. Katsumata K, Okazaki A, Kuwajima K. Effect of GroEL on the Re-folding Kinetics of α-Lactalbumin. J. Mol. Biol. 1996; 258: 827-838.
36. Kuwajima K. The molten globule state of alpha-lactalbumin. Faseb J. 1996; 10(1): 102-109.
37. Aoki K, Taguchi H, Shindo Y, Yoshida M, Ogasahara K, Yutani K, Tanaka N. Calorimetric observation of a GroEL-protein binding reaction with little contribution of hydrophobic interaction. J. Biol. Chem. 1997; 272: 32158-32162.
38. Motojima F, Makio T, Aoki K, Makino T, Kuwajima K, Yoshida M. Hydrophilic residues at the apical domain of GroEL contribute to GroES binding but attenuate polypeptide binding. Biochem. Biophys. Res. Commun. 2000; 267: 842-849.
39. Aoki K, Motojima F, Taguchi H, Yomo T, Yoshida M. GroEL binds artificial proteins with random sequences. J. Biol. Chem. 2000; 275(18): 13755-13758.
40. Suzuki M, Ueno T, Iizuka R, Miura T, Zako T, Akahori R, Miyake T, Shimamoto N, Aoki M, Tanii T, Ohdomari I, Funatsu T. Effect of the C-terminal truncation on the functional cycle of chaperonin GroEL: implication that the C-terminal region facilitates the transition from the folding-arrested to the folding-competent state. J. Biol. Chem. 2008; 283(35): 23931-23939.
41. Rye HS, Roseman AM, Chen S, Furtak K, Fenton WA, Saibil HR, Horwich AL. GroEL-GroES cycling: ATP and nonnative polypeptide direct alternation of folding-active rings. Cell 1999; 97(3): 325-338.
42. Martin J, Langer T, Boteva R, Schramel A, Horwich AL, Hartl FU. Chaperonin-mediated protein folding at the surface of groEL through a 'molten globule'-like intermediate. Nature 1991; 352(6330): 36-42.
43. Yifrach O, Horovitz A. Allosteric control by ATP of non-folded protein binding to GroEL. J. Mol. Biol. 1996; 255(3): 356-361.
44. Jackson GS, Staniforth RA, Halsall DJ, Atkinson T, Holbrook JJ, Clarke AR, Burston SG. Binding and hydrolysis of nucleotides in the chaperonin catalytic cycle: implications for the mechanism of assisted protein folding. Biochemistry 1993; 32(10): 2554-2563.
45. Chandrasekhar GN, Tilly K, Woolford C, Hendrix R, Georgopoulos C. Purification and properties of the groES morphogenetic protein of Escherichia coli. J. Biol. Chem. 1986; 261(26): 12414-12419.
46. Ranson NA, Clare DK, Farr GW, Houldershaw D, Horwich AL, Saibil HR. Allosteric signaling of ATP hydrolysis in GroEL-GroES complexes. Nat. Struct. Mol. Biol. 2006; 13(2): 147-152.
47. Spolar RS, Ha JH, Record MT Jr. Hydrophobic effect in protein folding and other noncovalent processes involving proteins. Proc. Natl. Acad. Sci. U.S.A. 1989; 86(21): 8382-8385.
48. Baldwin RL. Temperature dependence of the hydrophobic interaction in protein folding. Proc. Natl. Acad. Sci. U.S.A. 1986; 83(21): 8069-8072.
49. Sturtevant JM. Heat capacity and entropy changes in processes involving proteins. Proc. Natl. Acad. Sci. U.S.A. 1977; 74(6): 2236-2240.
50. Lin Z, Schwartz FP, Eisenstein E. The hydrophobic nature of GroEL-substrate binding. J. Biol. Chem. 1995; 270(3): 1011-1014.
51. Lin Z, Madan D, Rye HS. GroEL stimulates protein folding through forced unfolding. Nat. Struct. Mol. Biol. 2008; 15(3): 303-311.