In silico chaperonin-like cycle helps folding of proteins for structure prediction

Biophysical Journal

Volumn 94, Issue 7, 2008, Pages 2558-2565

  Furuta, Tadaomi ^a,b,e   Fujitsuka, Yoshimi ^a   Chikenji, George ^a,c   Takada, Shoji ^a,d,e  

^a KOBE UNIVERSITY   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c NAGOYA UNIVERSITY   (Japan)

^d KYOTO UNIVERSITY   (Japan)

^e JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CHAPERONIN; PROTEIN;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; PROTEIN CONFORMATION; PROTEIN FOLDING; ULTRASTRUCTURE;

CHAPERONINS; COMPUTER SIMULATION; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS;

EID: 41649094425     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.107.115261     Document Type: Article

References (43)

1. Sigler, P. B., Z. Xu, H. S. Rye, S. G. Burston, W. A. Fenton, and A. L. Horwich. 1998. Structure and function in GroEL-mediated protein folding. Annu. Rev. Biochem. 67:581-608.
2. Hartl, F. U., and M. Hayer-Hartl. 2002. Molecular chaperones in the cytosol: from nascent chain to folded protein. Science. 295:1852-1858.
3. Braig, K., Z. Otwinowski, R. Hegde, D. C. Boisvert, A. Joachimiak, A. L. Horwich, and P. B. Sigler. 1994. The crystal structure of the bacterial chaperonin GroEL at 2.8 Å. Nature. 371:578-586.
4. Xu, Z., A. L. Horwich, and P. B. Sigler. 1997. The crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex. Nature. 388:741-750.
5. Weissman, J. S., Y. Kashi, W. A. Fenton, and A. L. Horwich. 1994. GroEL-mediated protein folding proceeds by multiple rounds of binding and release of nonnative forms. Cell. 78:693-702.
6. Weissman, J. S., C. M. Hohl, O. Kovalenko, Y. Kashi, S. Chen, K. Braig, H. R. Saibil, W. A. Fenton, and A. L. Horwich. 1995. Mechanism of GroEL action: productive release of polypeptide from a sequestered position under GroES. Cell. 83:577-587.
7. Rye, H. S., S. G. Burston, W. A. Fenton, J. M. Beechem, Z. Xu, P. B. Sigler, and A. L. Horwich. 1997. Distinct actions of cis and trans ATP within the double ring of the chaperonin GroEL. Nature. 388:792-798.
8. Weber, F., F. Keppel, C. Georgopoulos, M. K. Hayer-Hartl, and F. U. Hartl. 1998. The oligomeric structure of GroEL/GroES is required for biologically significant chaperonin function in protein folding. Nat. Struct. Biol. 5:977-985.
9. Eliss, R. J. 1994. Molecular chaperones. Opening and closing the Anfinsen cage. Curr. Biol. 4:633-635.
10. Saibil, H. R., D. Zheng, A. M. Roseman, A. S. Hunter, G. M. Watson, S. Chen, A. auf der Mauer, B. P. O'Hara, S. P. Wood, N. H. Mann, L. K. Barnett, and R. J. Ellis. 1993. ATP induces large quaternary rearrangements in a cage-like chaperonin structure. Curr. Biol. 3:265-273.
11. Todd, M. J., G. H. Lorimer, and D. Thirumalai. 1996. Chaperonin- facilitated protein folding: optimization of rate and yield by an iterative annealing mechanism. Proc. Natl. Acad. Sci. USA. 93:4030-4035.
12. Betancourt, M. R., and D. Thirumalai. 1999. Exploring the kinetic requirements for enhancement of protein folding rates in the GroEL cavity. J. Mol. Biol. 287:627-644.
13. Shtilerman, M., G. H. Lorimer, and S. W. Englander. 1999. Chaperonin function: folding by forced unfolding. Science. 284:822-825.
14. Brinker, A., G. Pfeifer, M. J. Kerner, D. J. Naylor, F. U. Hartl, and M. Hayer-Hartl. 2001. Dual function of protein confinement in chaperonin-assisted protein folding. Cell. 107:223-233.
15. Zhou, H. X., and K. A. Dill. 2001. Stabilization of proteins in confined spaces. Biochemistry. 40:11289-11293.
16. Klimov, D. K., D. Newfield, and D. Thirumalai. 2002. Simulations of β-hairpin folding confined to spherical pores using distributed computing. Proc. Natl. Acad. Sci. USA. 99:8019-8024.
17. Takagi, F., N. Koga, and S. Takada. 2003. How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: molecular simulations. Proc. Natl. Acad. Sci. USA. 100:11367-11372.
18. Tand, Y.-C., H.-C. Chang, A. Roeben, D. Wischnewski, N. Wischnewski, M. J. Kerner, F. U. Hartl, and M. Hayer-Hartl. 2006. Structural features of the GroEL-GroES nano-cage required for rapid folding of encapsulated protein. Cell. 125:903-914.
19. Vincent, J. J., C. H. Tai, B. K. Sathyanarayana, and B. Lee. 2005. Assessment of CASP6 predictions for new and nearly new fold targets. Proteins. 61:67-83.
20. Reference deleted in proof.
21. Aloy, P., A. Stark, C. Hadley, and R. B. Russell. 2003. Predictions without templates: new folds, secondary structure, and contacts in CASP5. Proteins. 53:436-456.
22. Moult, J., K. Fidelis, B. Rost, T. Hubbard, and A. Tramontano. 2005. Critical assessment of methods of protein structure prediction (CASP)-round 6. Proteins. 61:3-7.
23. Moult, J., K. Fidelis, A. Zemla, and T. Hubbard. 2003. Critical assessment of methods of protein structure prediction (CASP)-round V. Proteins. 53:334-339.
24. Simons, K. T., C. Kooperberg, E. Huang, and D. Baker. 1997. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol. 268:209-225.
25. Jones, D. T. 1997. Successful ab initio prediction of the tertiary structure of NK-lysin using multiple sequences and recognized supersecondary structural motifs. Proteins. 29:185-191.
26. Bowie, J. U., and D. Eisenberg. 1994. An evolutionary approach to folding small α-helical proteins that uses sequence information and an empirical guiding fitness function. Proc. Natl. Acad. Sci. USA. 91:4436-4440.
27. Simons, K. T., C. Strauss, and D. Baker. 2001. Prospects for ab initio protein structural genomics. J. Mol. Biol. 306:1191-1199.
28. Jones, D. T. 2001. Predicting novel protein folds by using FRAGFOLD. Proteins. 45:127-132.
29. Chikenji, G., Y. Fujitsuka, and S. Takada. 2003. A reversible fragment assembly method for de novo protein structure prediction. J. Chem. Phys. 119:6895-6903.
30. Fujitsuka, Y., S. Takada, Z. A. Luthey-Schulten, and P. G. Wolynes. 2004. Optimizing physical energy functions for protein folding. Proteins. 54:88-103.
31. Fukunishi, H., O. Watanabe, and S. Takada. 2002. On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: application to protein structure prediction. J. Chem. Phys. 116:9058-9067.
32. Fan, H., and A. E. Mark. 2004. Mimicking the action of folding chaperones in molecular dynamics simulations: application to the refinement of homology-based protein structures. Protein Sci. 13:992-999.
33. Liu, P., X. Huang, R. Zhou, and B. J. Berne. 2006. Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent. J. Phys. Chem. B. 110:19018-19022.
34. Takada, S. 2001. Protein folding simulation with solvent-induced force field: folding pathway ensemble of three-helix-bundle proteins. Proteins. 42:85-98.
35. Bonneau, R., C. E. Strauss, C. A. Rohl, D. Chivian, P. Bradley, L. Malmström, T. Robertson, and D. Baker. 2002. De novo prediction of three-dimensional structures for major protein families. J. Mol. Biol. 322:65-78.
36. Fujitsuka, Y., G. Chikenji, and S. Takada. 2006. SimFold energy function for de novo protein structure prediction: consensus with Rosetta. Proteins. 62:381-398.
37. Kihara, D., H. Lu, A. Kolinski, and J. Skolnick. 2001. TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints. Proc. Natl. Acad. Sci. USA. 98:10125-10130.
38. Zelma, A., C. Venclocas, J. Moult, and K. Fidelis. 2001. Processing and evaluation of predictions in CASP4. Proteins. 45:13-21.
39. Murzin, A. G., S. E. Brenner, T. Hubbard, and C. Chothia. 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:536-540.
40. Reference deleted in proof.
41. Plaxco, K. W., K. T. Simons, and D. Baker. 1998. Contact order, transition state placement, and the refolding rates of single domain proteins. J. Mol. Biol. 277:985-994.
42. Reference deleted in proof.
43. DeLano, W. L. 2002. The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA.