Inside the chaperonin toolbox: Theoretical and computational models for chaperonin mechanism

Physical Biology

Volumn 6, Issue 1, 2009, Pages

  Lucent, Del ^a   England, Jeremy ^a   Pande, Vijay ^a,b,c  

^a STANFORD UNIVERSITY   (United States)

^b Departments of Chemistry and Structural Biology   (United States)

^c STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHAPERONIN; PROTEIN;

ARTICLE; CONTROLLED STUDY; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN MICROARRAY; SIMULATION; THEORETICAL MODEL; ANIMAL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; HUMAN; METABOLISM; PROTEIN CONFORMATION; REVIEW;

ANIMALS; CHAPERONINS; COMPUTER SIMULATION; HUMANS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS;

EID: 62449109092     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/6/1/015003     Document Type: Article

References (61)

1. Fenton W A and Horwich A L 2003 Chaperonin-mediated protein folding: Fate of substrate polypeptide Q. Rev. Biophys. 36 229-56 (Pubitemid 37493574)
2. Hartl F U and Hayer-Hartl M 2002 Molecular chaperones in the cytosol: From nascent chain to folded protein Science 295 1852-8
3. Lin Z and Rye H S 2006 Groel-mediated protein folding: Making the impossible, possible Crit. Rev. Biochem. Mol. Biol. 41 211-39 (Pubitemid 44100582)
4. Spiess C, Meyer A S, Reissmann S and Frydman J 2004 Mechanism of the eukaryotic chaperonin: Protein folding in the chamber of secrets Trends Cell Biol. 14 598-604 (Pubitemid 39440608)
5. Kerner M J et al 2005 Proteome-wide analysis of chaperonin-dependent protein folding in escherichia coli Cell 122 209-20 (Pubitemid 41032985)
6. Ellis R J 1994 Molecular chaperones. Opening and closing the anfinsen cage Curr. Biol. 4 633-5 (Pubitemid 2111018)
7. Weissman J S, Kashi Y, Fenton W A and Horwich A L 1994 Groel-mediated protein folding proceeds by multiple rounds of binding and release of nonnative forms Cell 78 693-702 (Pubitemid 24268591)
8. Brinker A, Pfeifer G, Kerner M J, Naylor D J, Hartl F U and Hayer-Hartl M 2001 Dual function of protein confinement in chaperonin-assisted protein folding Cell 107 223-33 (Pubitemid 33035948)
9. Farr G W, Furtak K, Rowland M B, Ranson N A, Saibil H R, Kirchhausen T and Horwich A L 2000 Multivalent binding of nonnative substrate proteins by the chaperonin groel Cell 100 561-73
10. Fenton W A, Kashi Y, Furtak K and Horwich A L 1994 Residues in chaperonin groel required for polypeptide binding and release Nature 371 614-9 (Pubitemid 24315744)
11. Gulukota K and Wolynes P G 1994 Statistical mechanics of kinetic proofreading in protein folding in vivo Proc. Natl. Acad. Sci. USA 91 9292-6 (Pubitemid 24297900)
12. Todd M J, Lorimer G H and Thirumalai D 1996 Chaperonin-facilitated protein folding: Optimization of rate and yield by an iterative annealing mechanism Proc. Natl. Acad. Sci. USA 93 4030-5 (Pubitemid 26144240)
13. Dill K A, Bromberg S, Yue K, Fiebig K M, Yee D P, Thomas P D and Chan H S 1995 Principles of protein folding-a perspective from simple exact models Protein Sci. 4 561-602
14. Betancourt M R and Thirumalai D 1999 Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes Protein Sci. 8 361-9 (Pubitemid 29072436)
15. Chan H S and Dill K A 1996 A simple model of chaperonin-mediated protein folding Proteins: Structure, Function, and Genetics 24 345-51 (Pubitemid 26095966)
16. Sfatos C D, Gutin A M, Abkevich V I and Shakhnovich E I 1996 Simulations of chaperone-assisted folding Biochemistry 35 334-9 (Pubitemid 26036439)
17. Betancourt M R and Thirumalai D 1999 Exploring the kinetic requirements for enhancement of protein folding rates in the groel cavity J. Mol. Biol. 287 627-44 (Pubitemid 29168438)
18. Baumketner A, Jewett A and Shea J E 2003 Effects of confinement in chaperonin assisted protein folding: Rate enhancement by decreasing the roughness of the folding energy landscape J. Mol. Biol. 332 701-13 (Pubitemid 37075991)
19. Jewett A I, Baumketner A and Shea J E 2004 Accelerated folding in the weak hydrophobic environment of a chaperonin cavity: creation of an alternate fast folding pathway Proc. Natl. Acad. Sci. USA 101 13192-7 (Pubitemid 39209641)
20. Jewett A I and Shea J E 2006 Folding on the chaperone: yield enhancement through loose binding J. Mol. Biol. 363 945-57 (Pubitemid 44573225)
21. Cheung M S and Thirumalai D 2006 Nanopore-protein interactions dramatically alter stability and yield of the native state in restricted spaces J. Mol. Biol. 357 632-43 (Pubitemid 43290761)
22. Tehver R and Thirumalai D 2008 Kinetic model for the coupling between allosteric transitions in groel and substrate protein folding and aggregation J. Mol. Biol. 377 1279-95
23. Jewett A I and Shea J E 2008 Do chaperonins boost protein yields by accelerating folding or preventing aggregation? Biophys. J. 94 2987-93
24. Genevaux P, Keppel F, Schwager F, Langendijk-Genevaux P S, Hartl F U and Georgopoulos C 2004 In vivo analysis of the overlapping functions of dnak and trigger factor EMBO Rep. 5 195-200 (Pubitemid 38401201)
25. Lin Z and Rye H S 2004 Expansion and compression of a protein folding intermediate by groel Mol. Cell 16 23-34 (Pubitemid 39330149)
26. Tang Y C, Chang H C, Roeben A, Wischnewski D, Wischnewski N, Kerner M J, Hartl F U and Hayer-Hartl M 2006 Structural features of the groel-groes nano-cage required for rapid folding of encapsulated protein Cell 125 903-14 (Pubitemid 43795198)
27. Zhou H X and Dill K A 2001 Stabilization of proteins in confined spaces Biochemistry 40 11289-93 (Pubitemid 32911271)
28. Klimov D K, Newfield D and Thirumalai D 2002 Simulations of beta-hairpin folding confined to spherical pores using distributed computing Proc. Natl. Acad. Sci. USA 99 8019-24 (Pubitemid 34650998)
29. Takagi F, Koga N and Takada S 2003 How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: molecular simulations Proc. Natl. Acad. Sci. USA 100 11367-72 (Pubitemid 37205941)
30. Rathore N, Knotts T A t and de Pablo J J 2006 Confinement effects on the thermodynamics of protein folding: Monte Carlo simulations Biophys. J. 90 1767-73
31. Cheung M S, Klimov D and Thirumalai D 2005 Molecular crowding enhances native state stability and refolding rates of globular proteins Proc. Natl. Acad. Sci. USA 102 4753-8 (Pubitemid 40471526)
32. Zhang S Q and Cheung M S 2007 Manipulating biopolymer dynamics by anisotropic nanoconfinement Nano Lett. 7 3438-42 (Pubitemid 350216043)
33. Eggers D K and Valentine J S 2001 Molecular confinement influences protein structure and enhances thermal protein stability Protein Sci. 10 250-61 (Pubitemid 32229119)
34. Farr G W, Fenton W A and Horwich A L 2007 Perturbed atpase activity and not 'Close confinement' Of substrate in the cis cavity affects rates of folding by tail-multiplied groel Proc. Natl. Acad. Sci. USA 104 5342-7 (Pubitemid 47175682)
35. Chandler D 2005 Interfaces and the driving force of hydrophobic assembly Nature 437 640-7 (Pubitemid 41486526)
36. Nymeyer H and Garcia A E 2003 Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized born approximation with explicit solvent Proc. Natl. Acad. Sci. 100 13934-9 (Pubitemid 37499169)
37. Rhee Y M, Sorin E J, Jayachandran G, Lindahl E and Pande V S 2004 Simulations of the role of water in the protein-folding mechanism Proc. Natl. Acad. Sci. USA 101 6456-61 (Pubitemid 38585995)
38. Ruhong Z 2003 Free energy landscape of protein folding in water: explicit vs. Implicit solvent Proteins: Struct. Funct. Genet. 53 148-61 (Pubitemid 37193811)
39. Sorin E J, Rhee Y M, Shirts M R and Pande V S 2006 The solvation interface is a determining factor in peptide conformational preferences J. Mol. Biol. 356 248-56 (Pubitemid 43069740)
40. Hummer G, Rasaiah J C and Noworyta J P 2001 Water conduction through the hydrophobic channel of a carbon nanotube Nature 414 188-90 (Pubitemid 33051229)
41. Mashl R J, Joseph S, Aluru N R and Jakobsson E 2003 Anomalously immobilized water: A new water phase issue by confinement in nanotubes Nano Lett. 3 589-592 (Pubitemid 37140620)
42. Singh S, Houston J, van Swol F and Brinker C J 2006 Superhydrophobicity: drying transition of confined water Nature 442 526 (Pubitemid 44167905)
43. Sorin E J and Pande V S 2006 Nanotube confinement denatures protein helices J. Am. Chem. Soc. 128 6316-7 (Pubitemid 43727259)
44. Ziv G, Haran G and Thirumalai D 2005 Ribosome exit tunnel can entropically stabilize alpha-helices Proc. Natl. Acad. Sci. USA 102 18956-61 (Pubitemid 43049548)
45. Lucent D, Vishal V and Pande V S 2007 Protein folding under confinement: a role for solvent Proc. Natl. Acad. Sci. USA 104 10430-4 (Pubitemid 47185682)
46. Wang J D, Herman C, Tipton K A, Gross C A and Weissman J S 2002 Directed evolution of substrate-optimized groel/s chaperonins Cell 111 1027-39 (Pubitemid 36044693)
47. Machida K, Kono-Okada A, Hongo K, Mizobata T and Kawata Y 2008 Hydrophilic residues 526kndaad531 in the flexible c-terminal region of the chaperonin groel are critical for substrate protein folding within the central cavity J. Biol. Chem. 283 6886-96
48. Bulone D, Martorana V, San Biagio P L and Palma-Vittorelli M B 1997 Effects of electric charges on hydrophobic forces Phys. Rev. E 56 R4939
49. Bulone D, Martorana V V, San Biagio P L and Palma-Vittorelli M B 2000 Effects of electric charges on hydrophobic forces: II Phys. Rev. E 62 6799-809
50. Dzubiella J and Hansen J P 2003 Reduction of the hydrophobic attraction between charged solutes in water J. Chem. Phys. 119 12049-52
51. Dzubiella J and Hansen J P 2004 Competition of hydrophobic and coulombic interactions between nanosized solutes J. Chem. Phys. 121 5514-30
52. Weixin X and Yuguang M 2008 Polar confinement modulates solvation behavior of methane molecules J. Chem. Phys. 128 234506
53. England J, Lucent D and Pande V 2008 Rattling the cage: computational models of chaperonin-mediated protein folding Curr. Opin. Struct. Biol. 18 163-9
54. England J and Pande V 2008 Biophys. J. in press
55. England J, Lucent D and Pande V 2008 J. Am. Chem. Soc. in press
56. Jacob E, Horovitz A and Unger R 2007 Different mechanistic requirements for prokaryotic and eukaryotic chaperonins: a lattice study Bioinformatics 23 i240-248 (Pubitemid 47244406)
57. Fan H and Mark A E 2006 Mimicking the action of groel in molecular dynamics simulations: application to the refinement of protein structures Protein Sci. 15 441-8 (Pubitemid 43306238)
58. Furuta T, Fujitsuka Y, Chikenji G and Takada S 2008 In silico chaperonin-like cycle helps folding of proteins for structure prediction Biophys. J. 94 2558-65
59. Kyte J and Doolittle R F 1982 A simple method for displaying the hydropathic character of a protein J. Mol. Biol. 157 105-32
60. Chaudhry C, Farr G W, Todd M J, Rye H S, Brunger A T, Adams P D, Horwich A L and Sigler P B 2003 Role of the gamma-phosphate of atp in triggering protein folding by groel-groes: Function, structure and energetics Embo J. 22 4877-87 (Pubitemid 37222010)
61. Shilton B H, Shuman H A and Mowbray S L 1996 Crystal structures and solution conformations of a dominant-negative mutant of escherichia coli maltose-binding protein J. Mol. Biol. 264 364-76 (Pubitemid 26402703)