Nanopore-protein interactions dramatically alter stability and yield of the native state in restricted spaces

Journal of Molecular Biology

Volumn 357, Issue 2, 2006, Pages 632-643

  Cheung, Margaret S ^a   Thirumalai, D ^a  

^a Bldg 142   (United States)

Author keywords

Chaperonins; Folding in confined spaces; Folding kinetics; Macromolecular crowding; Nanopore protein interactions

Indexed keywords

ADENOSINE TRIPHOSPHATE; CHAPERONIN; PROTEIN;

ALLOSTERISM; AMINO ACID SEQUENCE; ARTICLE; EXPERIMENTATION; HYDROPHILICITY; HYDROPHOBICITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STABILITY; TEMPERATURE;

EID: 33344476423     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.12.048     Document Type: Article

References (46)

1. R.J. Ellis, and A.P. Minton Join the crowd Nature 425 2003 27 28
2. R.J. Ellis Macromolecular crowding: obvious but underappreciated Trends Biochem. Sci. 26 2001 597 604
3. S.B. Zimmerman, and A.P. Minton Macromolecular crowding: biochemical, biophysical, and physiological consequences Annu. Rev. Biophys. Biomol. Struct. 22 1993 27 65
4. H.X. Zhou, and K.A. Dill Stabilization of proteins in confined spaces Biochemistry 40 2001 11289 11293
5. M.M. Dedmon, C.N. Patel, G.B. Young, and G.J. Pielak FlgM gains structure in living cells Proc. Natl Acad. Sci. USA 99 2002 12681 12684
6. A.P. Minton Models for excluded volume interaction between an unfolded protein and rigid macromolecular cosolutes: macromolecular crowding and protein stability revisited Biophys. J. 88 2005 971 985
7. P. Nissen, H. Hansen, N. Ban, and P.B. Moore The structural basis of ribosome activity in peptide bond synthesis Science 289 2000 920 930
8. D.K. Klimov, D. Newfield, and D. Thirumalai Simulations of beta-hairpin folding confined to spherical pores using distributed computing Proc. Natl Acad. Sci. USA 99 2002 8019 8024
9. D. Thirumalai, and G.H. Lorimer Chaperonin-mediated protein folding Annu. Rev. Biophys. Biomol. Struct. 30 2003 245 269
10. F.U. Hartl Molecular chaperones in cellular protein folding Nature 381 1996 571 580
11. Z. Xu, and P.B. Sigler GroEL/GroES: structure and function of a two-stroke folding machine J. Struct. Biol. 124 1998 129 141
12. H.R. Saibil, and N.A. Ranson The chaperonin folding machine Trends Biochem. Sci. 27 2002 627 632
13. W.A. Fenton, and A.L. Horwich Chaperonin-mediated protein folding: fate of substrate polypeptide Quart. Rev. Biophys. 121 2003 229 256
14. R.J. Ellis Protein folding: importance of the anfinsen cage Curr. Biol. 13 2003 R881 R883
15. M.J. Todd, G.H. Lorimer, and D. Thirumalai Chaperonin-facilitated protein folding: optimization of rate and yield by an iterative annealing mechanism Proc. Natl Acad. Sci. USA 93 1996 4030 4035
16. D.K. Eggers, and J.S. Valentine Crowding and hydration effects on protein conformation: a study with sol-gel encapsulated proteins J. Mol. Biol. 314 2001 911 922
17. R. Ravindra, S. Zhao, H. Gies, and R. Winter Protein encapsulation in mesoporous silicate: the effects of confinement on protein stability, hydration, and volumetric properties J. Am. Chem. Soc. 126 2004 12224 12225
18. B. Campanini, S. Bologna, F. Cannone, G. Chirico, A. Mozzarelli, and S. Bettati Unfolding of green fluorescent protein mut2 in wet nanoporous silica gels Protein Sci. 14 2005 1125 1133
19. D. Bolis, A.S. Politou, G. Kelly, A. Pastore, and P.A. Temussi Protein stability in nanocages: a novel approach for influencing protein stability by molecular confinement J. Mol. Biol. 336 2004 203 212
20. B. van den Berg, R. Wain, C.M. Dobson, and R.J. Ellis Macromolecular crowding perturbs protein refolding kinetics: implications for folding inside the cell EMBO J. 19 2000 3870 3875
21. K. Sasahara, P. McPhie, and A.P. Minton Effect of dextran on protein stability and conformation attributed to macromolecular crowding J. Mol. Biol. 326 2003 1227 1237
22. N. Tokuriki, M. Kinjo, S. Negi, M. Hoshino, Y. Goto, I. Urabe, and T. Yomo Protein folding by the effects of macromolecular crowding Protein Sci. 13 2004 125 133
23. M.S. Cheung, D. Klimov, and D. Thirumalai Molecular crowding enhances native state stability and refolding rates Proc. Natl Acad. Sci. USA 102 2005 4753 4758
24. M.R. Betancourt, and D. Thirumalai Exploring the kinetic requirements for enhancement of protein folding rates in the GroEL cavity J. Mol. Biol. 287 1999 627 644
25. F. Takagi, N. Koga, and S. Takada How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: molecular simulations Proc. Natl Acad. Sci. USA 100 2003 11367 11372
26. M. Friedel, D.J. Sheeler, and J.-E. Shea Effects of confinement and crowding on the thermodynamics and kinetics of folding of a minimalist beta-barrel protein J. Chem. Phys. 118 2003 8106 8113
27. A.I. Jewett, A. Baumketner, and J.E. Shea Accelerated folding in the weak hydrophobic environment of a chaperonin cavity: creation of an alternate fast folding pathway Proc. Natl Acad. Sci. USA 101 2004 13192 13197
28. W.-X. Xu, J. Wang, and W. Wang Folding behavior of chaperonin-mediated substrate protein Proteins: Struct. Funct. Genet. 61 2005 774 794
29. A. Brinker, G. Pfeifer, M.J. Kerner, D.J. Naylor, F.U. Hartl, and M. Hayer-Hartl Dual function of protein confinement in chaperonin-assisted protein folding Cell 107 2001 223 233
30. H.S. Chan, and K.A. Dill A simple model of chaperonin-mediated protein folding Proteins: Struct. Funct. Genet. 24 1996 345 351
31. T.E. Gray, J. Eder, M. Bycroft, A.G. Day, and A.R. Fersht Refolding of barnase mutants and pro-barnase in the presence and absence of GroEL EMBO J. 12 1993 4145 4150
32. M. Jager, H. Nguyen, J.C. Crane, J.W. Kelly, and M. Gruebele The folding mechanism of a beta-sheet: the WW domain J. Mol. Biol. 311 2001 373 393
33. H. Orland, and D. Thirumalai A kinetic model for chaperonin assisted folding of protein J. Physique I 7 1997 553 560
34. J.C. Crane, E.K. Koepf, J.W. Kelly, and M. Gruebele Mapping the transition state of WW domain β-sheet J. Mol. Biol. 298 2000 283 292
35. S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucl. Acids Res. 25 1997 3389 3402
36. Z. Xu, A.L. Horwich, and P.B. Sigler The crystal stucture of the asymmetric groEL-groES-(ADP)7 chaperonin complex Nature 388 1997 741 750
37. E. Rhoades, E. Gussakovsky, and G. Haran Watching proteins fold one molecule at a time Proc. Natl Acad. Sci. USA 100 2003 3197 3202
38. C.R. Babu, V.J. Hilser, and A.J. Wand Direct access to the cooperative substructure of proteins and the protein ensemble via cold denaturation Nature Struct. Mol. Biol. 11 2004 352 357
39. R.W Peterson, K. Anbalagan, C. Tommos, and A.J. Wand Forced folding and structural analysis of metastable proteins J. Am. Chem. Soc. 126 2004 9498 9499
40. D.K. Klimov, and D. Thirumalai Mechanisms and kinetics of beta-hairpin formation Proc. Natl Acad. Sci. USA 97 2000 2544 2549
41. M.S. Cheung, J.M. Finke, B. Callahan, and J.N. Onuchic Exploring the interplay of topology and secondary structural formation in the protein folding problem J. Phys. Chem. B 107 2003 11193 11200
42. M.R. Betancourt, and D. Thirumalai Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes Protein Sci. 8 1999 361 369
43. K.Y. Sanbonmatsu, and A.E. Garcia Structure of Met-Enkephalin in explicit aqueous solution using replica exchange molecular dynamics Proteins: Struct. Funct. Genet. 46 2002 225 234
44. Y. Sugita, and Y. Okamoto Replica-exchange molecular dynamics methods for protein folding Chem. Phys. Letters 314 1999 141 151
45. J.D. Honeycutt, and D. Thirumalai The nature of folded states of globular proteins Biopolymers 32 1992 695 709
46. C.J. Camacho, and D. Thirumalai Kinetics and thermodynamics of folding in model proteins Proc. Natl Acad. Sci. USA 90 1993 6369 6372