Temperature dependence of protein folding kinetics in living cells

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 44, 2012, Pages 17863-17867

  Guo, Minghao ^a   Xu, Yangfan ^b   Gruebele, Martin ^a,b  

^a University of Illinois at Urbana Champaign   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Activation barrier; Fluorescence microscopy; F rster resonance energy transfer (FRET); Green fluorescent protein (GFP); Thermal denaturation

Indexed keywords

PHOSPHOGLYCERATE KINASE;

ARTICLE; BONE CELL; FLUORESCENCE ANALYSIS; HYDROPHOBICITY; IN VITRO STUDY; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STABILITY; TEMPERATURE SENSITIVITY;

CELL LINE, TUMOR; FLUORESCENCE RESONANCE ENERGY TRANSFER; HUMANS; KINETICS; PHOSPHOGLYCERATE KINASE; PROTEIN FOLDING;

EID: 84868130708     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1201797109     Document Type: Article

References (31)

1. Duan Y, Kollman PA (1998) Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282:740-744.
2. Snow CD, Nguyen H, Pande V, Gruebele M (2002) Absolute comparison of simulated and experimental protein folding dynamics. Nature 420:102-106.
3. Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) How fast-folding proteins fold. Science 334:517-520.
4. van den Berg B, Wain R, Dobson CM, Ellis RJ (2000) Macromolecular crowding perturbs protein refolding kinetics; implications for folding inside the cell. EMBO J 19:3870-3875.
5. Homouz D, Stagg L, Wittung-Stafshede P, Cheung MS (2009) Macromolecular crowding modulates folding mechanism of alpha/beta protein apoflavodoxin. Biophys J 96:671-680.
6. Dhar A, et al. (2010) Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding. Proc Natl Acad Sci USA 107:17586-17591.
7. Dhar A, Ebbinghaus S, Shen Z, Mishra T, Gruebele M (2010) The diffusion coefficient for PGK folding in eukaryotic cells. Biophys J 99:L69-L71.
8. Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG (1995) Funnels, pathways, and the energy landscape of protein folding: A synthesis. Protein Struct Funct Gene 21:167-195.
9. Ebbinghaus S, Gruebele M (2011) Protein folding landscapes in the living cell. J Phys Chem Lett 2:314-319.
10. Ebbinghaus S, Dhar A, McDonald JD, Gruebele M (2010) Protein folding stability and dynamics imaged in a living cell. Nat Methods 7:319-323.
11. Dhar A, et al. (2011) Protein stability and folding kinetics in the nucleus and endoplasmic reticulum of eucaryotic cells. Biophys J 101:421-430.
12. Sabelko J, Ervin J, Gruebele M (1999) Observation of strange kinetics in protein folding. Proc Nat Acad Sci USA 96:6031-6036.
13. Osvath S, Herenyi L, Zavodszky P, Fidy J, Kohler G (2006) Hierarchic finite level energy landscape model-To describe the refolding kinetics of phosphoglycerate kinase. J Biol Chem 281:24375-24380.
14. Osváth S, Sabelko J, Gruebele M (2003) Tuning the heterogeneous early folding dynamics of phosphoglycerate kinase. J Mol Biol 333:187-199.
15. Fersht AR (1999) Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding (W.H. Freeman, New York).
16. Mukherjee S, Waegele MM, Chowdhury P, Guo L, Gai F (2009) Effect of macromolecular crowding on protein folding dynamics at the secondary structure level. J Mol Biol 393:227-236.
17. Verkman AS (2002) Solute and macromolecule diffusion in cellular aqueous compartments. Trends Biochem Sci 27:27-33.
18. Minton AP (2005) Influence of macromolecular crowding upon the stability and state of association of proteins: Predictions and observations. J Pharmceut Sci 94:1668-1675.
19. Dedmon MM, Patel CN, Young GB, Pielak GJ (2002) FlgM gains structure in living cells. Proc Nat Acad Sci USA 99:12681-12684.
20. Cheung MS, Klimov D, Thirumalai D (2005) Molecular crowding enhances native state stability and refolding rates of globular proteins. Proc Nat Acad Sci USA 102:4753-4758.
21. Qin SB, Zhou H-X (2009) Atomistic modeling of macromolecular crowding predicts modest increases in protein folding and binding stability. Biophys J 97:12-19.
22. Miklos AC, Sarkar M, Wang YQ, Pielak GJ (2011) Protein crowding tunes protein stability. J Am Chem Soc 133:7116-7120.
23. Ando T, Skolnick J (2010) Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion. Proc Nat Acad Sci USA 107:18457-18462.
24. Cellmer T, Henry ER, Hofrichter J, Eaton WA (2008) Measuring internal friction of an ultrafast-folding protein. Proc Nat Acad Sci USA 105:18320-18325.
25. Ebbinghaus S, et al. (2007) An extended dynamical hydration shell around proteins. Proc Nat Acad Sci USA 104:20749-20752.
26. Liu F, Gruebele M (2009) The transition state transit time of WW domain folding is controlled by energy landscape roughness. J Chem Phys 131:195101.
27. Fan L, et al. (2008) XPD helicase structures and activities: Insights into the cancer and aging phenotypes from XPD mutations. Cell 133:789-800.
28. Dhar A, Gruebele M (2011) Fast relaxation imaging in living cells. Curr Protoc Prot Sci 28.1.1-28.2.19 Unit 28.1.
29. Ghaemmaghami S, et al. (2003) Global analysis of protein expression in yeast. Nature 425:737-741.
30. Privalov PL, Gill SJ (1988) Stability of protein structure and hydrophobic interaction. Adv Protein Chem 39:191-234.
31. Girdhar K, Scott G, Chemla YR, GruebeleM(2011) Better biomolecule thermodynamics from kinetics. J Chem Phys 135:015102.