Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts

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

Volumn 111, Issue 12, 2014, Pages 4449-4454

  Liu, Yu ^a   Tan, Yun Lei ^a   Zhang, Xin ^a   Bhabha, Gira ^b   Ekiert, Damian C ^b   Genereux, Joseph C ^a   Cho, Younhee ^a   Kipnis, Yakov ^c   Bjelic, Sinisa ^c   Baker, David ^c   Kelly, Jeffery W ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

Chemical probes; Fluorescence labeling; Pharmacologic chaperone

Indexed keywords

ADENOSINE TRIPHOSPHATE; CHAPERONE; CHAPERONIN; CHAPERONIN HOLDASE; PREALBUMIN; PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; CELL LYSATE; CYTOLYSIS; ENZYME ACTIVITY; FLUORESCENCE; MOLECULAR PROBE; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN HOMEOSTASIS;

CHEMICAL PROBES; FLUORESCENCE LABELING; PHARMACOLOGIC CHAPERONE;

ADENOSINE TRIPHOSPHATE; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; FLUORESCENT DYES; PROTEIN FOLDING;

EID: 84896923527     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1323268111     Document Type: Article

References (31)

1. Hartl FU, Hayer-Hartl M (2002) Molecular chaperones in the cytosol: From nascent chain to folded protein. Science 295(5561):1852-1858. (Pubitemid 34214115)
2. Kim YE, Hipp MS, Bracher A, Hayer-Hartl M, Hartl FU (2013) Molecular chaperone functions in protein folding and proteostasis. Annu Rev Biochem 82(2013):323-355.
3. Balch WE, Morimoto RI, Dillin A, Kelly JW (2008) Adapting proteostasis for disease intervention. Science 319(5865):916-919. (Pubitemid 351263754)
4. Chen B, Retzlaff M, Roos T, Frydman J (2011) Cellular strategies of protein quality control. Cold Spring Harb Perspect Biol 3(8):a004374.
5. Ebbinghaus S, Dhar A, McDonald JD, Gruebele M (2010) Protein folding stability and dynamics imaged in a living cell. Nat Methods 7(4):319-323.
6. Scheck RA, Schepartz A (2011) Surveying protein structure and function using bisarsenical small molecules. Acc Chem Res 44(9):654-665.
7. Ignatova Z, Gierasch LM (2004) Monitoring protein stability and aggregation in vivo by real-time fluorescent labeling. Proc Natl Acad Sci USA 101(2):523-528. (Pubitemid 38084669)
8. Griffin BA, Adams SR, Tsien RY (1998) Specific covalent labeling of recombinant protein molecules inside live cells. Science 281(5374):269-272. (Pubitemid 28334512)
9. Myung N, et al. (2013) Bifunctional coumarin derivatives that inhibit transthyretin amyloidogenesis and serve as fluorescent transthyretin folding sensors. Chem Commun (Camb) 49(80):9188-9190.
10. Cravatt BF, Wright AT, Kozarich JW (2008) Activity-based protein profiling: From enzyme chemistry to proteomic chemistry. Annu Rev Biochem 77:383-414.
11. Jiang L, et al. (2008) De novo computational design of retro-aldol enzymes. Science 319(5868):1387-1391. (Pubitemid 351354873)
12. Jing C, Cornish VW (2011) Chemical tags for labeling proteins inside living cells. Acc Chem Res 44(9):784-792.
13. Suh EH, et al. (2013) Stilbene vinyl sulfonamides as fluorogenic sensors of and traceless covalent kinetic stabilizers of transthyretin that prevent amyloidogenesis. J Am Chem Soc 135(47):17869-17880.
14. Bjelic S, et al. (2014) Exploration of alternate catalytic mechanisms and optimization strategies for retroaldolase design. J Mol Biol 426(1):256-271.
15. Nagano N, Orengo CA, Thornton JM (2002) One fold with many functions: The evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J Mol Biol 321(5):741-765.
16. Lassila JK, Baker D, Herschlag D (2010) Origins of catalysis by computationally designed retroaldolase enzymes. Proc Natl Acad Sci USA 107(11):4937-4942.
17. Heine A, Luz JG, Wong CH, Wilson IA (2004) Analysis of the class I aldolase binding site architecture based on the crystal structure of 2-deoxyribose-5-phosphate aldolase at 0.99A resolution. J Mol Biol 343(4):1019-1034. (Pubitemid 39345961)
18. Sekijima Y, et al. (2005) The biological and chemical basis for tissue-selective amyloid disease. Cell 121(1):73-85.
19. Banaszynski LA, Chen LC, Maynard-Smith LA, Ooi AG, Wandless TJ (2006) A rapid, reversible, and tunable method to regulate protein function in living cells using synthetic small molecules. Cell 126(5):995-1004. (Pubitemid 44310772)
20. Yu ZQ, Sawkar AR, Kelly JW (2007) Pharmacologic chaperoning as a strategy to treat Gaucher disease. FEBS J 274(19):4944-4950. (Pubitemid 47481193)
21. Kerner MJ, et al. (2005) Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli. Cell 122(2):209-220. (Pubitemid 41032985)
22. Teter SA, et al. (1999) Polypeptide flux through bacterial Hsp70: DnaK cooperates with trigger factor in chaperoning nascent chains. Cell 97(6):755-765. (Pubitemid 29278049)
23. Schröder H, Langer T, Hartl FU, Bukau B (1993) DnaK, DnaJ and GrpE form a cellular chaperone machinery capable of repairing heat-induced protein damage. EMBO J 12(11):4137-4144. (Pubitemid 23302027)
24. Rüdiger S, Buchberger A, Bukau B (1997) Interaction of Hsp70 chaperones with substrates. Nat Struct Biol 4(5):342-349. (Pubitemid 27190834)
25. Martin J, et al. (1991) Chaperonin-mediated protein folding at the surface of groEL through a 'molten globule'-like intermediate. Nature 352(6330):36-42. (Pubitemid 21896688)
26. Chang L, Thompson AD, Ung P, Carlson HA, Gestwicki JE (2010) Mutagenesis reveals the complex relationships between ATPase rate and the chaperone activities of Escherichia coli heat shock protein 70 (Hsp70/DnaK). J Biol Chem 285(28):21282-21291.
27. Tiwari S, Kumar V, Jayaraj GG, Maiti S, Mapa K (2013) Unique structural modulation of a non-native substrate by cochaperone DnaJ. Biochemistry 52(6):1011-1018.
28. Gidalevitz T, Ben-Zvi A, Ho KH, Brignull HR, Morimoto RI (2006) Progressive disruption of cellular protein folding in models of polyglutamine diseases. Science 311(5766):1471-1474. (Pubitemid 43376703)
29. Gupta R, et al. (2011) Firefly luciferase mutants as sensors of proteome stress. Nat Methods 8(10):879-884.
30. Bettencourt C, Lima M (2011) Machado-Joseph Disease: From first descriptions to new perspectives. Orphanet J Rare Dis 6:35.
31. Schaffar G, et al. (2004) Cellular toxicity of polyglutamine expansion proteins: Mechanism of transcription factor deactivation. Mol Cell 15(1):95-105. (Pubitemid 38850222)