Experimental detection of knotted conformations in denatured proteins

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

Volumn 107, Issue 18, 2010, Pages 8189-8194

  Mallam, Anna L ^a,b   Rogers, Joseph M ^a   Jackson, Sophie E ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

Denatured state; Knotted protein; Protein folding; Protein misfolding

Indexed keywords

POLYPEPTIDE;

ARTICLE; CONFORMATION; CONFORMATIONAL TRANSITION; IN VITRO STUDY; PREVALENCE; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN FOLDING;

ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; HAEMOPHILUS INFLUENZAE; METHYLTRANSFERASES; MODELS, MOLECULAR; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY;

LOTUS;

EID: 77952415889     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0912161107     Document Type: Article

References (38)

1. Clark PL (2004) Protein folding in the cell: Reshaping the folding funnel. Trends Biochem Sci 29:527-534.
2. Dobson CM (2003) Protein folding and misfolding. Nature 426:884-890.
3. Hartl FU, Hayer-Hartl M (2002) Molecular chaperones in the cytosol: From nascent chain to folded protein. Science 295:1852-1858.
4. Hartl FU, Hayer-Hartl M (2009) Converging concepts of protein folding in vitro and in vivo. Nat Struct Mol Biol 16:574-581.
5. Service RF (2008) Problem solved* (*sort of). Science 321:784-786.
6. Mallam AL (2009) How does a knotted protein fold?. FEBS J 276:365-375.
7. Taylor WR, Lin K (2003) Protein knots: A tangled problem. Nature 421:25.
8. Taylor WR (2000) A deeply knotted protein structure and how it might fold. Nature 406:916-919.
9. Yeates TO, Norcross TS, King NP (2007) Knotted and topologically complex proteins as models for studying folding and stability. Curr Opin Chem Biol 11:595-603.
10. Onuchic JN, Wolynes PG (2004) Theory of protein folding. Curr Opin Struc Biol 14:70-75.
11. Virnau P, Mirny LA, Kardar M (2006) Intricate knots in proteins: Function and evolution. PLOS Comput Biol 2:1074-1079. (Pubitemid 44495721)
12. Taylor WR (2007) Protein knots and fold complexity: Some new twists. Comput Biol Chem 31:151-162.
13. Tkaczuk KL, Dunin-Horkawicz S, Purta E, Bujnicki JM (2007) Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases. BMC Bioinformatics 8:73.
14. Dzubiella J (2009) Sequence-specific size, structure, and stability of tight protein knots. Biophys J 96:831-839.
15. Huang L, Makarov DE (2008) Translocation of a knotted polypeptide through a pore. J Chem Phys 129:121107.
16. Sulkowska JI, Sulkowski P, Szymczak P, Cieplak M (2008) Stabilizing effect of knots on proteins. Proc Natl Acad Sci USA 105:19714-19719.
17. King NP, Yeates EO, Yeates TO (2007) Identification of rare slipknots in proteins and their implications for stability and folding. J Mol Biol 373:153-166.
18. Wallin S, Zeldovich KB, Shakhnovich EI (2007) The folding mechanics of a knotted protein. J Mol Biol 368:884-893.
19. Sulkowska JI, Sulkowski P, Onuchic J (2009) Dodging the crisis of folding proteins with knots. Proc Natl Acad Sci USA 106:3119-3124.
20. Mallam AL, Jackson SE (2005) Folding studies on a knotted protein. J Mol Biol 346:1409-1421.
21. Mallam AL, Jackson SE (2007) The dimerization of an alpha/beta-knotted protein is essential for structure and function. Structure 15:111-122. (Pubitemid 46073770)
22. Purta E, Kaminska KH, Kasprzak JM, Bujnicki JM, Douthwaite S (2008) YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA. RNA 14:2234-2244.
23. Ero R, Peil L, Liiv A, Remme J (2008) Identification of pseudouridine methyltransferase in Escherichia coli. RNA 14:2223-2233.
24. Mallam AL, Onuoha SC, Grossmann JG, Jackson SE (2008) Knotted fusion proteins reveal unexpected possibilities in protein folding. Mol Cell 30:642-648.
25. Mallam AL, Morris ER, Jackson SE (2008) Exploring knotting mechanisms in protein folding. Proc Natl Acad Sci USA 105:18740-18745.
26. Mallam AL, Jackson SE (2007) A comparison of the folding of two knotted proteins: YbeA and YibK. J Mol Biol 366:650-665.
27. Mallam AL, Jackson SE (2006) Probing nature's knots: The folding pathway of a knotted homodimeric protein. J Mol Biol 359:1420-1436.
28. Lim K, et al. (2003) Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): A cofactor bound at a site formed by a knot. Proteins Struct Funct Genet 51:56-67. (Pubitemid 36293032)
29. Creighton TE (1988) Disulphide bonds and protein stability. Bioessays 8:57-63.
30. Mansfield ML (1997) Fit to be tied. Nat Struct Biol 4:166-167.
31. Virnau P, Kantor Y, Kardar M (2005) Knots in globule and coil phases of a model polyethylene. J Am Chem Soc 127:15102-15106. (Pubitemid 41547376)
32. Raymer DM, Smith DE (2007) Spontaneous knotting of an agitated string. Proc Natl Acad Sci USA 104:16432-16437.
33. Mansfield ML (2007) Efficient knot group identification as a tool for studying entanglements of polymers. J Chem Phys 127:244901.
34. Mansfield ML (2007) Development of knotting during the collapse transition of polymers. J Chem Phys 127:244902.
35. Mansfield ML (1994) Are there knots in proteins?. Nat Struct Biol 1:213-214.
36. Zagrovic B, Snow CD, Khaliq S, Shirts MR, Pande VS (2002) Native-like mean structure in the unfolded ensemble of small proteins. J Mol Biol 323:153-164. (Pubitemid 35168488)
37. Shortle D, Ackerman MS (2001) Persistence of native-like topology in a denatured protein in 8 M urea. Science 293:487-489. (Pubitemid 32679075)
38. Perham M, Chen M, Ma J, Wittung-Stafshede P (2005) Unfolding of heptameric co-chaperonin protein follows "fly casting" mechanism: Observation of transient nonnative heptamer. J Am Chem Soc 127:16402-16403.