Knotted Fusion Proteins Reveal Unexpected Possibilities in Protein Folding

Molecular Cell

Volumn 30, Issue 5, 2008, Pages 642-648

  Mallam, Anna L ^a   Onuoha, Shimobi C ^a   Grossmann, J Günter ^b   Jackson, Sophie E ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b DARESBURY LABORATORY   (United Kingdom)

Author keywords

PROTEINS

Indexed keywords

AMINO ACID; CARBOXYL GROUP; HOMODIMER; HYBRID PROTEIN; PROTEIN SUBUNIT;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CIRCULAR DICHROISM; CONTROLLED STUDY; GENE CONSTRUCT; NONHUMAN; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN STABILITY; PROTEIN STRUCTURE; RADIATION SCATTERING; ULTRAVIOLET RADIATION;

ARCHAEOGLOBUS FULGIDUS; DIMERIZATION; ESCHERICHIA COLI; HAEMOPHILUS INFLUENZAE; METHYLTRANSFERASES; PROTEIN FOLDING; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT FUSION PROTEINS; UREA;

EID: 44449146446     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2008.03.019     Document Type: Article

References (35)

1. Ahn H.J., Kim H.W., Yoon H.J., Lee B.I., Suh S.W., and Yang J.K. Crystal structure of tRNA(m1G37)methyltransferase: insights into tRNA recognition. EMBO J. 22 (2003) 2593-2603
2. Bateman A., Coin L., Durbin R., Finn R.D., Hollich V., Griffiths-Jones S., Khanna A., Marshall M., Moxon S., Sonnhammer E.L., et al. The Pfam protein families database. Nucleic Acids Res. 32 (2004) D138-D141
3. Carson M. Ribbons. Methods Enzymol. 277 (1997) 493-505
4. Elkins P.A., Watts J.M., Zalacain M., van Thiel A., Vitazka P.R., Redlak M., Andraos-Selim C., Rastinejad F., and Holmes W.M. Insights into catalysis by a knotted TrmD tRNA methyltransferase. J. Mol. Biol. 333 (2003) 931-949
5. Grossmann J.G., Hall J.F., Kanbi L.D., and Hasnain S.S. The N-terminal extension of rusticyanin is not responsible for its acid stability. Biochemistry 41 (2002) 3613-3619
6. Hayes M.V., Sessions R.L.B., and Clarke A.R. Engineered assembly of intertwined oligomers of an immunoglobulin domain. J. Mol. Biol. 285 (1999) 1857-1867
7. Hoffman J.L. Chromatographic analysis of the chiral and covalent instability of S-adenosyl-L-methionine. Biochemistry 25 (1986) 4444-4449
8. Kolesov G., Virnau P., Kardar M., and Mirny L.A. Protein knot server: detection of knots in protein structures. Nucleic Acids Res. 35 (2007) W425-W428
9. Kozin M.B., and Svergun D.I. Automated matching of high- and low-resolution structural models. J. Appl. Cryst. 34 (2001) 33-41
10. Lim K., Zhang H., Tempczyk A., Krajewski W., Bonander N., Toedt J., Howard A., Eisenstein E., and Herzberg O. Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): a cofactor bound at a site formed by a knot. Proteins Struct. Funct. Genet. 51 (2003) 56-67
11. Mallam A.L., and Jackson S.E. Folding studies on a knotted protein. J. Mol. Biol. 346 (2005) 1409-1421
12. Mallam A.L., and Jackson S.E. Probing Nature's knots: The folding pathway of a knotted homodimeric protein. J. Mol. Biol. 359 (2006) 1420-1436
13. Mallam A.L., and Jackson S.E. A comparison of the folding of two knotted proteins: YbeA and YibK. J. Mol. Biol. 366 (2007) 650-665
14. Mallam A.L., and Jackson S.E. The dimerization of an α/β-knotted protein is essential for structure and function. Structure 15 (2007) 111-122
15. Mansfield M.L. Fit to be tied. Nat. Struct. Biol. 4 (1997) 166-167
16. Marti-Renom M.A., Stuart A.C., Fiser A., Sanchez R., Melo F., and Sali A. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29 (2000) 291-325
17. Mosbacher T.G., Bechthold A., and Schulz G.E. Structure and function of the antibiotic resistance-mediating methyltransferase AviRb from Streptomyces viridochromogenes. J. Mol. Biol. 345 (2005) 535-545
18. Myers J.K., Pace C.N., and Scholtz J.M. Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding. Protein Sci. 4 (1995) 2138-2148
19. Nureki O., Watanabe K., Fukai S., Ishii R., Endo Y., Hori H., and Yokoyama S. Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme. Structure 12 (2004) 593-602
20. Pace C.N. Determination and analysis of urea and guanidine hydrochloride denaturation curves. Methods Enzymol. 131 (1986) 266-280
21. Petoukhov M.V., and Svergun D.I. Global rigid body modeling of macromolecular complexes against small-angle scattering data. Biophys. J. 89 (2005) 1237-1250
22. Raymer D.M., and Smith D.E. Spontaneous knotting of an agitated string. Proc. Natl. Acad. Sci. USA 104 (2007) 16432-16437
23. Rousseau F., Schymkowitz J.W.H., Wilkinson H.R., and Itzhaki L.S. Three-dimensional domain swapping in p13suc1 occurs in the unfolded state and is controlled by conserved proline residues. Proc. Natl. Acad. Sci. USA 98 (2001) 5596-5601
24. Rousseau F., Schymkowitz J.W.H., and Itzhaki L.S. The unfolding story of three-dimensional domain swapping. Structure 11 (2003) 243-251
25. Schuwirth B.S., Borovinskaya M.A., Hau C.W., Zhang W., Vila-Sanjurjo A., Holton J.M., and Doudna Cate J.H. Structures of the Bacterial Ribosome at 3.5 Å Resolution. Science 310 (2005) 827-834
26. Svergun D.I. Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J. Appl. Cryst. 25 (1992) 495-503
27. Svergun D.I., Petoukhov M.V., and Koch M.H. Determination of domain structure of proteins from X-ray solution scattering. Biophys. J. 80 (2001) 2946-2953
28. Taylor W.R. A deeply knotted protein structure and how it might fold. Nature 406 (2000) 916-919
29. Taylor W.R. Protein knots and fold complexity: some new twists. Comput. Biol. Chem. 31 (2007) 151-162
30. Taylor W.R., and Lin K. Protein knots: A tangled problem. Nature 421 (2003) 25
31. Virnau P., Kantor Y., and Kardar M. Knots in globule and coil phases of a model polyethylene. J. Am. Chem. Soc. 127 (2005) 15102-15106
32. Virnau P., Mirny L.A., and Kardar M. Intricate Knots in Proteins: Function and Evolution. PLoS Comput. Biol. 2 (2006) e122 10.1371/journal.pcbi.0020122
33. Volkov V.V., and Svergun D.I. Uniqueness of ab initio shape determination in small-angle scattering. J. Appl. Cryst. 36 (2003) 860-864
34. Wallin S., Zeldovich K.B., and Shakhnovich E.I. The folding mechanics of a knotted protein. J. Mol. Biol. 368 (2007) 884-893
35. Yeates T.O., Norcross T.S., and King N.P. Knotted and topologically complex proteins as models for studying folding and stability. Curr. Opin. Chem. Biol. 11 (2007) 1-9