Knot localization in proteins

Biochemical Society Transactions

Volumn 41, Issue 2, 2013, Pages 538-541

  Rawdon, Eric J ^a,b   Millett, Kenneth C ^c   Sulkowska, Joanna I ^d,e   Stasiak, Andrzej ^e  

^a UNIVERSITY OF ST THOMAS   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF WARSAW   (Poland)

^e UNIVERSITY OF LAUSANNE   (Switzerland)

Author keywords

Knotting fingerprint; Protein backbone; Protein knot; Slipknotted protein

Indexed keywords

CLOACIN; PYOCIN; UBIQUITIN THIOLESTERASE;

ALGORITHM; AMINO ACID SEQUENCE; ESCHERICHIA COLI; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN KNOTTING; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; REVIEW;

ANIMALS; HUMANS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS;

EID: 84875384720     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST20120329     Document Type: Review

References (23)

1. Trabi, M. and Craik, D.J. (2002) Circular proteins: no end in sight. Trends Biochem. Sci. 27, 132-138
2. Boutz, D.R., Cascio, D., Whitelegge, J., Perry, L.J. and Yeates, T.O. (2007) Discovery of a thermophilic protein complex stabilized by topologically interlinked chains. J. Mol. Biol. 368, 1332-1344
3. Cao, Z.B., Roszak, A.W., Gourlay, L.J., Lindsay, J.G. and Isaacs, N.W. (2005) Bovine mitochondrial peroxiredoxin III forms a two-ring catenane. Structure 13, 1661-1664
4. Mansfield, M.L. (1994) Are there knots in proteinsNat. Struct. Biol. 1, 213-214
5. Mansfield, M.L. (1997) Fit to be tied. Nat. Struct. Biol. 4, 166-167
6. Taylor, W.R. (2000) A deeply knotted protein structure and how it might fold. Nature 406, 916-919
7. King, N.P., Yeates, E.O. and Yeates, T.O. (2007) Identification of rare slipknots in proteins and their implications for stability and folding. J. Mol. Biol. 373, 153-166
8. Millett, K.C., Rawdon, E.J., Stasiak, A. and Sukowska, J.I. (2012) Identifying knots in proteins. Biochem. Soc. Trans. 41, 533-537
9. Millett, K.C., Dobay, A. and Stasiak, A. (2005) Linear random knots and their scaling behavior. Macromolecules 38, 601-606
10. Millett, K.C. and Sheldon, B.M. (2005) Tying down open knots: a statistical method for identifying open knots with applications to proteins. Ser. Knots Everything 36, 203-217
11. Sukowska, J.I., Rawdon, E.J., Millett, K.C., Onuchic, J.N. and Stasiak, A. (2012) Conservation of complex knotting and slipknotting patterns in proteins. Proc. Natl. Acad. Sci. U.S.A. 109, E1715-E1723
12. Banavar, J.R., Hoang, T.X., Maddocks, J.H., Maritan, A., Poletto, C., Stasiak, A. and Trovato, A. (2007) Structural motifs of biomolecules. Proc. Natl. Acad. Sci. U.S.A. 104, 17283-17286
13. Darcy, I.K., Scharein, R.G. and Stasiak, A. (2008) 3D visualization software to analyze topological outcomes of topoisomerase reactions. Nucleic Acids Res. 36, 3515-3521
14. Tubiana, L., Orlandini, E. and Micheletti, C. (2011) Probing the entanglement and locating knots in ring polymers: a comparative study of different arc closure schemes. Prog. Theor. Phys. Suppl. 191, 192-204
15. Sayre, T.C., Lee, T.M., King, N.P. and Yeates, T.O. (2011) Protein stabilization in a highly knotted protein polymer. Protein Eng., Des. Sel. 24, 627-630
16. Sukowska, J.I., Sukowski, P., Szymczak, P. and Cieplak, M. (2008) Stabilizing effect of knots on proteins. Proc. Natl. Acad. Sci. U.S.A. 105, 19714-19719
17. Virnau, P., Mirny, L.A. and Kardar, M. (2006) Intricate knots in proteins: function and evolution. PLoS Comput. Biol. 2, 1074-1079
18. Sukowska, J.I., Sukowski, P. and Onuchic, J.N. (2009) Jamming proteins with slipknots and their free energy landscape. Phys. Rev. Lett. 103, 268103
19. Bornschlogl, T., Anstrom, D.M., Mey, E., Dzubiella, J., Rief, M. and Forest, K.T. (2009) Tightening the knot in phytochrome by single-molecule atomic force microscopy. Biophys. J. 96, 1508-1514
20. Comoglio, F. and Rinaldi, M. (2011) A topological framework for the computation of the HOMFLY polynomial and its application to proteins. PLoS ONE 6, e18693
21. Kolesov, G., Virnau, P., Kardar, M. and Mirny, L.A. (2007) Protein knot server: detection of knots in protein structures. Nucleic Acids Res. 35, W425-W428
22. Lai, Y.L., Chen, C.C. and Hwang, J.K. (2012) pKNOT v.2: the protein KNOT web server. Nucleic Acids Res. 40, W228-W231
23. Lua, R.C. (2012) PyKnot: a PyMOLtool for the discovery and analysis of knots in proteins. Bioinformatics 28, 2069-2071