Conservation of complex knotting and slipknotting patterns in proteins

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

Volumn 109, Issue 26, 2012, Pages

  Sułkowska, Joanna I ^a   Rawdon, Eric J ^b   Millett, Kenneth C ^c   Onuchic, Jose N ^d   Stasiak, Andrzej ^e  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF ST THOMAS   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d RICE UNIVERSITY   (United States)

^e UNIVERSITY OF LAUSANNE   (Switzerland)

Author keywords

Knot theory; Protein knots; Topology

Indexed keywords

CLOACIN; HALOACID; PYOCIN; TRANSCRIPTION FACTOR SNF; UBIQUITIN THIOLESTERASE;

AMINO ACID SEQUENCE; ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE;

PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS;

EID: 84862983938     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1205918109     Document Type: Article

References (50)

1. Mansfield ML (1994) Are there knots in proteins? Nat Struct Biol 1:213-214.
2. 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. (Pubitemid 47390715)
3. Lua RC, Grosberg AY (2006) Statistics of knots, geometry of conformations, and evolution of proteins. PLoS Comput Biol 2:e45.
4. Virnau P, Mirny LA, Kardar M (2006) Intricate knots in proteins: Function and evolution. PLoS Comput Biol 2:e122.
5. Sulkowska JI, Sulkowski P, Onuchic JN (2009) Dodging the crisis of folding proteins with knots. Proc Natl Acad Sci USA 106:3119-3124.
6. King NP, JacobitzAW, Sawaya MR, Goldschmidt L, Yeates TO (2010) Structure and folding of a designed knotted protein. Proc Natl Acad Sci USA 107:20732-20737.
7. Sulkowska JI, Sulkowski P, Szymczak P, Cieplak M (2008) Stabilizing effect of knots on proteins. Proc Natl Acad Sci USA 105:19714-19719.
8. Mallam AL, Rogers JM, Jackson SE (2010) Experimental detection of knotted conformations in denatured proteins. Proc Natl Acad Sci USA 107:8189-8194.
9. Prentiss MC, Wales DJ,Wolynes PG (2010) The energy landscape, folding pathways and the kinetics of a knotted protein. PLoS Comput Biol 6:e1000835.
10. Noel JK, Sulkowska JI, Onuchic JN (2010) Slipknotting upon native-like loop formation in a trefoil knot protein. Proc Natl Acad Sci USA 107:15403-15408.
11. Shakhnovich E (2011) Protein folding: To knot or not to knot? Nat Mater 10:84-86.
12. Sayre TC, Lee TM, King NP, Yeates TO (2011) Protein stabilization in a highly knotted protein polymer. Protein Eng Des Sel 24:627-630.
13. Alam MT, et al. (2002) The importance of being knotted: Effects of the C-terminal knot structure on enzymatic and mechanical properties of bovine carbonic anhydrase II. FEBS Lett 519:35-40. (Pubitemid 34521988)
14. Wang T, Arakawa H, Ikai A (2001) Force measurement and inhibitor binding assay of monomer and engineered dimer of bovine carbonic anhydrase B Biochem. Biochem Biophys Res Commun 285:9-14. (Pubitemid 32916120)
15. Mallam AL, Jackson SE (2007) A comparison of the folding of two knotted proteins: YbeA and YibK. J Mol Biol 366:650-665. (Pubitemid 46136200)
16. Bornschlogl T, et al. (2009) Tightening the knot in phytochrome by single-molecule atomic force microscopy. Biophys J 96:1508-1504.
17. Ohta S, et al. (2004) Origin of mechanical strength of bovine carbonic anhydrase studied by molecular dynamics simulation. Biophys J 87:4007-4020. (Pubitemid 39602905)
18. Tkaczuk KL, et al. (2007) Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases. BMC Bioinformatics 8:73.
19. Lai YL, Yen SC, Yu SH, Hwang JK (2007) pKNOT: The protein KNOT web server. Nucleic Acids Res 35:W420-W424.
20. Wallin S, Zeldovich KB, Shakhnovich EI (2007) The folding mechanics of a knotted protein. J Mol Biol 368:884-893. (Pubitemid 46527616)
21. Dzubiella J (2009) Sequence-specific size, structure, and stability of tight protein knots. Biophys J 96:831-839.
22. Huang L, Makarov DE (2008) Translocation of a knotted polypeptide through a pore. J Chem Phys 129:121107.
23. Faisca PFN, et al. (2010) The folding of knotted proteins: Insights from lattice simulations. Phys Biol 7:016009.
24. Tuszynska I, Bujnicki JM (2010) Predicting atomic details of the unfolding pathway for YibK, a knotted protein from the SPOUT superfamily. J Biomol Struct Dyn 27:511-520.
25. Potestio R, Micheletti C, Orland H (2010) Knotted versus unknotted proteins: evidence of knot-promoting loops. PLoS Comput Biol 6:e1000864.
26. Andreeva A, Murzin AG (2010) Structural classification of proteins and structural genomics: New insights into protein folding and evolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 66:1190-1197.
27. Bölinger D, et al. (2010) A Stevedore's protein knot. PLoS Comput Biol 6:e1000731.
28. Berman HM, et al. (2000) The protein data bank. Nucleic Acids Res 28:235-242. (Pubitemid 30047768)
29. Taylor WR (2000) A deeply knotted protein structure and how it might fold. Nature 406:916-919.
30. Millett K, Dobay A, Stasiak A (2005) Linear random knots and their scaling behavior. Macromolecules 38:601-606. (Pubitemid 40184336)
31. Katritch V, Olson WK, Vologodskii A, Dubochet J, Stasiak A (2000) Tightness of random knotting. Phys Rev E Stat Nonlin Soft Matter Phys 61:5545-5549.
32. Marcone B, Orlandini E, Stella AL, Zonta F (2005) What is the length of a knot in a polymer? J Phys A Math Gen 38:L15-L21. (Pubitemid 40097451)
33. Tubiana L, Orlandini E, 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.
34. Koniaris K, Muthukumar M (1991) Self-entanglement in ring polymers. J Chem Phys 95:2873-2881.
35. Finn RD, et al. (2006) Pfam: Clans, web tools and services. Nucleic Acids Res 34:D247-D251.
36. Taylor WR (2005) Protein folds, knots and tangles. Physical and numerical models in knot theory, eds JA Calvo, KC Millet, EJ Rawdon, and A Stasiak (World Scientific, Singapore), pp 171-202.
37. Schmidberger JW,Wilce JA,Weightman AJ, Whisstock JC,Wilce MCJ (2008) The crystal structure of DehI reveals a new alpha-haloacid dehalogenase fold and active-site mechanism. J Mol Biol 378:284-294.
38. Darcy IK, Sumners DW (2000) Rational tangle distance on knots and links. Math Proc Cambridge Philos Soc 128:497-510.
39. Flammini A, Maritan A, Stasiak A (2004) Simulations of action of DNA topoisomerases to investigate boundaries and shapes of spaces of knots. Biophys J 87:2968-2975. (Pubitemid 40468557)
40. Darcy IK, Scharein RG, Stasiak A (2008) 3D visualization software to analyze topological outcomes of topoisomerase reactions. Nucleic Acids Res 36:3515-3521. (Pubitemid 351917516)
41. Hasegawa H, Holm L (2009) Advances and pitfalls of protein structural alignment. Curr Opin Struct Biol 19:341-348.
42. Holm L, Sander C (1996) Mapping the protein universe. Science 273:595-602. (Pubitemid 26262103)
43. Edgar RC (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-1797.
44. Flores SC, Lu LJ, Yang J, Carriero N, Gerstein MB (2007) Hinge atlas: Relating protein sequence to sites of structural flexibility. BMC Bioinformatics 8:167.
45. Orlandini E, Stella AL, Vanderzande C (2009) The size of knots in polymers. Phys Biol 6:025012.
46. Fernandez-Fuentes N, Zhai J, Fiser A (2006) ArchPRED: A template based loop structure prediction server. Nucleic Acids Res 34:W173-W176. (Pubitemid 44529758)
47. Grant BJ, Rodrigues AP, ElSawy KM, McCammon JA, Caves LS (2006) Bio3D: An R package for the comparative analysis of protein structures. Bioinformatics 22:2695-2696. (Pubitemid 44642612)
48. Freyd P, et al. (1985) A new polynomial invariant of knots and links. Bull Am Math Soc 12:239-246.
49. Przytycki JH, Traczyk P (1987) Invariants of links of Conway type. Kobe J Math 4:115-139.
50. Ewing B, Millett KC (1997) Computational algorithms and the complexity of link polynomials. Progress in Knot Theory and Related Topics (Hermann, Paris), pp 51-68.