Effects of Knots on Protein Folding Properties

PLoS ONE

Volumn 8, Issue 9, 2013, Pages

  Soler, Miguel A ^a,b   Faísca, Patrícia F N ^a,b  

^a Centro de Fisica da Materia Condensada   (Portugal)

^b UNIVERSITY OF LISBON   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; MONTE CARLO METHOD; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN KNOTTING; PROTEIN STABILITY; PROTEIN STRUCTURE; THERMODYNAMICS; THERMOSTABILITY;

MODELS, MOLECULAR; MONTE CARLO METHOD; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STABILITY; PROTEINS; TEMPERATURE;

EID: 84883379881     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0074755     Document Type: Article

References (51)

1. Sulkowska JI, Rawdon EJ, Millett KC, Onuchic JN, Stasiak A, (2012) Conservation of complex knotting and slipknotting patterns in proteins. Proceedings of the National Academy of Sciences of the USA 109: 1715-1723.
2. King NP, Yeates EO, Yeates TO, (2007) Identification of rare slipknots in proteins and their implications for stability and folding. Journal of Molecular Biology 373: 153-166.
3. Bolinger D, Sulkowska JI, Hsu HP, Mirny LA, Kardar M, et al. (2010) A Stevedore's Protein Knot. Plos Computational Biology 6: e1000731.
4. Virnau P, Mirny LA, Kardar M, (2006) Intricate knots in proteins: Function and evolution. Plos Computational Biology 2: 1074-1079.
5. Sulkowska JI, Rawdon EJ, Millett KC, Onuchic JN, Stasiak A, (2012) Conservation of complex knotting and slipknotting patterns in proteins. Proceedings of the National Academy of Sciences of the USA109: 1715-E1723.
6. Lai YL, Chen CC, Hwang JK, (2012) pKNOT v.2: the protein KNOT web server. Nucleic Acids Research 40: W228-W231.
7. Mallam AL, (2009) How does a knotted protein fold? Febs Journal 276: 365-375.
8. Virnau P, Mallam A, Jackson S, (2011) Structures and folding pathways of topologically knotted proteins. Journal of Physics-Condensed Matter 23: 033101.
9. Yeates T, Norcross TS, King NP, (2007) Knotted and topologically complex proteins as models for studying folding and stability. Current Opinion in Chemical Biology 11: 595-603.
10. Andersson FI, Pina DG, Mallam AL, Blaser G, Jackson SE, (2009) Untangling the folding mechanism of the 5(2)-knotted protein UCH-L3. Febs Journal 276: 2625-2635.
11. Mallam AL, Jackson SE, (2007) A comparison of the folding of two knotted proteins: YbeA and YibK. Journal of Molecular Biology 366: 650-665.
12. Mallam AL, Jackson SE, (2006) Probing Nature's knots: The folding pathway of a knotted homodimeric protein. Journal of Molecular Biology 359: 1420-1436.
13. Mallam AL, Onuoha SC, Grossmann JG, Jackson SE, (2008) Knotted fusion proteins reveal unexpected possibilities in protein folding. Molecular Cell 30: 642-648.
14. Mallam AL, Morris ER, Jackson SE, (2008) Exploring knotting mechanisms in protein folding. Proceedings of the National Academy of Sciences of the USA105: 18740-18745.
15. Mallam AL, Rogers JM, Jackson SE, (2010) Experimental detection of knotted conformations in denatured proteins. Proceedings of the National Academy of Sciences of the USA107: 8189-8194.
16. Mallam AL, Jackson SE, (2012) Knot formation in newly translated proteins is spontaneous and accelerated by chaperonins. Nature Chemical Biology 8: 147-153.
17. King NP, Jacobitz AW, Sawaya MR, Goldschmidt L, Yeates TO, (2010) Structure and folding of a designed knotted protein. Proceedings of the National Academy of Sciences of the USA 107: 20732-20737.
18. Faisca PFN, Travasso RDM, Charters T, Nunes A, Cieplak M, (2010) The folding of knotted proteins: insights from lattice simulations. Physical Biology 7: 016009.
19. Soler MA, Faísca PFN, (2012) How Difficult Is It to Fold a Knotted Protein? In Silico Insights from Surface-Tethered Folding Experiments. Plos One 7: e52343.
20. Wallin S, Zeldovich KB, Shakhnovich EI, (2007) The folding mechanics of a knotted protein. Journal of Molecular Biology 368: 884-893.
21. Sulkowska JI, Sulkowski P, Onuchic J, (2009) Dodging the crisis of folding proteins with knots. Proceedings of the National Academy of Sciences of the USA106: 3119-3124.
22. Sulkowska JI, Noel JK, Onuchic JN, (2012) Energy landscape of knotted protein folding. Proceedings of the National Academy of Sciences of the USA 109: 17783-17788.
23. Noel JK, Sulkowska JI, Onuchic JN, (2010) Slipknotting upon native-like loop formation in a trefoil knot protein. Proceedings of the National Academy of Sciences of the USA 107: 15403-15408.
24. Skrbic T, Micheletti C, Faccioli P, (2012) The Role of Non-Native Interactions in the Folding of Knotted Proteins. Plos Computational Biology 8: e1002504.
25. Sułkowska JI, Noel JK, Onuchic JN, (2012) Energy landscape of knotted protein folding. Proceedings of the National Academy of Sciences of the USA 109: 17783-17788.
26. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E, (1953) Equations of state calculations by fast computing machines. Journal of Chemical Physics 21: 1087-1092.
27. Sayre TC, Lee TM, King NP, Yeates TO, (2011) Protein stabilization in a highly knotted protein polymer. Protein Engineering Design & Selection 24: 627-630.
28. Sulkowska JI, Sulkowski P, Szymczak P, Cieplak M, (2008) Stabilizing effect of knots on proteins. Proceedings of the National Academy of Sciences of the USA 105: 19714-19719.
29. Alam MT, Yamada T, Carlsson U, Ikai A, (2002) The importance of being knotted: effects of the C-terminal knot structure on enzymatic and mechanical properties of bovine carbonic anhydrase II. Febs Letters 519: 35-40.
30. Dill KA, Chan HS, (1997) From Levinthal to pathways to funnels. Nature Structural Biology 4: 10-19.
31. Li L, Mirny LA, Shakhnovich EI, (2000) Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus. Nature Structural Biology 7: 336-342.
32. Abkevich VI, Gutin AM, Shakhnovich EI, (1994) Specific nucleus as the transition state for protein folding- evidence from the lattice model. Biochemistry 33: 10026-10036.
33. Faisca PFN, (2009) The nucleation mechanism of protein folding: a survey of computer simulation studies. Journal of Physics-Condensed Matter 21: 373102.
34. Faisca PFN, da Gama MMT, (2005) Native geometry and the dynamics of protein folding. Biophysical Chemistry 115: 169-175.
35. Faisca PFN, Nunes A, Travasso RDM, Shakhnovich EI, (2010) Non-native interactions play an effective role in protein folding dynamics. Protein Science 19: 2196-2209.
36. Krobath H, Faisca PFN, (2013) Interplay between native topology and non-native interactions in the folding of tethered proteins. Physical Biology 10: 016002.
37. Gin BC, Garrahan JP, Geissler PL, (2009) The Limited Role of Nonnative Contacts in the Folding Pathways of a Lattice Protein. Journal of Molecular Biology 392: 1303-1314.
38. Li MS, Co NT, Reddy G, Hu CK, Straub JE, et al. (2010) Factors Governing Fibrillogenesis of Polypeptide Chains Revealed by Lattice Models. Physical Review Letters 105: 218101.
39. Bhattacherjee A, Wallin S, (2012) Coupled Folding-Binding in a Hydrophobic/Polar Protein Model: Impact of Synergistic Folding and Disordered Flanks. Biophysical Journal 102: 569-578.
40. Faísca PFN, Travasso RDM, Parisi A, Rey A, (2012) Why Do Protein Folding Rates Correlate with Metrics of Native Topology? Plos One 7: e35599.
41. Li YW, Wust T, Landau DP, (2013) Generic folding and transition hierarchies for surface adsorption of hydrophobic-polar lattice model proteins. Physical Review E 87: 2706-2706.
42. Taketomi H, Ueda Y, Go N, (1975) Studies on protein folding, unfolding and fluctuations by computer simulations. 1. Effect of specific amino-acid sequence represented by specific inter-unit interactions. International Journal of Peptide and Protein Research 7: 445-459.
43. Quake SR, (1995) Fast Monte Carlo algorithms for knotted polymers. Physical Review E 52: 1176-1180.
44. Faisca PFN, Ball RC, (2002) Thermodynamic control and dynamical regimes in protein folding. Journal of Chemical Physics 116: 7231-7237.
45. Taylor WR, (2000) A deeply knotted protein structure and how it might fold. Nature 406: 916-919.
46. Feig M, Karanicolas J, Brooks CL, (2004) MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. Journal of Molecular Graphics & Modelling 22: 377-395.
47. Capraro DT, Roy M, Onuchic JN, Jennings PA, (2008) Backtracking on the folding landscape of the beta-trefoil protein interleukin-1 beta? Proceedings of the National Academy of Sciences of the USA 105: 14844-14848.
48. Gutin AM, Abkevich VI, Shakhnovich EI, (1996) Chain length scaling of protein folding time. Physical Review Letters 77: 5433-5436.
49. Li MS, Klimov DK, Thirumalai D, (2002) Dependence of Folding Rates on Protein Length. The Journal of Physical Chemistry B 106: 8302-8305.
50. Sanchez-Ruiz JM, (2010) Protein kinetic stability. Biophysical Chemistry 148: 1-15.
51. Kwiecinska JI, Cieplak M, (2005) Chirality and protein folding. Journal of Physics: Condensed Matter 17: S1565.