How Difficult Is It to Fold a Knotted Protein? In Silico Insights from Surface-Tethered Folding Experiments

PLoS ONE

Volumn 7, Issue 12, 2012, 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

TREFOIL PEPTIDE;

AMINO ACID SEQUENCE; ARTICLE; COMPUTER MODEL; COMPUTER SIMULATION; MONTE CARLO METHOD; PROBABILITY; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STRUCTURE; RNA TRANSLATION; SURFACE PROPERTY; THERMODYNAMICS;

MODELS, THEORETICAL; MONTE CARLO METHOD; PROTEIN FOLDING; PROTEINS;

LOTUS;

EID: 84871448220     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0052343     Document Type: Article

References (54)

1. Mansfield ML, (1994) Are there knots in proteins. Nature Structural Biology 1: 213-214.
2. 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 United States of America 109: 1715-1723.
3. Virnau P, Mirny LA, Kardar M, (2006) Intricate knots in proteins: Function and evolution. Plos Computational Biology 2: 1074-1079.
4. Bolinger D, Sulkowska JI, Hsu HP, Mirny LA, Kardar M, et al. (2010) A Stevedore's Protein Knot. Plos Computational Biology 6(4): e1000731.
5. 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.
6. Sulkowska JI, Sulkowski P, Szymczak P, Cieplak M, (2008) Stabilizing effect of knots on proteins. Proceedings of the National Academy of Sciences of the United States of America 105: 19714-19719.
7. Sayre TC, Lee TM, King NP, Yeates TO, (2011) Protein stabilization in a highly knotted protein polymer. Protein Engineering Design & Selection 24: 627-630.
8. 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.
9. 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.
10. Wallin S, Zeldovich KB, Shakhnovich EI, (2007) The folding mechanics of a knotted protein. Journal of Molecular Biology 368: 884-893.
11. Skrbic T, Micheletti C, Faccioli P, (2012) The Role of Non-Native Interactions in the Folding of Knotted Proteins. Plos Computational Biology 8(6): e1002504.
12. Sulkowska JI, Sulkowski P, Onuchic J, (2009) Dodging the crisis of folding proteins with knots. Proceedings of the National Academy of Sciences of the United States of America 106: 3119-3124.
13. 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 United States of America 107: 15403-15408.
14. Mallam AL, Jackson SE, (2007) A comparison of the folding of two knotted proteins: YbeA and YibK. Journal of Molecular Biology 366: 650-665.
15. Mallam AL, Jackson SE, (2006) Probing Nature's knots: The folding pathway of a knotted homodimeric protein. Journal of Molecular Biology 359: 1420-1436.
16. Mallam AL, Rogers JM, Jackson SE, (2010) Experimental detection of knotted conformations in denatured proteins. Proceedings of the National Academy of Sciences of the United States of America 107: 8189-8194.
17. Mallam AL, Onuoha SC, Grossmann JG, Jackson SE, (2008) Knotted fusion proteins reveal unexpected possibilities in protein folding. Molecular Cell 30: 642-648.
18. Mallam AL, Jackson SE, (2012) Knot formation in newly translated proteins is spontaneous and accelerated by chaperonins. Nature Chemical Biology 8: 147-153.
19. 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 United States of America 107: 20732-20737.
20. Mallam AL, Morris ER, Jackson SE, (2008) Exploring knotting mechanisms in protein folding. Proceedings of the National Academy of Sciences of the United States of America 105: 18740-18745.
21. Faisca PFN, Travasso RDM, Charters T, Nunes A, Cieplak M, (2010) The folding of knotted proteins: insights from lattice simulations. Physical Biology 7: 016009.
22. Sulkowska JI, Sulkowski P, Szymczak P, Cieplak M, (2010) Untying Knots in Proteins. Journal of the American Chemical Society 132: 13954-13956.
23. Klimov DK, Thirumalai D, (1998) Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism. Journal of Molecular Biology 282: 471-492.
24. 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.
25. Faisca PFN, da Gama MMT, (2005) Native geometry and the dynamics of protein folding. Biophysical Chemistry 115: 169-175.
26. Faisca PFN, da Gama MMT, Nunes A, (2005) The Gō Model revisited: Native structure and the geometric coupling between local and long-range contacts. Proteins-Structure Function and Bioinformatics 60: 712-722.
27. Faisca PFN, Travasso RDM, Ball RC, Shakhnovich EI, (2008) Identifying critical residues in protein folding: Insights from phi-value and Pfold analysis. Journal of Chemical Physics 129: 095108.
28. 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.
29. Faisca PFN, Travasso RDM, Parisi A, Rey A, (2012) Why Do Protein Folding Rates Correlate with Metrics of Native Topology? Plos One 7(4): e35599.
30. Gutin AM, Abkevich VI, Shakhnovich EI, (1996) Chain length scaling of protein folding time. Physical Review Letters 77: 5433-5436.
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. Dill KA, Bromberg S, Yue KZ, Fiebig KM, Yee DP, et al. (1995) Principles of protein folding - A perspective from simple exact models. Protein Science 4: 561-602.
33. Camacho CJ, Thirumalai D, (1993) Kinetics and thermodynamics of folding in model proteins. Proceedings of the National Academy of Sciences of the United States of America 90: 6369-6372.
34. Chan HS, Dill KA, (1998) Protein folding in the landscape perspective: Chevron plots and non-Arrhenius kinetics. Proteins-Structure Function and Bioinformatics 30: 2-33.
35. Kaya H, Chan HS, (2003) Contact order dependent protein folding rates: Kinetic consequences of a cooperative interplay between favorable nonlocal interactions and local conformational preferences. Proteins-Structure Function and Genetics 52: 524-533.
36. Wang PY, Klimov DK, (2008) Lattice simulations of cotranslational folding of single domain proteins. Proteins-Structure Function and Bioinformatics 70: 925-937.
37. 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.
38. 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.
39. Taketomi H, Ueda Y, Go N, (1975) Studies on protein folding, unfolding and fluctuations by computer-simulation. 1. Effect of specific amino acid sequence represented by specific inter-unit interactions. International Journal of Peptide and Protein Research 7: 445-459.
40. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E, (1953) Equation of state calculation by fast computing machines. Journal of Chemical Physics 21: 1087-1092.
41. Quake SR, (1995) Fast Monte Carlo algorithms for knotted polymers. Physical Review E 52: 1176-1180.
42. Faisca PFN, Ball RC, (2002) Thermodynamic control and dynamical regimes in protein folding. Journal of Chemical Physics 116: 7231-7237.
43. Finkelstein AV, Ptitsyn OB (2002) Protein Physics. London: Academic Press.
44. Chodera JD, Swope WC, Pitera JW, Seok C, Dill KA, (2007) Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations. Journal of Chemical Theory and Computation 3: 26-41.
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. Lai YL, Chen CC, Hwang JK, (2012) pKNOT v.2: the protein KNOT web server. Nucleic Acids Research 40: W228-W231.
48. Shakhnovich EI, Gutin AM, (1993) Engineering of stable and fast-folding sequences of model proteins. Proceedings of the National Academy of Sciences of the United States of America 90: 7195-7199.
49. Sułkowska JI, Noel JK, Onuchic JN, (2012) Energy landscape of knotted protein folding. Proceedings of the National Academy of Sciences 109: 17783-17788.
50. Plaxco KW, Simons KT, Baker D, (1998) Contact order, transition state placement and the refolding rates of single domain proteins. Journal of Molecular Biology 277: 985-994.
51. Faisca PFN, da Gama MMT, Ball RC, (2004) Folding and form: Insights from lattice simulations. Physical Review E 69: 051917.
52. O'Brien EP, Hsu STD, Christodoulou J, Vendruscolo M, Dobson CM, (2010) Transient Tertiary Structure Formation within the Ribosome Exit Port. Journal of the American Chemical Society 132: 16928-16937.
53. O'Brien EP, Christodoulou J, Vendruscolo M, Dobson CM, (2011) New Scenarios of Protein Folding Can Occur on the Ribosome. Journal of the American Chemical Society 133: 513-526.
54. O'Brien EP, Christodoulou J, Vendruscolo M, Dobson CM, (2012) Trigger Factor Slows Co-translational Folding through Kinetic Trapping while Sterically Protecting the Nascent Chain from Aberrant Cytosolic Interactions. Journal of the American Chemical Society 134: 10920-10932.