Mechanically tightening a protein slipknot into a trefoil knot

Journal of the American Chemical Society

Volumn 136, Issue 34, 2014, Pages 11946-11955

  He, Chengzhi ^a   Lamour, Guillaume ^a   Xiao, Adam ^a   Gsponer, Joerg ^a   Li, Hongbin ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR DYNAMICS; TOPOLOGY;

AMINO ACID RESIDUES; MECHANICAL RESISTANCE; MECHANICAL UNFOLDING; MOLECULAR MECHANISM; POLYPEPTIDE CHAIN; SINGLE MOLECULE FORCE SPECTROSCOPY; STEERED MOLECULAR DYNAMICS; TOPOLOGICAL FEATURES;

PROTEINS;

AMINO ACID; KNOTTIN; POLYPEPTIDE; PROTEIN; SLIPKNOTTED PROTEIN; TIGHTENED TREFOIL KNOT; TREFOIL PEPTIDE; UNCLASSIFIED DRUG;

ARTICLE; ATOMIC FORCE MICROSCOPY; CONTROLLED STUDY; KINETICS; MOLECULAR DYNAMICS; MONTE CARLO METHOD; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; STEERED MOLECULAR DYNAMIC; STEREOSPECIFICITY; AMINO ACID SEQUENCE; CHEMISTRY; GENETICS; MOLECULAR GENETICS; PROTEIN ENGINEERING; PROTEIN UNFOLDING; THERMODYNAMICS;

AMINO ACID SEQUENCE; MICROSCOPY, ATOMIC FORCE; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; MONTE CARLO METHOD; PROTEIN CONFORMATION; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN UNFOLDING; PROTEINS; THERMODYNAMICS;

EID: 84906762121     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja503997h     Document Type: Article

References (57)

1. Guo, Z. Y.; Thirumalai, D. Biopolymers 1995, 36, 83
2. Onuchic, J. N.; LutheySchulten, Z.; Wolynes, P. G. Annu. Rev. Phys. Chem. 1997, 48, 545
3. Thirumalai, D.; Klimov, D. K.; Woodson, S. A. Theor. Chem. Acc. 1997, 96, 14
4. Onuchic, J. N.; Wolynes, P. G. Curr. Opin. Struct. Biol. 2004, 14, 70
5. Mansfield, M. L. Nat. Struct. Biol. 1994, 1, 213
6. Taylor, W. R. Nature 2000, 406, 916
7. King, N. P.; Yeates, E. O.; Yeates, T. O. J. Mol. Biol. 2007, 373, 153
8. Sulkowska, J. I.; Sulkowski, P.; Onuchic, J. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 3119
9. Bolinger, D.; Sulkowska, J. I.; Hsu, H. P.; Mirny, L. A.; Kardar, M.; Onuchic, J. N.; Virnau, P. PLoA Comput. Biol. 2010, 6 e1000731
10. Kolesov, G.; Virnau, P.; Kardar, M.; Mirny, L. A. C. P. Nucleic Acids Res. 2007, 35, W425
11. Lai, Y.-L.; Yen, S.-C.; Yu, S.-H.; Hwang, J.-K. Nucleic Acids Res. 2007, 35, W420
12. Lai, Y. L.; Chen, C. C.; Hwang, J. K. Nucleic Acids Res. 2012, 40, W228
13. Lua, R. C.; Grosberg, A. Y. PLoS Comput. Biol. 2006, 2, e45
14. Virnau, P.; Mirny, L. A.; Kardar, M. C. P. PLoS Comput. Biol. 2006, 2, e122
15. Mallam, A. L.; Jackson, S. E. Structure (London, U.K.) 2007, 15, 111
16. Noel, J. K.; Sulkowska, J. I.; Onuchic, J. N. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 15403
17. Alam, M. T.; Yamada, T.; Carlsson, U.; Ikai, A. C. P. s. FEBS Lett. 2002, 519, 35
18. Sulkowska, J. I.; Sulkowski, P.; Szymczak, P.; Cieplak, M. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 19714
19. Sulkowska, J. I.; Rawdon, E. J.; Millett, K. C.; Onuchic, J. N.; Stasiak, A. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, E1715
20. Sulkowska, J. I.; Noel, J. K.; Onuchic, J. N. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 17783
21. Mallam, A. L.; Jackson, S. E. J. Mol. Biol. 2005, 346, 1409
22. Mallam, A. L.; Jackson, S. E. J. Mol. Biol. 2007, 366, 650
23. Yeates, T.; Norcross, T. S.; King, N. P. Curr. Opinion Chem. Biol. 2007, 11, 595
24. Mallam, A. L.; Morris, E. R.; Jackson, S. E. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 18740
25. Mallam, A. L.; Onuoha, S. C.; Grossmann, J. G. n.; Jackson, S. E. Mol. cell 2008, 30, 642
26. Faisca, P. F. N.; Travasso, R. D. M.; Charters, T.; Nunes, A.; Cieplak, M. Phys. Biol. 2010, 7 16009
27. Li, W. F.; Terakawa, T.; Wang, W.; Takada, S. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 18625
28. Mallam, A. L.; Jackson, S. E. Nat. Chem. Biol. 2012, 8, 147
29. Beccara, S. A.; Skrbic, T.; Covino, R.; Micheletti, C.; Faccioli, P. PLoS Comput. Biol. 2013, 9 e1003002
30. Soler, M. A.; Faisca, P. F. N. PLoS One 2013, 8 e74755
31. Sulkowska, J. I.; Sulkowski, P.; Szymczak, P.; Cieplak, M. J. Am. Chem. Soc. 2010, 132, 13954
32. Keller, J.; Leulliot, N.; Cambillau, C.; Campanacci, V.; Porciero, S.; Prangishvili, D.; Forterre, P.; Cortez, D.; Quevillon-Cheruel, S.; Tilbeurgh, H. Virol. J. 2007, 4, 10
33. He, C. Z.; Genchev, G. Z.; Lu, H.; Li, H. B. J. Am. Chem. Soc. 2012, 134, 10428
34. Cao, Y.; Lam, C.; Wang, M. J.; Li, H. B. Angew. Chem., Int. Ed. 2006, 45, 642
35. Cao, Y.; Li, H. B. Nat. Mater. 2007, 6, 109
36. Marko, J. F.; Siggia, E. D. Macromolecules 1995, 28, 8759
37. Bell, G. I. Science 1978, 200, 618
38. Evans, E.; Ritchie, K. C. P. Biophys. J. 1997, 72, 1541
39. Carrion-Vazquez, M.; Oberhauser, A. F.; Fowler, S. B.; Marszalek, P. E.; Broedel, S. E.; Clarke, J.; Fernandez, J. M. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 3694
40. Rief, M.; Fernandez, J. M.; Gaub, H. E. Phys. Rev. Lett. 1998, 81, 4764
41. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. J. Comput. Chem. 2005, 26, 1781
42. MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586
43. Mackerell, A. D., Jr.; Feig, M.; Brooks, C. L., III J. Comput. Chem. 2004, 25, 1400
44. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graphics Modell. 1996, 14, 33
45. Paci, E.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 6521
46. Haberthur, U.; Caflisch, A. J. Comput. Chem. 2008, 29, 701
47. Peng, Q.; Li, H. B. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 1885
48. Guo, Z. Y.; Thirumalai, D. Biopolymers 1995, 36, 83
49. Hagen, S. J.; Hofrichter, J.; Szabo, A.; Eaton, W. A. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 11615
50. Lu, H.; Isralewitz, B.; Krammer, A.; Vogel, V.; Schulten, K. Biophys. J. 1998, 75, 662
51. Lu, H.; Schulten, K. Proteins: Struct., Funct., Genet. 1999, 35, 453
52. Carrion-Vazquez, M.; Marszalek, P. E.; Oberhauser, A. F.; Fernandez, J. M. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 11288
53. Rico, F.; Gonzalez, L.; Casuso, I.; Puig-Vidal, M.; Scheuring, S. Science 2013, 342, 741
54. Wang, T.; Ikai, A. Jpn. J. Appl. Phys., Part 1 1999, 38, 3912
55. Bornschlogl, T.; Anstrom, D. M.; Mey, E.; Dzubiella, J.; Rief, M.; Forest, K. T. Biophys. J. 2009, 96, 1508
56. Dzubiella, J. J. Phys. Chem. Lett. 2013, 4, 1829
57. Sulkowska, J. I.; Sulkowski, P.; Szymczak, P.; Cieplak, M. C. Phy. Rev. Lett. 2008, 100 058106