Translocation of a β-hairpin-forming peptide through a cylindrical tunnel

Journal of Chemical Physics

Volumn 121, Issue 20, 2004, Pages 10268-10277

  Kirmizialtin, Serdal ^a   Ganesan, Venkat ^b,c   Makarov, Dmitrii E ^a,c  

^a Section of Molecular Genetics and Microbiology   (United States)

^b The University of Texas at Austin   (United States)

^c UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYLINDRICAL TUNNELS; HOMOPOLYMER MODELS; PROTEIN STABILITY;

CRYSTAL STRUCTURE; DNA; ENTROPY; ESCHERICHIA COLI; FREE ENERGY; PROTEINS; RNA;

POLYPEPTIDES;

NANOMATERIAL; PEPTIDE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN TRANSPORT; THERMODYNAMICS;

COMPUTER SIMULATION; MODELS, MOLECULAR; NANOSTRUCTURES; PEPTIDES; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN TRANSPORT; THERMODYNAMICS;

EID: 10844297348     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1807832     Document Type: Article

References (64)

1. U. K. Kaemmli and M. Favre, J. Mol. Biol. 80, 575 (1973).
2. F. Jähnig, Proc. Natl. Acad. Sci. U.S.A. 80, 3691 (1983).
3. V. R. Lingappa, J. Chaidez, C. S. Yost, and J. Hedgepetch, Proc. Natl. Acad. Sci. U.S.A. 81, 456 (1984).
4. K. M. Choi and R. Brimacombe, Nucleic Acids Res. 26, 887 (1998).
5. I. S. Gabashvili, S. T. Gregory, M. Valle, R. Grassucci, M. Worbs, M. C. Wahl, A. E. Dahlberg, and J. Frank, Mol. Cell 8, 181 (2001).
6. B. Hardesty and G. Kramer, Prog. Nucleic Acid Res. Mol. Biol. 65, 41 (2001).
7. P. Nissen, H. Hansen, N. Ban, P. B. Moore, and T. Steitz, Science 289, 920 (2000).
8. A. Yonath, K. R. Leonard, and H. G. Wittman, Science 236, 813 (1987).
9. J. R. Verschoor, S. Warner, S. Srivastava, R. A. Grassucci, and J. Frank, Nucleic Acids Res. 15, 655 (1998).
10. H. Zhou and A. K. Dill, Biochemistry 40, 11289 (2001).
11. Y. Wei, J. Xu, Q. Feng, H. Dong, and M. Lin, Mater. Lett. 44, 6 (2000).
12. D. K. Eggers and J. S. Valentine, Protein Sci. 10, 250 (2000).
13. F. Takagi, N. Koga, and S. Takada, Proc. Natl. Acad. Sci. U.S.A. 100, 11367 (2003).
14. G. Ping, J. M. Yuan, M. Vallieres, H. Dong, Z. Sun, Y. Wei, F. Y. Li, and S. H. Lin, J. Chem. Phys. 118, 8042 (2003).
15. M. Friedel, D. J. Sheeler, and J. E. Shea, J. Chem. Phys. 118, 8106 (2003).
16. D. K. Klimov, D. Newfield, and D. Thirumalai, Proc. Natl. Acad. Sci. U.S.A. 99, 8019 (2002).
17. G. Kramer, V. Ramachandiran, and B. Hardesty, Recent Res. Devel. Anal. Biochem. 1, 39 (2001).
18. I. Mingarro, I. Nilson, P. Whitley, and G. Heijine, Cell Biol. 1, 3 (2000).
19. W. J. Netzer and F. U. Hartl, Nature (London) 388, 343 (1998).
20. P. Whitley, I. Nilson, and G. Heijine, J. Biol. Chem. 271, 6241 (1995).
21. W. Sung and P. J. Park, Phys. Rev. Lett. 77, 783 (1996).
22. E. A. Di Marzio and A. J. Mandell, J. Chem. Phys. 107, 5510 (1997).
23. M. Muthkumar, Phys. Rev. Lett. 86, 3188 (2000).
24. M. Muthkumar, J. Chem. Phys. 118, 5174 (2003).
25. S. S. Chern, A. E. Cárdenas, and R. D. Coalson, J. Chem. Phys. 115, 7772 (2001).
26. E. Slonkina and A. B. Kolomeisky, J. Chem. Phys. 118, 7112 (2002).
27. M. P. Morrissey, Z. Ahmed, and E. I. Shakhnovich, Polymer 45, 557 (2003).
28. J. J. Kasianovicz, E. Brandin, D. Branton, and D. W. Deamer, Proc. Natl. Acad. Sci. U.S.A. 93, 13770 (1996).
29. M. Akeson, D. Branton, J. J. Kasianovicz, E. Brandin, and D. W. Deamer, Biophys. J. 77, 3227 (1999).
30. B. Hanss, E. Leal-Pinto, L. A. Bruggeman, T. D. Copeland, and P. E. Klotman, Proc. Natl. Acad. Sci. U.S.A. 95, 1921 (1998).
31. A. Meller, L. Nivon, E. Brandin, D. Golovchenko, and D. Branton, Proc. Natl. Acad. Sci. U.S.A. 97, 1079 (2000).
32. A. Meller, L. Nivon, and D. Branton, Phys. Rev. Lett. 86, 3435 (2001).
33. S. Howorka, L. Movileanu, X. Lu, M. Magnon, S. Cheley, O. Braha, and H. Bayley, J. Am. Chem. Soc. 122, 2411 (2000).
34. T. Veitshans, D. Klimov, and D. Thirumalai, Folding Des. 2, 1 (1996).
35. R. H. Pain, Mechanisms of Protein Folding, 2nd ed. (Oxford University Press, New York, 2000).
36. R. Du, A. Y. Grosberg, T. Tanaka, and M. Rubinstein, Phys. Rev. Lett. 84, 2417 (2000).
37. M. Karplus and A. Šali, Curr. Opin. Struct. Biol. 5, 58 (1995).
38. M. Karplus, Physica A 263, 389 (1999).
39. Y. Duan and P. A. Kollman, Science 282, 740 (1998).
40. B. Zagrovic, E. J. Sorin, and V. Pande, J. Mol. Biol. 313, 151 (2001).
41. B. Zagrovic, C. D. Snow, S. Khaliq, M. R. Shirts, and V. S. Pande, J. Mol. Biol. 323, 153 (2002).
42. J. D. Honeycutt and D. Thirumalai, Biopolymers 32, 695 (1992).
43. J. N. Onuchic, Z. Luthey-Schulten, and P. G. Wolynes, Annu. Rev. Phys. Chem. 48, 545 (1997).
44. E. I. Shakhnovich, Curr. Opin. Struct. Biol. 7, 29 (1997).
45. A. K. Dill, Protein Sci. 8, 1166 (1999).
46. C. Clementi, P. A. Jennings, and J. N. Onuchic, Proc. Natl. Acad. Sci. U.S.A. 97, 5871 (2000).
47. Z. Guo and D. Thirumalai, Biopolymers 36, 83 (1995).
48. Z. Guo and C. L. Brooks, Biopolymers 42, 745 (1997).
49. M. G. Paterlini and D. M. Ferguson, Chem. Phys. 236, 243 (1998).
50. U. Hansmann and Y. Okamoto, J. Comput. Chem. 18, 920 (1997).
51. A. P. Lyubartsev, A. A. Martsinovski, S. V. Shevkunov, and P. N. Velyaminov, J. Chem. Phys. 96, 1776 (1992).
52. D. D. Frantz, D. L. Freeman, and J. D. Doll, J. Chem. Phys. 93, 2769 (1990).
53. B. A. Berg and T. Neuhaus, Phys. Lett. B 267, 249 (1991).
54. Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 314, 141 (1999).
55. D. Frenkel and B. Smit, Understanding Molecular Simulation, 2nd ed. (Academic, San Diego, 2002).
56. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 63, 1195 (1989).
57. P. Li and D. E. Makarov, J. Chem. Phys. 119, 9260 (2003).
58. D. Klimov and D. Thirumalai, Phys. Rev. Lett. 79, 317 (1997).
59. C. J. Camacho and D. Thirumalai, Proc. Natl. Acad. Sci. U.S.A. 90, 6369 (1993).
60. P. G. De Gennes, Scaling Concepts in Polymer Physics (Cornell University Press, Ithaca, N.Y., 1979).
61. D. L. Nelson, A. L. Lehninger, and M. M. Cox, Lehninger Principles of Biochemistry (Worth, New York, 2000).
62. B. Maier, L. Potter, M. So, H. S. Seifert, and M. P. Sheetz, Proc. Natl. Acad. Sci. U.S.A. 99, 16012 (2002).
63. R. B. Best, D. J. Brockwell, J. L. Toca-Herrera, A. W. Blake, D. A. Smith, S. E. Radford, and J. Clarke, Anal. Chim. Acta 479, 87 (2003).
64. R. Lavery, A. Lebrun, J.-F. Allemand, D. Bensimon, and V. Croquette, J. Phys.: Condens. Matter 14, R383 (2002).