A statistical model for translocation of structured polypeptide chains through nanopores

Journal of Physical Chemistry B

Volumn 113, Issue 30, 2009, Pages 10348-10356

  Ammenti, Alessandro ^a   Cecconi, Fabio ^b   Marconi, Umberto Marini Bettolo ^c   Vulpiani, Angelo ^d  

^a UNIVERSITY OF PERUGIA   (Italy)

^b INFM   (Italy)

^c UNIVERSITY OF CAMERINO   (Italy)

^d UNIVERSITÀ DI ROMA LA SAPIENZA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

FREE ENERGY; MOLECULAR DYNAMICS; NANOPORES; PROBABILITY DENSITY FUNCTION; PROTEINS; REACTION KINETICS;

CARBON BACKBONE; CENTER OF MASS; CONFINEMENT EFFECTS; CYLINDRICAL NANOPORES; DRIFT-DIFFUSION MODEL; ENERGY PROFILE; GLOBULAR PROTEINS; KINETIC CHARACTERIZATION; MOLECULAR DYNAMICS SIMULATIONS; NATIVE-CENTRIC MODELS; POLYPEPTIDE CHAIN; PULLING FORCE; REACTION COORDINATES; STATISTICAL MODELS; TRANSLOCATION PROCESS; TRANSPORT DYNAMICS; UBIQUITIN; UMBRELLA SAMPLING;

SIMULATORS;

EID: 67651202364     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp900947f     Document Type: Article

References (41)

1. Singer, S. J. Annu. Rev. Cell Biol. 1990, 6, 247-296.
2. Schatz, G.; Dobberstein, B. Science 1996, 271, 1519-1526.
3. Wickner, W.; Schekman, R. Science 2005, 310, 247-296.
4. Lodish, H.; Baltimore, D.; Berk, A.; Zipursky, S. L.; Matsudaira, P.; Durnell, J. Molecular cell biology; Freeman: New York, 1996.
5. Agarraberes, F.; Dice, J. Biochem. Biophys. Acta 2001, 1513, 1-24.
6. Kasianowicz, J.; Brandin, E.; Branton, D.; Deamer, D. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 13770-13773.
7. Meller, A. J. Phys.: Condens. Matter 2003, 15, R581-R607.
8. Sutherland, T.; Long, Y.-T.; Stefureac, R.; Bediako-Amoa, I.; Kraatz, H.-B.; Lee, J. Nano Lett. 2004, 4, 1273-1277.
9. Oukhaled, G.; Mathé, J.; Biance, A. L.; Bacri, L.; Betton, J. M.; Lairez, D.; Pelta, J.; Auvray, L. Phys. Rev. Lett. 2007, 98, 158101-158104.
10. Jiali, L.; Gershow, M.; Stein, D.; Brandin, E.; Golovchenko, J. Nat. Mater. 2003, 2, 611-615.
11. Yeh, I.-C.; Hammer, G. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 12177-12182.
12. Meller, A.; Nivon, L.; Brandin, E.; Golovchenko, J.; Branton, D. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 1079-1084.
13. Lingappa, V. R.; Katz, F. N.; Lodish, H. F.; Blobel, G. J. Biol. Chem. 1978, 253, 8667-8670.
14. Römisch, K.; Collie, N.; Soto, N.; Logue, J.; Lindsay, M.; Scheper, W.; Cheng, C.-H. C. J. Cell Sci. 2003, 116, 2875-2883.
15. Rapaport, T. Nature 2007, 450, 663-669.
16. Goloubinoff, P.; De-Los-Rios, P. Trends Biochem. Sci. 2007, 32, 372.
17. Sung, W.; Park, P. J. Phys. Rev. Lett. 1996, 77, 783-786.
18. Lubensky, D.; Nelson, D. Biophys. J. 1999, 77, 1824-1838.
19. Muthukumar, M. Phys. Rev. Lett. 2001, 86, 3188-3191.
20. Tian, P.; Andricioaei, I. J. Mol. Biol. 2005, 350, 1017-1034.
21. Tian, P.; Andricioaei, I. Biophys. J. 2006, 90, 2718-2730.
22. Wells, D.; Abramkina, V.; Aksimentiev, A. J. Chem. Phys. 2007, 127, 125101.
23. Wintrode, P.; Makhatadze, G.; Privalov, P. Proteins: Struct., Funct., Genet 1994, 18, 246-253.
24. Briggs, M.; Roder, H. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 2017-2021.
25. Marianayagam, N.; Jackson, S. Biophys. Chem. 2004, 111, 159-171.
26. Huang, L.; Kirmizialtin, S.; Makarov, D. J. Chem. Phys. 2005, 123, 124903.
27. Matysiak, S.; Montesi, A.; Pasquali, M.; Kolomeisky, A.; Clementi, C. Phys. Rev. Lett. 2006, 96, 118103/1-118103/4.
28. Fyta, M.; Melchionna, S.; Succi, S.; Kaxiras, E. Phys. Rev. E 2008, 78, 036704/1-036704/7.
29. Kumar, S.; Rosenberg, J.; Bouzida, D.; Swendsen, R.; Kollman, P. J. Comput. Chem. 1992, 13, 1011-1021.
30. Souaille, M.; Roux, B. Comput. Phys. Commun. 2001, 135, 40-57.
31. Risken, H. The Fokker-Planck equation. Methods of solution and applications, 2nd ed.; Springer Series in Synergetics; Springer: Berlin, New York, 1989
32. Redner, S. A guide to first-passage processes; Cambridge University Press: Cambridge, U.K., 2001.
33. Clementi, C.; Nymeyer, H.; Onuchic, J. J. Mol. Biol. 2000, 298, 937-953.
34. Miyazawa, S.; Jernigan, R. J. Mol. Biol. 1996, 256, 623-644.
35. Schlick, T. Molecular Modeling and Simulation - An Interdisciplinary Guide., 2nd ed.; Interdisciplinary applied mathematics mathematical biology; Springer: New York, 2002.
36. Ferrenberg, A.; Swendsen, R. Phys. Rev. Lett. 1989, 63, 1195-1198.
37. Berezhkovskii, A.; Pustovoit, M.; Bezrukov, S. J. Chem. Phys. 2002, 116, 9952-9956.
38. Berezhkovskii, A.; Gopich, I. Biophys. J. 2003, 84, 787-793.
39. Murli, A.; Rizzardi, M. ACM Trans. Math. Software 1990, 16, 158-168.
40. Metzler, R.; Klafter, J. Biophys. J. 2003, 85, 2776-2779.
41. Costantini, G.; Cecconi, F.; Marini-Bettolo-Marconi, U. J. Chem. Phys. 2006, 125, 204711.