Simulations of stochastic sensing of proteins

Journal of the American Chemical Society

Volumn 127, Issue 51, 2005, Pages 18252-18261

  Kong, Chung Yin ^a   Muthukumar, M ^a  

^a UNIVERSITY OF MASSACHUSETTS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEXATION; COMPUTER SIMULATION; HEAVY IONS; MOLECULAR DYNAMICS; POISSON EQUATION; POLYMERS;

CHANNEL CURRENTS; CONFORMATIONAL FLUCTUATIONS; IONIC CURRENTS; STOCHASTIC SENSING;

PROTEINS;

ALPHA HEMOLYSIN; HEMOLYSIN; POLYMER; PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; COMPLEX FORMATION; DYNAMICS; ENTROPY; GENETIC ENGINEERING; ION CURRENT; PROTEIN ANALYSIS; PROTEIN CONFORMATION; SIMULATION; STOCHASTIC MODEL;

BACTERIAL TOXINS; BIOTIN; COMPUTER SIMULATION; HEMOLYSIN PROTEINS; MODELS, CHEMICAL; MODELS, MOLECULAR; POLYETHYLENE GLYCOLS; STOCHASTIC PROCESSES; STREPTAVIDIN;

EID: 29844451576     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja055695o     Document Type: Article

References (42)

1. Braha, O.; Walker, B.; Cheley, S.; Kasianowicz, J. J.; Song, L. Z.; Gouaux, J. E.; Bayley, H. Chem. Biol. 1997, 4, 497.
2. Gu, L. Q.; Braha, O.; Conlan, S.; Cheley, S.; Bayley, H. Nature 1999, 398, 686.
3. Sanchez-Quesada, J.; Ghadiri, M. R.; Bayley, H.; Braha, O. J. Am. Chem. Soc. 2000, 122, 11757.
4. Braha, O.; Gu, L. Q.; Zhou, L.; Lu, X. F.; Cheley, S.; Bayley, H. Nat. Biotechnol. 2000, 18, 1005.
5. Howorka, S.; Movileanu, L.; Lu, X. F.; Magnon, M.; Cheley, S.; Braha, O.; Bayley, H. J. Am. Chem. Soc. 2000, 122, 2411.
6. Movileanu, L.; Howorka, S.; Braha, O.; Bayley, H. Nat. Biotechnol. 2000, 18, 1091.
7. Movileanu, L.; Bayley, H. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 10137.
8. Bayley, H.; Cremer, P. S. Nature 2001, 413, 226.
9. Cheley, S.; Gu, L. Q.; Bayley, H. Chem. Biol. 2002, 9, 829.
10. Kasianowicz, J. J.; Brandin, E.; Branton, D.; Deamer, D. W. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 13770-13773.
11. Bezrukov, S. M.; Vodyanoy, I.; Brutyan, R. A.; Kasianowicz, J. J. Macromolecules 1996, 29, 8517-8522.
12. Akeson, M.; Branton, D.; Kasianowicz, J. J.; Brandin, E.; Deamber, D. W. Biophys. J. 1999, 77, 3227-3233.
13. Henrickson, S. E.; Misakian, M.; Robertson, B.; Kasianowicz, J. J. Phys. Rev. Lett. 2000, 85, 3057-3060.
14. Meller, A.; Nivon, L.; Brandin, E.; Golovchenko, J.; Branton, D. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 1079-1084.
15. Meller, A.; Nivon, L.; Branton, D. Phys. Rev. Lett. 2001, 86, 3435-3438.
16. Kong, C.; Muthukumar, M. Electrophoresis 2002, 23, 2697.
17. Muthukumar, M. Phys. Rev. Lett. 2001, 86, 3188.
18. Muthukumar, M. J. Chem. Phys. 2003, 118, 5174.
19. Kong, C. Y.; Muthukumar, M. J. Chem. Phys. 2004, 120, 3460.
20. (a) Daoud, M.; Degennes, P. G. J. Physique 1977, 38, 85.
21. (b) Sotta, P.; Lesne, A.; Victor, J. M. J. Chem. Phys. 2000, 113, 6966.
22. Hermsen, G. F.; de Geeter, B. A.; van der Vegt, N. F. A.; Wessling, M. Macromolecules 2002, 35, 5267.
23. Subramanian, G.; Williams, D. R. M.; Pincus, P. A. Europhys. Lett. 1995, 29, 285.
24. Milchev, A.; Yamakov, V.; Binder, K. Europhys. Lett. 1999, 47, 675.
25. Cifra, P.; Bleha, T. Macromolecules 2001, 34, 605.
26. Song, L. Z.; Hobaugh, M. R.; Shustak, C.; Cheley, S.; Bayley, H.; Gouaux, J. E. Science 1996, 274, 1859.
27. Korchev, Y. E.; Bashford, C. L.; Alder, G. M.; Kasianowicz, J. J.; Pasternak, C. A. J. Membr. Biol. 1995, 147, 233-239.
28. Chaiet, L.; Wolf, F. J. Arch. Biochem. Biophys. 1964, 106, 1-5.
29. Green, N. M. Adv. Protein Chem. 1975, 29, 85-133.
30. Miyamoto, S.; Kollman, P. A. Proteins 1993, 16, 226.
31. Chilkoti, A.; Tan, P. H.; Stayton, P. S. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 1754.
32. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Oxford: New York, 1987.
33. Aksimentiev, A.; Schulten, K. Biophys. J. 2005, 88, 3745.
34. Eisenberg, R. S. J. Membr. Biol. 1996, 150, 1.
35. Kurnikova, M. G.; Coalson, R. D.; Graf, P.; Nitzan, A. Biophys. J. 1999, 76, 642.
36. Corry, B.; Kuyucak, S.; Chung S. H. Biophys. J. 2000, 78, 2364.
37. Selberherr, S. Analysis and Simulation of Semiconductor Device; Sringer-Verlag: New York, 1984.
38. Hollerbach, U.; Chen, D.-P.; Eisenberg, R. S. J. Sci. Comput. 2002, 16, 373.
39. Schuss, Z.; Nadler, B.; Eisenberg, R. S. Phys. Rev. E 2001, 64, 0361161.
40. De Gennes, P. G. Scaling Concepts in Polymer Physics; Cornell University Press: Ithaca, NY, 1979.
41. Boucher, E. A.; Hines, P. M. J. Polym. Sci., Polym. Phys. Ed. 1976, 14, 2241.
42. Molyneux, P. Water-Soluble Synthetic Polvtners: Properties and Behavior, CRC Press: Boca Raton, FL, 1983; Vol. 1.