MD simulations on the influences of an external force on the water transportation behavior through a cyclic peptide nanotube

Computational Materials Science

Volumn 78, Issue , 2013, Pages 47-54

  Liu, Dongyan ^a   Fan, Jianfen ^a   Song, Xuezeng ^a   Li, Rui ^a   Li, Hui ^a  

^a SOOCHOW UNIVERSITY   (China)

Author keywords

External force; Gating mechanism; Molecular dynamics; Transmembrane peptide nanotube; Water transportation

Indexed keywords

CYCLIC PEPTIDE NANOTUBES; EXTERNAL FORCE; GATING MECHANISMS; MOLECULAR CONFIGURATIONS; PEPTIDE NANOTUBES; SIMULTANEOUS FORMATION; STEERED MOLECULAR DYNAMICS; WATER TRANSPORTATION;

DEFORMATION; MOLECULAR DYNAMICS; MOLECULES; PEPTIDES;

NANOTUBES;

EID: 84879098633     PISSN: 09270256     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.commatsci.2013.05.013     Document Type: Article

References (53)

1. H.S. Kim, J.D. Hartgerink, and M.R. Ghadiri J. Am. Chem. Soc. 120 1998 4417 4424
2. H.F. Liu, J. Chen, Q. Shen, W. Fu, and W. Wu Mol. Pharm. 7 2010 1985 1994
3. H. Hwang, G.C. Schatz, and M.A. Ratner J. Phys. Chem. A 133 2009 4780 4787
4. A. Khalfa, W. Treptow, B. Maigret, and M. Tarek Chem. Phys. 358 2009 161 170
5. E. Khurana, R.H. DeVane, A. Kohlmeyer, and M.L. Klein Nano Lett. 8 2008 3626 3630
6. M.R. Ghadiri, J.R. Granja, R.A. Milligan, D.E. McRee, and N. Khazanovich Nature 366 1993 324 327
7. J. Sánchez-Quesada, M.P. Isler, and M.R. Ghadiri J. Am. Chem. Soc. 124 2002 10004 10005
8. H.F. Liu, J. Chen, and Q. Shen Mol. Pharm. 7 2010 1985 1994
9. M. Engels, D. Bashford, and M.R. Ghadiri J. Am. Chem. Soc. 177 1995 9151 9158
10. M. Tarek Biophys. J. 85 2003 2287 2298
11. J. Liu, J.F. Fan, M. Tang, and W.Q. Zhou J. Phys. Chem. A 114 2010 2376 2383
12. J. Liu, J.F. Fan, M. Tang, M. Cen, J.F. Yang, Z. Liu, and W.Q. Zhou J. Phys. Chem. B 114 2010 12183 12192
13. J. Liu, J.F. Fan, M. Cen, X.Z. Song, D.Y. Liu, W.Q. Zhou, Z. Liu, and J.F. Yang J. Chem. Inf. Model. 52 2012 2132 2138
14. J. Gullingsrud, D. Kosztin, and K. Schulten Biophys. J. 80 2001 2074 2081
15. A.E. Aliaga, H. Ahumada, K. Sepúlveda, J.S. Gomez-Jeria, C. Garrido, B.E. Weiss-López, and M.M. Campos-Vallette J. Phys. Chem. C 115 2011 3982 3989
16. F.Q. Zhu, and G. Hummer Biophys. J. 97 2009 2456 2463
17. S.H. Ghaderi, and E. Hajiesmaili Comput. Mater. Sci. 55 2012 344 349
18. J.Y. Pang, and G.Y. Xu Comput. Mater. Sci. 65 2012 324 330
19. G. Hummer, J.C. Rasaiah, and J.P. Noworyta Nature 414 2001 188 190
20. S. Ebrahimi, A. Montazeri, and H. Rafii-Tabar Comput. Mater. Sci. 69 2013 29 39
21. Y. Wang, Y.J. Zhao, and J.P. Huang J. Phys. Chem. B 115 2011 13275 13279
22. X.J. Gong, J.Y. Li, H. Zhang, R.Z. Wan, H.J. Lu, S. Wang, and H.P. Fang Phys. Rev. Lett. 101 1-4 2008 257801
23. J.Y. Su, and H.X. Guo ACS Nano 5 2011 351 359
24. G.C. Zuo, R. Shen, S.J. Ma, and W.L. Guo ACS Nano 4 2010 205 210
25. R.Z. Wan, J.Y. Li, H.J. Lu, and H.P. Fang J. Am. Chem. Soc. 127 2005 7166 7170
26. J.Y. Li, X.J. Gong, H.J. Lu, Ding Li, H.P. Fang, and R.H. Zhou Proc. Natl. Acad. Sci. USA 104 2007 3687 3692
27. X.J. Gong Nat. Nanotechnol. 2 2007 709 712
28. S. Wang, H.J. Lu, Y.S. Tu, C.L. Wang, and H.P. Fang Chin. Phys. Lett. 26 1-3 2009 068702
29. E. Khurana, S.O. Nielsen, B. Ensing, and M.L. Klein J. Phys. Chem. B 110 2006 18965 18972
30. H. Hwang, G.C. Schatz, and M.A. Ratner J. Phys. Chem. A 113 2009 4780 4787
31. R. García-Fandiño, L. Castedo, J.R. Granja, and S.A. Vázquez J. Phys. Chem. B 114 2010 4973 4983
32. R. Vijayaraj, S.S. Raman, R.M. Kumar, and V. Subramanian J. Phys. Chem. B 114 2010 16574 16583
33. A. Ghorai, A. Gayen, G. Kulsi, E. Padmanaban, A. Laskar, B. Achari, C. Mukhopadhyay, and P. Chattopadhyay Org. Lett. 13 2011 5512 5515
34. J.C. Zhu, J. Cheng, Z.X. Liao, Z.H. Lai, and B. Liu J. Comput. Aided Mol. Des. 22 2008 773 781
35. E. Khurana, R.H. DeVane, A. Kohlmeyer, and M.L. Klein Nano Lett. 8 2008 3626 3630
36. L.Q. Gu, M.D. Serra, J.B. Vincent, G. Vigh, S. Cheley, O. Braha, and H. Bayley Proc. Natl. Acad. Sci. USA. 97 8 2000 3959 3964
37. C. Chipot, and M. Tarek Phys. Biol. 3 2006 S20 S25
38. H. Okamoto, T. Nakanishi, Y. Nagai, M. Kasahara, and K. Takeda J. Am. Chem. Soc. 125 2003 2756 2769
39. T. Róg, K. Murzyn, J. Milhaud, M. Karttunen, and M. Pasenkiewicz-Gierula J. Phys. Chem. B 113 2009 2378 2387
40. B. Eisenberg Acc. Chem. Res. 31 1998 117 123
41. S. Leekumjorn, and A.K. Sum J. Phys. Chem. B 111 2007 6026 6033
42. Y. Yano, A. Yamamoto, M. Ogura, and K. Matsuzaki Biochemistry-US 50 2011 6806 6814
43. L.E. Townsley, W.A. Tucker, S. Sham, and J.F. Hinton Biochemistry-US 40 2001 11676 11686
44. S.-W. Chiu, S. Subramaniam, and E. Jakobsson Biophys. J. 76 1999 1939 1950
45. B.L. de Groot, D.P. Tieleman, P. Pohl, and H. Grubmüller Biophys. J. 82 2002 2042 2934
46. G.J. Martyna, D.J. Tobias, and M.L. Klein J. Chem. Phys. 5 1994 4177 4189
47. T.A. Darden, D.M. York, and L.G. Pedersen J. Chem. Phys. 98 1993 10089 10092
48. B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, and M. Karplus J. Comput. Chem. 4 1983 187 217
49. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein J. Chem. Phys. 79 1983 926 935
50. J.C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R.D. Skeel, L. Kale, and K. Schulten J. Comput. Chem. 26 2005 1781 1802
51. W. Humphrey, A. Dalke, and K. Schulten J. Mol. Graph 14 1996 33 38
52. B. Isralewitz, M. Gao, and K. Schulten Curr. Opin. Struct. Biol. 11 2001 224 230
53. U. Zimmerli, P.G. Gonnet, J.H. Walther, and P. Koumoutsakos Nano Lett. 5 2005 1017 1022