A steered molecular dynamics study on peptide sequence prediction from force-extension profiles

Polymer

Volumn 48, Issue 10, 2007, Pages 3013-3020

  Zhang, Linxi ^a   Sun, Tingting ^b   Cheng, Jun ^b   Ma, Haizhu ^b  

^a WENZHOU UNIVERSITY   (China)

^b ZHEJIANG UNIVERSITY   (China)

Author keywords

Force extension profiles; LNB sequence; Steered molecular dynamics (SMD)

Indexed keywords

COMPUTER SIMULATION; DESORPTION; HYDROPHILICITY; HYDROPHOBICITY; PEPTIDES; SURFACE MORPHOLOGY;

FORCE EXTENSION PROFILES; LNB SEQUENCE; PEPTIDE SEQUENCES; STEERED MOLECULAR DYNAMICS (SMD);

MOLECULAR DYNAMICS;

ADSORPTION; DESORPTION; HYDROPHILIC PROPERTY; HYDROPHOBIC PROPERTY; MOLECULAR STRUCTURE; PROTEIN;

EID: 34247186335     PISSN: 00323861     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.polymer.2007.03.046     Document Type: Article

References (53)

1. Lavery R., Lebrun A., Allemand J.F., Bensimon D., and Croquette V. J Phys Condens Matter 14 (2002) R383-R414
2. Becker N., Oroudjev E., Mutz S., Cleveland J.P., Hansma P.K., Hayashi C.Y., et al. Nat Mater 2 (2003) 278-283
3. Best R.B., Brockwell D.J., Toca-Herrera J.L., Blake A.W., Smith D.A., Radford S.E., et al. Anal Chim Acta 479 (2003) 87-105
4. Best R.B., Li B., Steward A., Daggett V., and Clarke J. Biophys J 81 (2001) 2344-2356
5. Brockwell D.J., Beddard G.S., Clarkson J., Zinober R.C., Blake A., Trinick J., et al. Biophys J 83 (2002) 458-472
6. Erickson H.P. Science 276 (1997) 1090-1092
7. Fisher T.E., Marsalek P.E., and Fernandez J.M. Nat Struct Biol 7 (2000) 719-730
8. Fisher T.E., Oberhauser A.F., Vezquez M.C., Marsalek P.E., and Fernandez J. Trends Biochem Sci 24 (1999) 379-384
9. Hansma H.G., and Pietrasanta L.I. Curr Opin Chem Biol 2 (1998) 579-584
10. Hansma H.G., Pietrasanta L.I., Auerbach I.D., Sorenson C., Golan R., and Holden P.A. J Biomater Sci Polymer Ed 11 (2000) 675-683
11. Kellermayer M.S.Z., Smith S.B., Granzier H.L., and Bustamante C. Science 276 (1997) 1112-1119
12. Li H., Carrion-Vazquez M., Oberhauser A.F., Marsalek P.E., and Fernandez J.M. Nat Struct Biol 7 (2000) 1117-1120
13. Li H., Oberhauser A.F., Fowler S.B., Clarke J., and Fernandez J.M. Proc Natl Acad Sci USA 97 (2000) 6527-6531
14. Marsalek P.E., Lu H., Li H., Carrion-Vazquez M., Oberhauser A.F., Schulten K., et al. Nature 402 (1999) 100-103
15. Oberhauser A.F., Badilla-Fernandez C., Carrion-Vazquez M., and Fernandez J.M. J Mol Biol 319 (2002) 433-447
16. Oberhauser A.F., Hansma P.K., Carrion-Vazquez M., and Fernandez J.M. Proc Natl Acad Sci USA 98 (2001) 468-472
17. Oberhauser A.F., Marszalek P.E., Erickson H., and Fernandez J.M. Nature 393 (1998) 181-185
18. Pennisi M.E. Science 283 (1999) 168-169
19. Rief M., Fernandez J.M., and Gaub H.E. Phys Rev Lett 81 (1998) 4764-4767
20. Rief M., Gautel M., Oesterhelt F., Fernandez J.M., and Gaub H.E. Science 276 (1997) 1109-1112
21. Rief M., Pascual J., Saraste M., and Gaub H.E. J Mol Biol 286 (1999) 553-561
22. Smith B.L., Schaffer T.E., Viani M., Thompson J.B., Frederick N.A., Kindt J., et al. Nature 399 (1999) 761-763
23. Thompson J.B., Hansma H.G., Hansma P.K., and Plaxco K.W. J Mol Biol 322 (2002) 645-652
24. Thompson J.B., Kindt J.H., Drake B., Hansma H.G., Morse D.E., and Hansma P.K. Nature 414 (2001) 773-776
25. Tskhovrebova L., Trinic J.A., Sleep J.A., and Simmons R.M. Nature 387 (1997) 308-312
26. Viani M.B., Schaffer T.E., Paloczi G.T., Pietrasanta L.I., Smith B.L., Thompson J.B., et al. Rev Sci Instrum 70 (1999) 4300-4303
27. Viani M.B., Schaffer T.E., Chand A., Rief M., Gaub H.E., and Hansma P.K. J Appl Phys 86 (1999) 2258-2262
28. Zhuang X., and Rief M. Curr Opin Struct Biol 13 (2003) 88-97
29. Zinober R.C., Brockwell D.J., Beddard G.S., Blake A.W., Olmsted P.D., Radford S.E., et al. Protein Sci 11 (2002) 2759-2765
30. Binning G., Quate C.F., and Gerber G. Phys Rev Lett 56 (1986) 930-933
31. Ashkin A., and Dziedzic J.M. Science 235 (1987) 1517-1520
32. Evans E., Ritchie K., and Merkel R. Biophys J 68 (1995) 2580-2587
33. Israelachvili J.N. Intermolecular and surface forces (1992), Academic Press, London
34. Isralewitz B., Baudry J., Gullingsrud J., Kosztin D., and Schulten K. J Mol Graph Model 19 (2001) 13-25
35. Isralewitz B., Gao M., and Schulten K. Curr Opin Struct Biol 11 (2001) 224-230
36. Izrailev S., Stepaniants S., Balsera M., Oono Y., and Sechulten K. Biophys J 72 (1997) 1568-1581
37. Lu H., and Schulten K. Proteins Struct Func Genetics 35 (1999) 453-463
38. Meller A., Nivon L., and Branton D. Phys Rev Lett 86 (2001) 3435-3439
39. Chen P., Gu J., Brandin E., Kim Y.R., Wang Q., and Branton D. Nano Lett 4 (2004) 2293-2298
40. Fologea D., Gershow M., Ledden B., McNabb D.S., Golovchenko J.A., and Li J. Nano Lett 5 (2005) 1905-1909
41. Braslavsky I., Hebert B., Kartalov E., and Quake S.R. Proc Natl Acad Sci USA 100 (2003) 3960-3964
42. Gracheva M.E., Xiong A., Aksimentiev A., Schulten K., Timp G., and Leburton J.P. Nanotechnology 17 (2006) 622-633
43. Lagerqvist J., Zwolak M., and Di Ventra M. Nano Lett 6 (2006) 779-782
44. Voulgarakis N.K., Redondo A., Bishop A.R., and Rasmussen K.ø. Nano Lett 6 (2006) 1483-1486
45. Dill K.A. Biochemistry 24 (1985) 1501-1509
46. Lau K.F., and Dill K.A. Macromolecules 22 (1989) 3986-3997
47. Kolinsky A., Skolnick J., and Yaris R. Biopolymers 26 (1987) 937-962
48. Honeycutt J.D., and Thirumalai D. Proc Natl Acad Sci USA 87 (1990) 3526-3529
49. Kirmizialtin S., Ganesan V., and Makarov D.E. J Chem Phys 121 (2004) 10268-10277
50. Guo Z., and Thirumalai D. J Chem Phys 97 (1992) 525-535
51. Veitshans T., Klimov D., and Thirumalai D. Fold Des 2 (1996) 1-22
52. Li F.Y., Yuan J.M., and Mou C.Y. Phys Rev E 63 (2001) 021905-021910
53. Beeman D. J Comp Phys 20 (1976) 130-139