Visualizing nature at work from the nano to the macro scale

Nanobiotechnology

Volumn 1, Issue 1, 2005, Pages 7-21

  Sanner, Michel F ^a   Stolz, Martin ^b   Burkhard, Peter ^c   Kong, Xiong Peng ^d   Min, Guongwei ^d   Sun, Jung Tien ^e   Driamov, Sergey ^f   Aebi, Ueli ^b   Stoffler, Daniel ^a,b  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF BASEL   (Switzerland)

^c UNIVERSITY OF CONNECTICUT   (United States)

^d NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e New York School of Medicine   (United States)

^f UNIVERSITY HOSPITAL BASEL   (Switzerland)

Author keywords

Atherosclerosis; Data visualization; Electron microscopy; Molecular modeling; Nanoparticles; Nuclear pore complex; Osteoarthritis; Scanning force microscopy; Urinary tract infection; Visual programming

Indexed keywords

EID: 24644442127     PISSN: 15511286     EISSN: None     Source Type: Journal    
DOI: 10.1385/Nano:1:1:7     Document Type: Article

References (59)

1. Goodsell, D. S. (2004), Bionanotechnology: lessons from nature. Wiley-Liss, New York.
2. Steinmetz, M., Stoffler, D., Hoenger, A., Bremer, A., and Aebi, U. (1997), J. Struct. Biol. 119, 295-320.
3. Orlova, E. V. and Saibil, H. R. (2004), Curr. Opin. Struct. Biol. 14, 584-590.
4. Dubochet, J., Adrian, M., Chang, J. J., et al. (1988), Q. Rev. Biophys. 21, 129-228.
5. Harrison, S. C. (2004), Nat. Struct. Mol. Biol. 11, 293-295.
6. Fu, R. and Cross, T. A. (1999), Annu. Rev. Biophys. Biomol. Struct. 28, 235-268.
7. Binning, G. and Rohrer, H. (1982), Helv. Phys. Acta 55, 726.
8. Binning, G., Quate, C. F., and Gerber, C. (1986), Phys. Rev. Lett. 56, 930-933.
9. Müller, D. J., Schabert, F. A., Büldt, G., and Engel, A. (1995), Biophys. J. 68, 1681-1686.
10. Stoffler, D., Goldie, K. N., Feja, B., and Aebi, U. (1999), J. Mol. Biol. 287, 741-752.
11. Stolz, M., Stoffler, D., Aebi, U., and Goldsbury, C. (2000), J. Struct. Biol. 131, 171-180.
12. Tao, Y., Olson, N. H., Xu, W., Anderson, D. L., Rossmann, M. G., and Baker, T. S. (1998), Cell 95, 431-437.
13. Raman, S., Machaidze, G., Lustig, A., Cole, J., and Burkhard, P. (2004), Nat. Mat, submitted.
14. Burkhard, P., Meier, M., and Lustig, A. (2000), Protein Sci, 9, 2294-2301.
15. Burkhard, P., Ivaninskii, S., and Lustig, A. (2002), J. Mol. Biol. 318, 901-910.
16. Burkhard, P., Stetefeld, J., and Strelkov, S.V. (2001), Trends Cell Biol. 11, 82-88.
17. Tao, Y., Strelkov, S. V., Mesyanzhinov, V. V., and Rossmann, M. G. (1997), Structure 5, 789-798.
18. Stetefeld, J., Frank, S., Jenny, M., et al. (2003), Structure (Camb.) 11, 339-346.
19. Malashkevich, V.N., Kammerer, R.A., Efimov, V.P., Schulthess, T., and Engel, J. (1996), Science 274, 761-765.
20. De Jong, M., Valkema, R., Jamar, F., et al. (2002), Sem. Nucl. Med. 32, 133-140.
21. Aebi, U., Ten Heggeler, B., Onorato, L., Kistler, J., and Showe, M. K. (1977), Proc. Natl. Acad. Sci. USA 74, 5514-5518.
22. Kistler, J., Aebi, U., Onorato, L., Ten Heggeler, B., and Showe, M. K. (1978), J. Mol. Biol. 126, 571-589.
23. Buhle, E. L. and Aebi, U. (1984), J. Ultrastruct. Res. 89, 165-178.
24. Bachmann, M. F. and Zinkernagel, R. M. (1996), Immunol. Today 17, 553-558.
25. Nieba, L. and Bachmann, M. F. (2000), Mod. Asp. Immunobiol. 1, 56-39.
26. Baschong, W., Hasler, L., Haner, M., Kistler, J., and Aebi, U. (2003), J. Struct. Biol. 143, 258-262.
27. Zinkernagel, R. M. (1996), Science 271, 173-178.
28. Hicks, R. M. (1975), Biol. Rev. Camb. Philos. Soc. 50, 215-246.
29. Sun, T.-T., Liang, F. X., and Wu, X. R. (1999), Adv. Exp. Med. Biol. 462, 7-18.
30. Hooton, T. M. and Stamm, W. E. (1997), Infect. Dis. Clin. North Am. 11, 551-581.
31. Walz, T., Haner, M., Wu, X. R., et al. (1995), J. Mol. Biol. 248, 887-900.
32. Min, G., Zhou, G., Schapira, M., Sun, T. T., and Kong, X. P. (2003), J. Cell Sci. 116, 4087-4094.
33. Kachar, B., Liang, F., Lins, U., et al. (1999), J. Mol. Biol. 285, 595-608.
34. Min, G., Stolz, M., Zhou, G., et al. (2002), J. Mol. Biol. 317, 697-706.
35. Reichelt, R., Holzenburg, A., Buhle, Jr., E. L., Jarnik, M., Engel, A., and Aebi, U. (1990), J. Cell Biol. 110, 883-894.
36. Fahrenkrog, B. and Aebi, U. (2003), Nat. Rev. Mol. Cell Biol. 4, 757-766.
37. Jarnik, M. and Aebi, U. (1991), J. Struct. Biol. 107, 291-308.
38. Panté, N. and Aebi, U. (1996), Crit. Rev. Biochem. Mol. Biol. 31, 153-199.
39. Lutzmann, M., Kunze, R., Buerer, A., Aebi, U., and Hurt, E. (2002). Modular self-assembly of a Y-shaped multiprotein complex made from seven nucleoporins. EMBO J. 21, 387-397.
40. Fahrenkrog, B., Koser, J., and Aebi, U. (2004), The nuclear pore complex: a jack of all trades? Trends Biochem. Sci., 29, 175-182.
41. Stoffler, D., Feja, B., Fahrenkrog, B., et al. (2003), J. Mol. Biol. 328, 119-130.
42. Beck, M., Forster, F., Ecke, M., et al. (2004), Science 306, 1387-1390.
43. Fahrenkrog, B., Maco, B., Fager, A., et al. (1992), J. Struct. Biol. 140, 254-267.
44. Shah, S., Tugendreich, S., and Forbes, D. (1998), J. Cell Biol. 1998, 141, 31-49.
45. Bastos, R., Lin, A., Enarson, M., and Burke, B. (1996), J. Cell Biol. 134, 1141-1156.
46. Pasterkamp, G., Falk, E., Woutman, H., and Borst, C. (2000), J. Am. Coll. Cardiol. 36, 13-21.
47. Sinclair, D.A., Smith, I.R., Wickramasinghe, H.K., and McAvoy, B. R. (1982), Ultrasonics Symposium Proceedings IEEE, New York, NY, Vol 2, p. 1090.
48. Stolz, M., Raiteri, R., Daniels, A. U., VanLandingham, M. R., Baschong, W., and Aebi, U. (2004), Biophys. J. 86, 3269-3283.
49. Hunziker, P., Stolz, M., and Aebi, U. (2002), Chimia 56, 520-526.
50. Oberleithner, H., Schneider, S. W., Albermann, L., et al. (2003), J. Membr. Biol. 196, 163-172.
51. Rotsch, C. and Radmacher, M. (2000), Biophys. J. 78, 520-535.
52. Stolz, M., Imer, R., Staufer, U., and Aebi, U. (2003), Bioworld 2-4, www.bioworld.ch.
53. Stolz, M., Imer, R., Staufer, U., Friederich, N. F., and Aebi, U. (2004), http://www.nccr-nano.org/nccr/media/nanonews/nanonews_03.
54. Sanner, M. F. (2005), Using the Python Programming Language for Bioinformatics. Encyclopedia of Genomics, proteomics and bioinformatics. Addision-Wesiey, John Wiley & Sons, Ltd. (in press).
55. Sanner, M. F. (2005), Structures, Special issue in visualization, simulation and representation of biological complexes (in press).
56. Lutz, M. (2001), Programming Python 2nd ed. O'Reilly & Associates, Inc., Sebastapol, CA, www.python.org.
57. Sanner, M. F. (1999), J. Mol. Graphics Mod. 17, 57-61.
58. Sanner, M. F., Stoffler, D., and Olson A. J. (2002), In: Proceedings of the 10th International Python Conference. February 4-7, 2002, pp. 103-115.
59. Stoffler, D., Coon, S. I., Huey, R., Olson, A. J., and Sanner, M. F. (2003), In: Proceedings of the Thirty-Sixth Annual Hawaii International Conference on System Sciences (CD/ROM), January 6-9, 2003, Computer Society Press.