Molecular dynamics study of forced dissociation process of wheat germ agglutinin dimer

e-Journal of Surface Science and Nanotechnology

Volumn 7, Issue , 2009, Pages 825-830

  Tagami, Katsunori ^a   Sekiguchi, Hiroshi ^b   Ikai, Atsushi ^b  

^a ADVANCESOFT CORPORATION   (Japan)

^b TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

Atomic force microscopy; Biological molecules proteins; Computer simulations; Force spectroscopy; Semiempirical models and model calculations

Indexed keywords

ATOMIC FORCE MICROSCOPY; BIOINFORMATICS; COMPUTER SIMULATION; DISSOCIATION; MOLECULAR DYNAMICS; MONOMERS;

BIOLOGICAL MOLECULES-PROTEINS; DISSOCIATION PATHWAYS; DISSOCIATION PROCESS; FORCE SPECTROSCOPY; MOLECULAR DYNAMICS SIMULATIONS; MONOMER STRUCTURES; SEMI-EMPIRICAL MODELS AND MODEL CALCULATIONS; WHEAT GERM AGGLUTININ;

DIMERS;

EID: 77951791648     PISSN: None     EISSN: 13480391     Source Type: Journal    
DOI: 10.1380/ejssnt.2009.825     Document Type: Article

References (34)

1. A. F. Oberhauser, P. K. Hansma, M. C. Vazquez, and J. M. Fernandez, Proc. Natl. Acad. Sci. 98, 468 (2001).
2. J. M. Fernandez and H. Li, Science 303, 1674 (2004).
3. C. Möller, D. Fotiadis, K. Suda, A. Engel, M. Kessler, and D. J. Müller, J. Struct. Biol. 142, 369 (2003).
4. M. T. Alam, T. Yamada, U. Carlsson, and A. Ikai, FEBS Lett. 519, 35 (2002).
5. A. F. Oberhauser, C. B. Fernandez, M. C. Vazquez, and J. M. Fernandez, J. Mol. Biol. 319, 433 (2002).
6. H. Lu, B. Isralewitz, A. Krammer, V. Vogel, and K. Schulten, Biophys. J. 75, 662 (1998).
7. M. Gao, M. Wilmanns, and K. Schulten, Biophys. J. 83, 3435 (2002).
8. H. Lu and K. Schulten, Biophys. J. 79, 51 (2000).
9. E. H. Lee, M. Gao, N. Pinotsis, M. Wilmanns, and K. Schulten, Structure 14, 497 (2006).
10. S. Ohta, M. T. Alam, H. Arakawa, and A. Ikai, Biophys. J. 87, 4007 (2004).
11. V. P. Hytönen and V. Vogel, PLoS Comput. Biol. 4, e24 (2008).
12. D. N. Greene, T. Garcia, R. B. Sutton, K. M. Gernert, G. M. Benian, and A. F. Oberhauser, Biophys. J. 95, 136 (2008).
13. M. Seeber, F. Fanelli, E. Paci, and A. Caflisch, Biophys. J. 91, 3276 (2006).
14. S. Paramore and G. A. Voth, Biophys. J. 91, 3436 (2006).
15. D. Craig, A. Krammer, K. Schulten, and V. Vogel, Proc. Natl. Acad. Sci. 98, 5590 (2001).
16. F. Li, S. D. Redick, H. P. Erickson, and V. T. Moy, Biophys. J. 84, 1252 (2003).
17. E. L. Florin, V. T. Moy, and H. E. Gaub, Science 264, 415 (1994).
18. C. Yuan, A. Chen, P. Kolb, and V. T. Moy, Biochemistry 39, 10219 (2000).
19. R. Ros, F. Schwesinger, D. Anselmetti, M. Kubon, R. Schäfer, A. Plückthun, and L. Tiefenauer, Proc. Natl. Acad. Sci. 95, 7402 (1998).
20. F. Schwesinger, R. Ros, T. Strunz, D. Anselmetti, H. Güntherodt, A. Honegger, L. Jermutus, L. Tiefenauer, and A. Plückthun, Proc. Natl. Acad. Sci. 97, 9972 (2000).
21. P. Hinterdorfer, W. Baumgartner, H. J. Gruber, K. Schilcher, and H. Schindler, Proc. Natl. Acad. Sci. 93, 3477 (1996).
22. J. Fritz, A. G. Katopodis, F. Kolbinger, and D. Anselmetti, Proc. Natl. Acad. Sci. 95, 12283 (1998).
23. C. M. Yip, C. C. Yip, and M. D. Ward, Biochemistry 37, 5439 (1998).
24. H. Grubmüller, B. Heymann, and P. Tavan, Science 271, 997 (1996).
25. S. Izrailev, S. Stepaniants, M. Balsera, Y. Oono, and K. Schulten, Biophys. J. 72, 1568 (1997).
26. L. Shen, J. Shen, X. Luo, F. Cheng, Y. Xu, K. Chen, E. Arnold, J. Ding, and H. Jiang, Biophys. J. 84, 3547 (2003).
27. M. V. Bayas, K. Schulten, and D. Leckband, Biophys. J. 84, 2223 (2003).
28. T. Kim, A. Rhee, and C. M. Yip, J. Am. Chem. Soc. 128, 5330 (2006).
29. S. Lü and M. Long, Mol. Cell. Biomech. 2, 161 (2005).
30. Z. Xuan, L. Ling, and R. Chen, Eur. Biophys. J. 29, 7 (2000).
31. L. Kale, R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, and K. Schulten, J. Comp. Phys. 151, 283 (1999).
32. Unpublished. The corresponding parameter files are found on the website http://www.charmm.org.
33. R. Afrin et al., to be published.
34. W. Humphrey, A. Dalke, and K. Schulten, J. Molec. Graphics 14, 33 (1996).