The antigen-antibody unbinding process through steered molecular dynamics of a complex of an Fv fragment and lysozyme

Journal of Physics Condensed Matter

Volumn 20, Issue 25, 2008, Pages

  Hanasaki, Itsuo ^a   Haga, Tomoaki ^a   Kawano, Satoyuki ^a  

^a OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIGEN-ANTIBODY REACTIONS; BINDING ENERGY; BIOMOLECULES; GAUSSIAN DISTRIBUTION; MOLECULAR DYNAMICS; OPTIMIZATION;

ANTIGEN MOLECULES; ANTIGEN-ANTIBODY UNBINDING; LYSOZYME; MOLECULAR DYNAMICS (SMD) SIMULATIONS;

ENZYMES;

EID: 44649169116     PISSN: 09538984     EISSN: 1361648X     Source Type: Journal    
DOI: 10.1088/0953-8984/20/25/255238     Document Type: Article

References (34)

1. Koshland D E Jr 1958 Proc. Natl Acad. Sci. USA. 44 98-104
2. Perozzo R, Folkers G and Scapozza L 2004 J. Recept. Signal Transduct. 24 1
3. Holdgate G A and Ward W H J 2005 Drug Discov. Today 10 1543
4. Piehler J 2005 Curr. Opin. Struct. Biol. 15 4
5. Clausen-Schaumann H, Seitz M, Krautbauer R and Gaub H E 2000 Curr. Opin. Chem. Biol. 4 524
6. Willemsen O H, Snel M M E, Cambi A, Greve J, De Grooth B G and Figdor C G 2000 Biophys. J. 79 3267
7. Allison D, Hinterdorfer P and Han W 2002 Curr. Opin. Biotechnol. 13 47
8. Hinterdorfer P and Dufrne Y F 2006 Nat. Methods 3 347
9. Allen M P and Tildesley D J 1987 Computer Simulation of Liquids (Oxford: Clarendon)
10. Isralewitz B, Gao M and Schulten K 2001 Curr. Opin. Struct. Biol. 11 224-30
11. Sotomayor M and Schulten K 2007 Science 316 1144
12. Heymann B and Grubmüller H 1999 Chem. Phys. Lett. 303 1-9
13. Heymann B and Grubmüller H 2001 Biophys. J. 81 1295-313
14. Curcio R, Caflisch A and Paci E 2005 Protein Sci. 14 2499-514
15. Paci E, Caflisch A, Plückthun A and Karplus M 2001 J. Mol. Biol. 314 589-605
16. Berquand A, Xia N, Castner D G, Clare B H, Abbott N L, Dupres V, Adriaensen Y and Dufrne Y F 2005 Langmuir 21 5517
17. Jarzynski C 1997 Phys. Rev. Lett. 78 2690
18. Park S, Khalili-Araghi F, Tajkhorshid E and Schulten K 2003 J. Chem. Phys. 119 3559-66
19. Kollman P A, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case D A and Cheatham T E III 2000 Acc. Chem. Res. 33 889
20. Darve E and Pohorille A 2001 J. Chem. Phys. 115 9169
21. Rodriguez-Gomez D, Darve E and Pohorille A 2004 J. Chem. Phys. 120 3563
22. Wang J, Deng Y and Roux B 2006 Biophys. J. 91 2798
23. Case D A, Darden T A, Cheatham T E III, Simmerling C L, Wang J, Duke R E, Luo R, Merz K M, Pearlman D A, Crawley M, Walker R C, Zhang W, Wang B, Hayik S, Roitberg A, Seabra G, Wong K F, Paesani F, Wu X, Brozell S, Tsui V, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Beroza P, Mathews D H, Schafmeister C, Ross W S and Kollman P A 2006 AMBER9 (San Francisco, CA: University of California)
24. Duan Y, Wu C, Chowdhury S, Lee M C, Xiong G, Zhang W, Yang R, Cieplak P, Luo R and Lee T 2003 J. Comput. Chem. 24 1999-2012
25. Lee M C and Duan Y 2004 Proteins 55 620-34
26. Kondo H, Shiroishi M, Matsushima M, Tsumoto K and Kumagai I 1999 J. Biol. Chem. 274 27623-31
27. Onufriev A, Bashford D and Case D A 2004 Proteins 55 383-94
28. Lu H and Schulten K 1999 Chem. Phys. 247 141
29. Jensen M, Park S, Tajkhorshid E and Schulten K 2002 Proc. Natl Acad. Sci. USA 99 6731
30. Park S and Schulten K 2004 J. Chem. Phys. 120 5946
31. Orzechowski M and Cieplak P 2005 J. Phys.: Condens. Matter 17 S1627-40
32. Humphrey W, Dalke A and Schulten K 1996 J. Mol. Graph. 14 33-8
33. Hinterdorfer P, Baumgartner W, Gruber H J, Schilcher K and Schindler H 1996 Proc. Natl Acad. Sci. USA 93 3477
34. Lin S, Wang Y, Huang L, Lin C, Hsu S and Lee C 2007 Biosens. Bioelectron. 22 1013