Effective binding force calculation in dimeric proteins

Molecular Simulation

Volumn 30, Issue 11-12, 2004, Pages 807-816

  Maragliano, Luca ^a   Ferrario, Mauro ^a   Ciccotti, Giovanni ^b  

^a UNIVERSITY OF MODENA AND REGGIO EMILIA   (Italy)

^b SAPIENZA UNIVERSITY OF ROME   (Italy)

Author keywords

Blue Moon; Dimers; Molecular dynamics; Photobacterium leiognathi

Indexed keywords

COMPUTER SIMULATION; DIMERS; ENZYMES; HYDROPHOBICITY; MOLECULAR DYNAMICS; MONOMERS; POLYPEPTIDES;

BLUE MOON; GLICINE (GLY); MOLECULAR RECOGNITION; PHOTOBACTERIUM LEIOGNATHI;

PROTEINS;

EID: 11144256402     PISSN: 08927022     EISSN: None     Source Type: Journal    
DOI: 10.1080/0892702042000270205     Document Type: Conference Paper

References (23)

1. Janin, J. (1996) "Protein-protein recognition", Prog. Biophys. Mol. Biol. 64, 145.
2. Chakrabarti, P. and Janin, J. (2002) "Dissecting proteinprotein recognition sites", PROTEINS: Struct. Fund. Genet. 47, 334.
3. LoConte, L., Chothia, C. and Janin, J. (1999) "The atomic structure of protein-protein recognition sites", J. Mol. Biol. 285, 2177.
4. Stitesand, W. (1997) "Protein-protein interactions: interface structure, binding thermodynamics and mutational analysis", Chem. Rev. 97, 1233.
5. Creighton, T. (1993) Proteins. Structure and Molecular Properties (W.H. Freeman and Company, New York).
6. Bordo, D., Matak, D., Djinovic-Carugo, K., Rosano, C., Pesce, A., Bolognesi, M., Stroppolo, M., Falconi, M., Battistoni, A. and Desideri, A. (1999) "Evolutionary constraints for dimer formation in prokaryotic Cu, Zn Superoxide dismutase", J. Mol. Biol. 285, 283.
7. Sergi, A., Ciccotti, G., Falconi, M., Desideri, A. and Ferrario, M. (2002) "Effective binding force calculation in a dimeric protein by molecular dynamics simulation", J. Chem. Phys. 116, 6329.
8. Carter, E.A., Ciccotti, G., Hynes, J.T. and Kapral, R. (1989) "A new ensemble for molecular dynamics simulation of rare events", Chem. Phys. Lett. 156, 472.
9. Sprik, M. and Ciccotti, G. (1998) "Free energy from constrained molecular dynamics", J. Chem. Phys. 109, 7737.
10. Goldstein, H. (1980) Classical Mechanics (Addison-Wesley, Reading, MA.
11. Coluzza, I., Sprik, M. and Ciccotti, G. (2003) "Constrained reaction coordinate dynamics for systems with constraints", Mol. Phys. 101, 2885-2894.
12. Stroppolo, M., Pesce, A., Falconi, M., O'Neill, P., Bolognesi, M. and Desideri, A. (2000) "Single mutation at the subunit interface confers extra efficiency to Cu, Zn Superoxide dismutase", FEBS Lett. 483, 17.
13. Melchionna, S. and Cozzini, S. (2000) DL-protein User Manual, Tech. Rep., http:/www.sissa.it/cm/DLPROTEIN
14. Gunsteren, W.V and Berendsen, H.J.C. (1987) Gromos Manual, Tech. Rep., University of Groningen, Groningen.
15. Berendsen, H., Postma, J., Gusteren, W. and Hermans, J. (1983) "The missing term in effective pair potential", J. Phys. Chem. 91, 6269.
16. Ciccotti, G. and Ryckaert, J. (1986) "Molecular dynamics simulations of rigid molecules", Comp. Phys. Rep. 4, 345.
17. Frenkel, D. and Smit, B. (2002) Understanding Molecular Simulations (Academic Press, New York).
18. Esmann, U., Perera, L., Berkowitz, M., Darden, T., Lee, H. and Pedersen, L. (1995) "A smooth particle mesh Ewald method", J. Chem. Phys. 105, 8577.
19. Martyna, G.J., Tuckerman, M.E., Tobias, D.J. and Klein, M.L. (1996) "Explicit reversible integrators for extended systems dynamics", Mol. Phys. 87, 1117.
20. Andersen, H. (1983) "Rattle: a "velocity" version of the shake algorithm for molecular dynamics calculation", J. Comput. Phys. 52, 24.
21. Tuckerman, M.E., Berne, B.J. and Martyna, G.J. (1992) "Reversible multiple time scale molecular dynamics", J. Chem. Phys. 97, 1990.
22. Nosè, S. (1991) "Constant temperature molecular-dynamics methods", Prog. Theor. Phys. Suppl. 1, 103.
23. Stroppolo, M., Pesce, A., D'Orazio, M., O'Neill, P., Bordo, D., Rosano, C., Milani, M., Battistoni, A., Bolognesi, M. and Desideri, A. (2001) "Single mutations at the subunit interface modulate copper reactivity in Photobacterium leiognathi Cu, Zn Superoxide dismutase", J. Mol. Biol. 308, 555.