Protocol for MM/PBSA molecular dynamics simulations of proteins

Biophysical Journal

Volumn 85, Issue 1, 2003, Pages 159-166

  Fogolari, Federico ^a,c   Brigo, Alessandro ^b   Molinari, Henriette ^a  

^a UNIVERSITY OF VERONA   (Italy)

^b UNIVERSITY OF PADOVA   (Italy)

^c Ca Vignal 1 ^*  (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; SOLVENT;

ALGORITHM; ARTICLE; CALCULATION; ELECTRIC POTENTIAL; FORCE; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR MECHANICS; PROTEIN FOLDING; SIMULATION;

EID: 0038650794     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)74462-2     Document Type: Article

References (53)

1. Antosiewicz, J., J. A. McCammon, and M. K. Gilson. 1994. Prediction of pH-dependent properties of proteins. J. Mol. Biol. 238:415-436.
2. Baginski, M., F. Fogolari, and J. M. Briggs. 1997. Electrostatic and non-electrostatic contributions to the binding free energies of anthracycline antibiotics to DNA. J. Mol. Biol. 274:253-267.
3. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: a program for macromolecular energy minimization and dynamics calculations. J. Comput. Chem. 4:187-217.
4. David, L., R. Luo, and M. K. Gilson. 2000. Comparison of generalized Bom and Poisson models: energetics and dynamics of HIV protease. J. Comput. Chem. 21:295-309.
5. Davis, M. E., and J. A. McCammon. 1990. Electrostatics in biomolecular structure and dynamics. Chem. Rev. 90:509-521.
6. Debye, P. 1929. Polar Molecules. Chemical Catalog, New York.
7. Eisenberg, D., and A. D. McLachlan. 1986. Solvation energy in protein folding and binding. Nature. 319:199-203.
8. Essmann, U., L. Perera, M. L. Berkowitz, J. Darden, H. Lee, and L. G. Pedersen. 1995. A smooth particle mesh Ewald method. J. Chem. Phys. 103:8577-8593.
9. Fogolari, F., and J. M. Briggs. 1997. On the variational approach to the Poisson-Boltzmann free energies. Chem. Phys. Lett. 281:135-139.
10. Fogolari, F., A. Brigo, and H. Molinari. 2002. The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology. J. Mol. Recognit. 15:377-392.
11. Fogolari, F., G. Esposito, P. Viglino, and H. Molinari. 2001. Molecular mechanics and dynamics of biomolecules using a solvent continuum model. J. Comput. Chem. 22:1830-1842.
12. Fogolari, F., P. Zuccato, G. Esposito, and P. Viglino. 1999. Biomolecular electrostatics with the linearized Poisson-Boltzmann equation. Biophys. J. 76:1-16.
13. Friedrichs, M., R. Zhou, S. R. Edinger, and R. A. Friesner. 1999. Poisson-Boltzmann analytical gradients for molecular modeling calculations. J. Phys. Chem. B. 103:3057-3061.
14. Gilson, M. K., M. E. Davis, B. A. Luty, and J. A. McCammon. 1993. Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation. J. Phys. Chem. 97:3591-3600.
15. Gilson, M. K., J. A. McCammon, and J. D. Madura. 1995. Molecular dynamics simulation with a continuum electrostatic model of the solvent. J. Comput. Chem. 16:1081-1095.
16. Halgren, T. A., and W. Damm. 2001. Polarizable force fields. Curr. Opin. Struct. Biol. 11:236-242.
17. Harvey, S. C. 1989. Treatment of electrostatic effects in macromolecular modeling. Proteins. 5:78-92.
18. Hill, T. L. 1956. An Introduction to Statistical Thermodynamics. Dover Publications, New York.
19. Honig, B., and A. Nicholls. 1995. Classical electrostatics in biology and chemistry. Science. 268:1144-1149.
20. Huber, G. A. 1998. Future directions for combining molecular and continuum models in protein simulations. Prog. Biophys. Mol. Biol. 69:483-496.
21. Im, W., D. Beglov, and B. Roux. 1998. Continuum solvation model: electrostatic forces from numerical solutions to the Poisson-Boltzmann equation. Comp. Phys. Comm. 111:59-75.
22. Jorgensen, W. L., J. Chandrasekar, J. D. Madura, R. Impey, and M. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
23. Kollman, P. A., I. Massova, C. Reyes, B. Kuhn, S. Huo, L. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D. A. Case, and T. E. Cheatham 3rd. 2000. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc. Chem. Res. 33:889-897.
24. Lazaridis, T., and M. Karplus. 1999. Effective energy function for proteins in solution. Proteins. 35:133-152.
25. Lee, M. R., D. Baker, and P. A. Kollman. 2001. 2.1 and 1.8 A average C(alpha) RMSD structure predictions on two small proteins, HP-36 and s15. J. Am. Chem. Soc. 123:1040-1046.
26. Lu, B. Z., W. Z. Chen, C. X. Wang, and X.-J. Xu. 2002. Protein molecular dynamics with electrostatic force entirely determined by a single Poisson-Boltzmann calculation. Proteins. 48:497-504.
27. Luo, R., L. David, and M. K. Gilson. 2002. Accelerated Poisson-Boltzmann calculations for static and dynamic systems. J. Comput. Chem. 23:1244-1253.
28. MacKerell, A. D., Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher 3rd, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
29. Madura, J. D., M. E. Davis, M. K. Gilson, R. Wade, B. A. Luty, and J. A. McCammon. 1994. Biological applications of electrostatics calculations and Brownian dynamics simulations. Rev. Comp. Chem. 5:229-267.
30. Madura, J. D., J. M. Briggs, R. Wade, M. E. Davis, B. A. Luty, A. Ilin, J. Antosiewicz, M. K. Gilson, B. Bagheri, L. Ridgway Scott, and J. A. McCammon. 1995. Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program. Comp. Comm. Phys. 91:57-95.
31. Marcus, R. A. 1955. Calculation of thermodynamic properties of polyelectrolytes. J. Chem. Phys. 23:1057-1068.
32. McCammon, J. A., and S. C. Harvey. 1987. Dynamics of Proteins and Nucleic Acids. Cambridge University Press, Cambridge.
33. Neria, E., S. Fischer, and M. Karplus. 1996. Simulation of activation free energies in molecular systems. J. Chem. Phys. 105:1902-1921.
34. Nicholls, A., K. A. Sharp, and B. Honig. 1991. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins. 11:281-296.
35. Niedermeier, C., and K. Schulten. 1992. Molecular dynamics simulations in heterogeneous dielectrica and Debye-Huckel media: application to the protein bovine pancreatic trypsin inhibitor. Mol. Simul. 8:361-387.
36. Perutz, M. F. 1978. Electrostatic effects in proteins. Science. 201:1187-1191.
37. Qiu, D., P. Shenkin, F. Hollinger, and W. Still. 1997. The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii. J. Phys. Chem. 101:3005-3014.
38. Romagnoli, S., R. Ugolini, F. Fogolari, G. Schaller, K. Urech, M. Giannattasio, L. Ragona, and H. Molinari. 2000. NMR structural determination of viscotoxin A3 from Viscum album L. Biochem. J. 350:569-577.
39. Roux, B., and T. Simonson. 1999. Implicit solvent models. Biophys. Chem. 78:1-20.
40. Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comp. Phys. 23:327-341.
41. Schutz, C. N., and A. Warshel. 2001. What are the dielectric "constants" of proteins and how to validate electrostatic models? Proteins. 44:400-417.
42. Sharp, K. A. 1991. Incorporating solvent and ion screening into molecular dynamics using the finite-difference Poisson-Boltzmann method. J. Comput. Chem. 12:454-468.
43. Sharp, K. A., and B. Honig. 1990. Calculating total electrostatic energies with the non-linear Poisson-Boltzmann equation. J. Phys. Chem. 94:7684-7692.
44. Simonson, T. 1999. Dielectric relaxation in proteins: microscopic and macroscopic models. Int. J. Quant. Chem. 73:45-57.
45. Simonson, T. 2001. Macromolecular electrostatics: continuum models and their growing pains. Curr. Opin. Struct. Biol. 11:243-252.
46. Sitkoff, D., K. A. Sharp, and B. Honig. 1994. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 98:1978-1988.
47. Smart, J. L., T. J. Marrone, and J. A. McCammon. 1997. Conformational sampling with Poisson-Boltzmann forces and a stochastic dynamics/Monte Carlo method: application to alanine dipeptide. J. Comput. Chem. 18:1750-1759.
48. Smart, J. L., and J. A. McCammon. 1999. Phosphorylation stabilizes the N-terminal of α-helices. Biopolymers. 49:225-233.
49. Sridharan, S., A. Nicholls, and K. A. Sharp. 1995. A rapid method for calculating derivatives of solvent accessible surface areas of molecules. J. Comput. Chem. 16:1038-1044.
50. Still, W. C., A. Tempczyk, R. C. Hawley, and T. Hendrickson. 1990. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 112:6127-6129.
51. Tanford, C. 1978. The hydrophobic effect and the organization of living matter. Science. 200:1012-1018.
52. Verlet, L. 1967. Computer experiments on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Phys. Rev. 159:98-103.
53. Zhou, H. X. 1994. Macromolecular electrostatic energy within the nonlinear Poisson-Boltzmann equation. J. Chem. Phys. 100:3152-3162.