Developing polarized protein-specific charges for protein dynamics: MD free energy calculation of pKa shifts for Asp26/Asp 20 in thioredoxin

Biophysical Journal

Volumn 95, Issue 3, 2008, Pages 1080-1088

  Ji, Changge ^a   Mei, Ye ^a   Zhang, John Z H ^a,b  

^a NANJING UNIVERSITY   (China)

^b NEW YORK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASPARAGINE; THIOREDOXIN;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ELECTRICITY; KINETICS; PROTEIN CONFORMATION; ULTRASTRUCTURE;

ASPARAGINE; COMPUTER SIMULATION; ELECTROSTATICS; KINETICS; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN CONFORMATION; THIOREDOXINS;

EID: 51049101330     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.108.131110     Document Type: Article

References (45)

1. Lifson, S., and A. Warshel. 1968. Consistent force field calculations of conformations vibrational spectra and enthalpies of cycloalkane and n-alkane molecules. J. Chem. Phys. 49:5116-5129.
2. 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.
3. Pearlman, D. A., D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham III, S. DelBolt, D. Ferguson, G. Seibel, and P. Kollman. 1995. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput. Phys. Commun. 91:1-41.
4. Hagler, A. T., E. Huler, and S. Lifson. 1977. Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals. J. Am. Chem. Soc. 96:5319-5327.
5. Nemethy, G., M. S. Pottle, and H. A. Scheraga. 1984. Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids. J. Phys. Chem. 87:1883-1887.
6. Berendsen, H. J. C., J. P. M. Postma, W. F. van Gunsteren, A. diNola, and J. R. Haak. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690.
7. Perutz, M. 1978. Electrostatic effects in proteins. Science. 201:1187-1191.
8. Warshel, A., and S. Russell. 1984. Calculations of electrostatic effects in biological systems and in solutions. Q. Rev. Biophys. 17:283-342.
9. Matthew, J. B. 1985. Electrostatic effects in proteins. Annu. Rev. Biophys. Biophys. Chem. 14:387-417.
10. Honig, B., and A. Nicholls. 1995. Classical electrostatics in biology and chemistry. Science. 268:1144-1149.
11. Davis, M. E., and J. A. McCammon. 1990. Electrostatics in biomolecular structure and dynamics. Chem. Rev. 90:509-521.
12. a, proton-transfer reactions, and general acid catalysis reactions in enzymes. Biochemistry. 20:3167-3177.
13. Schaefer, M., H. V. Vlijmen, and M. Karplus. 1998. Electrostatic contributions to molecular free energies in solution. Adv. Protein Chem. 51:1-57.
14. Simonson, T. 2003. Electrostatics and dynamics of proteins. Rep. Prog. Phys. 66:737-787.
15. Warshel, A. 1978. Energetics of enzyme catalysis. Proc. Natl. Acad. Sci. USA. 75:5250-5254.
16. Sternberg, M., F. Hayes, A. Russell, P. Thomas, and A. Fersht. 1987. Prediction of electrostatic effects of engineering of protein charges. Nature. 330:86-88.
17. Halgren, T. A. 2001. Polarizable force fields. Curr. Opin. Struct. Biol. 11:236-242.
18. Kaminski, G. A., H. A. Stern, B. J. Berne, R. A. Friesner, Y. X. X. Cao, R. B. Murphy, R. H. Zhou, and T. A. Halgren. 2002. Development of a polarizable force field for proteins via ab initio quantum chemistry: first-generation model and gas phase tests. J. Comput. Chem. 23:1515-1531.
19. Jorgensen, W. L. 2007. Special issue on polarization. J. Chem. Theory Comput. 3:1877.
20. Warshel, A., M. Kato, and A. V. Pisliakov. 2007. Polarizable force fields: history, test cases, and prospects. J. Chem. Comput. 3:2034-2045.
21. Honig, B., K. A. Sharp, and A.-S. Yang. 1993. Macroscopic models of aqueous solutions: biological and chemical applications. J. Phys. Chem. 97:1101-1109.
22. Tannor, D. J., B. Marten, R. Murphy, R. A. Friesner, D. Sitkoff, D. A. Nicholls, M. Ringnalda, W. A. Goddard, and B. Honig. 1994. Accurate first principles calculation of molecular charge distributions and solvation energies from ab initio quantum mechanics and continuum dielectric theory. J. Am. Chem. Soc. 116:11875-11882.
23. Zhang, D. W., and J. Z. H. Zhang. 2003. Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein-molecule interaction energy. J. Chem. Phys. 119:3599-3605.
24. Gao, A. M., D. W. Zhang, J. Z. H. Zhang, and Y. K. Zhang. 2004. An efficient linear scaling method for ab initio calculation of electron density of proteins. Chem. Phys. Lett. 394:293-297.
25. Mei, Y., D. W. Zhang, and J. Z. H. Zhang. 2005. A new method for direct linear scaling calculation of electron density of protein. J. Phys. Chem. A. 109:2 [Letter.].
26. Mei, Y., E. L. Wu, K. L. Han, and J. Z. H. Zhang. 2006. Treating hydrogen bonding in ab initio calculation of biopolymers. Int. J. Quantum Chem. 106:1267-1276.
27. Mei, Y., C. G. Ji, and J. Z. H. Zhang. 2006. A new quantum method for electrostatic solvation energy of protein. J. Chem. Phys. 125:94906-94912.
28. Bayly, C. I., P. Cieplak, W. Cornell, and P. A. Kollman. 1993. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J. Phys. Chem. 97:10269-10280.
29. Cornell, W. D., P. Cieplak, C. I. Bayly, and P. A. Kollman. 1993. Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation. J. Am. Chem. Soc. 115:9620-9631.
30. a calculations with explicit and implicit solvent models. J. Am. Chem. Soc. 126:4167-4180.
31. Miertuš, S., E. Scrocco, and J. Tomasi. 1981. Electrostatic interaction of a solute with a continuum. A direct utilization of ab initio molecular potentials for the prevision of solvent effects. Chem. Phys. 55:117-129.
32. Fedorov, D. G., K. Kitaura, H. Li, J. H. Jensen, and M. S. Gordon. 2006. The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO). J. Comput. Chem. 27:976-985.
33. Reference deleted in proof.
34. Gogonea, V., and K. M. Merz, Jr. 1999. Fully quantum mechanical description of proteins in solution. Combining linear scaling quantum mechanical methodologies with the Poisson-Boltzmann equation. J. Phys. Chem. A. 103:5171-5188.
35. Case, D. A., T. A. Darden, T. E. Cheatham III, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, K. M. Merz, B. Wang, D. A. Pearlman, M. Crowley, S. Brozell, V. Tsui, H. Gohlke, J. Mongan, V. Hornak, G. Cui, P. Beroza, C. Schafmeister, J. W. Caldwell, W. S. Ross, and P. A. Kollman. 2004. AMBER 8, University of California, San Francisco.
36. Rocchia, W., S. Sridharan, A. Nicholls, E. Alexov, A. Chiabrera, and B. Honig. 2002. Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects. J. Comput. Chem. 23:128-137.
37. Cornell, W. D., P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, Jr., D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:5179-5197.
38. as of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry. 29:10219-10225.
39. Antosiewicz, J., J. McCammon, and M. Gilson. 1994. Prediction of pH-dependent properties of proteins. J. Mol. Biol. 238:415-436.
40. as of ionizable groups in proteins. J. Phys. Chem. 100:17373-17387.
41. Warshel, A., F. Sussman, and G. King. 1986. Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process. Biochemistry. 25:8368-8372.
42. Warshel, A., P. K. Sharma, M. Kato, and W. W. Parson. 2006. Modeling electrostatic effects in proteins. Biochim. Biophys. Acta. 1764:1647-1676.
43. a calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols. J. Phys. Chem. B. 109:17715-17733.
44. Ryckaert, J., G. Ciccotti, and H. Berendsen. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23:327-341.
45. Kato, M., and A. Warshel. 2006. Using a charging coordinate in studies of ionization induced partial unfolding. J. Phys. Chem. B. 110:11566-11570.