Reproducing basic pKa values for Turkey ovomucoid third domain using a polarizable force field

Journal of Physical Chemistry B

Volumn 113, Issue 22, 2009, Pages 7844-7850

  Click, Timothy H ^a,b   Kaminski, George A ^a,b  

^a CENTRAL MICHIGAN UNIVERSITY   (United States)

^b WORCESTER POLYTECHNIC INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ELECTROMAGNETIC WAVE POLARIZATION; HYDROGEN; SOLVATION;

ACIDIC RESIDUES; ACIDITY CONSTANTS; AVERAGE ERRORS; CLOSE PROXIMITY; CONTINUUM SOLVATION MODELS; DEPROTONATED FORM; ENERGY CALCULATION; EXPERIMENTAL VALUES; FIXED CHARGES; FORCE FIELDS; GENERALIZED BORN; NON-POLAR; OPLS-AA FORCE FIELD; OVOMUCOID; POISSON-BOLTZMANN; POLARIZABLE FORCE FIELD; PROTEIN RESIDUES; PROTONATED; SOLVATION MODELS;

ACIDITY;

ARGININE; HISTIDINE; LYSINE; OVOMUCOID;

ANIMAL; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; PH; PROTEIN TERTIARY STRUCTURE; TURKEY (BIRD);

ANIMALS; ARGININE; HISTIDINE; HYDROGEN-ION CONCENTRATION; LYSINE; MODELS, MOLECULAR; OVOMUCIN; PROTEIN STRUCTURE, TERTIARY; TURKEYS;

EID: 66549089348     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp809412e     Document Type: Article

References (42)

1. Antosiewicz, J.; Mccammon, J. A.; Gilson, M. K. J. Mol. Biol. 1994, 238, 415-436.
2. Antosiewicz, J.; McCammon, J. A.; Gilson, M. K. Biochemistry 1996, 35, 7819-7833.
3. Barth, P.; Alber, T.; Harbury, P. B. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 4898-4903.
4. Dixit, S. B.; Bhasin, R.; Rajasekaran, E.; Jayaram, B. J. Chem. Soc., Faraday Trans. 1997, 93, 1105-1113.
5. Forsyth, W. R.; Antosiewiez, J. M.; Robertson, A. D. Proteins 2002, 48, 388-403.
6. Forsyth, W. R.; Gilson, M. K.; Antosiewicz, J.; Jaren, O. R.; Robertson, A. D. Biochemistry 1998, 37, 8643-8652.
7. Forsyth, W. R.; Robertson, A. D. Biochemistry 2000, 39, 80678072.
8. Havranek, J. J.; Harbury, P. B. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 11145-11150.
9. Jorgensen, W. L.; Briggs, J. M, J. Am. Chem. Soc. 1989, 111, 41904197.
10. Kallies, B.; Mitzner, R. J. Phys. Chem. B 1997, 101, 2959-2967.
11. Kaminski, G. A. J. Chem. Theory Comput. 2005, 1, 248-254.
12. Kaminski, G. A. J. Phys. Chem. B 2005, 109, 5884-5890.
13. Khandogin, J.; York, D. M. Proteins: Struct., Funct., Bioinf. 2004, 56, 724-737.
14. Klicic, J. J.; Friesner, R. A.; Liu, S. Y.; Guida, W. C J. Phys. Chem. A 2002, 106, 1327-1335.
15. Li, H.; Hains, A. W.; Everts, J. E.; Robertson, A. D.; Jensen, J. H. J. Phys. Chem. B 2002, 106, 3486-3494.
16. Li, H.; Robertson, A. D.; Jensen, J. H. Proteins: Struct., Funct., Bioinf. 2004, 55, 689-704.
17. MacDermaid, C M.; Kaminski, G. A. J. Phys. Chem. B 2007, 111, 9036-9044.
18. Mehler, E. L.; Guarnieri, F. Biophys. J. 1999, 77, 3-22.
19. Nielsen, J. E.; Vriend, G. Proteins 2001, 43, 403-412.
20. Ohno, K.; Sakurai, M. J. Comput. Chem. 2006, 27, 906-916.
21. Sandberg, L.; Edholm, O. Proteins 1999, 36, 474-483.
22. Schaller, W.; Robertson, A. D. Biochemistry 1995,34, 4714-4723.
23. Simonson, T.; Carlsson, J.; Case, D. A. J. Am. Chem. Soc. 2004, 126, 4167-4180.
24. Song, J. K.; Laskowski, M.; Qasim, M, A.; Markley, J. L. Biochemistry 2003, 42, 2847-2856.
25. Zhang, M. J.; Vogel, H. J. J. Biol. Chem. 1993,268, 22420-22428.
26. Tanford, C; Kirkwood, J. G. J. Am. Chem. Soc. 1957, 79, 5333-9.
27. Harris, T. K.; Turner, G. J. IUBMB Life 2002, 53, 85-98.
28. Hoogstraten, C G.; Choe, S.; Westler, W. M.; Markley, J. L. Protein Sci. 1995, 4, 2289-2299.
29. Bode, W.; Wei, A. Z.; Huber, R.; Meyer, E.; Travis, J.; Neumann, S. EMBO J. 1986, 5, 2453-2458.
30. Maple, J. R.; Cao, Y. X.; Damm, W. G.; Halgren, T. A.; Kaminski, G. A.; Zhang, L. Y.; Friesner, R. A. J. Chem. Theory Comput. 2005, 1, 694-715.
31. Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. J. Phys. Chem, B 2001, 105, 6474-6487.
32. Gallicchio, E.; Zhang, L. Y.; Levy, R. M. J. Comput. Chem. 2002, 23, 517-529.
33. Impact, version. 3.0; Schrödinger, LLC: New York, 2004.
34. Kaminski, G. A.; Stern, H. A.; Berne, B. J.; Friesner, R. A. J. Phys. Chem. A 2004, 108, 621-627.
35. Dunning, T. H. J.Chem. Phys. 1989, 90, 1007-1023.
36. Kaminski, G. A.; Stern, H. A.; Berne, B. J.; Friesner, R. A.; Cao, Y. X. X.; Murphy, R. B.; Zhou, R. H.; Halgren, T. A. J. Comput. Chem. 2002, 23, 1515-1531.
37. Dean, J. A.; Lange, N. A. Lange's handbook of chemistry, 15th ed.; McGraw-Hill: New York, 1999.
38. Lide, D. R. CRC handbook of chemistry and physics: a readyreference book of chemical and physical data, 87th ed.; CRC Press: Boca Raton, FL, 2006.
39. Ghosh, A.; Rapp, C S.; Friesner, R. A. J. Phys. Chem. B 1998, 102, 10983-10990.
40. Tannor, D. J.; Marten, B.; Murphy, R.; Friesner, R. A.; Sitkoff, D.; Nicholls, A.; Ringnalda, M.; Goddard, W. A.; Honig, B. J. Am. Chem. Soc. 1994, 116, 11875-11882.
41. Zhou, R. H.; Berne, B. J. Proc. Natl. Acad Sci. U.S.A. 2002, 99, 12777-12782.
42. Ji, C G.; Mei, Y.; Zhang, J. Z. H. Biophys. J. 2008, 95, 1080-1088.