Importance of electrostatic polarizability in calculating cysteine acidity constants and copper(I) binding energy of Bacillus subtilis CopZ

Journal of Computational Chemistry

Volumn 33, Issue 11, 2012, Pages 1142-1151

  Click, Timothy H ^a   Ponomarev, Sergei Y ^a   Kaminski, George A ^a  

^a Worcester Polytechnic Institute   (United States)

Author keywords

polarizable force fields; protein pK a shifts; protein cation interactions

Indexed keywords

ACIDITY CONSTANTS; BACILLUS SUBTILIS; BINDING CONSTANT; COPPER BINDING; CYSTEINE RESIDUES; ELECTROSTATIC POLARIZATION; EXPERIMENTAL DATA; EXPERIMENTAL VALUES; EXPLICIT TREATMENTS; ION BINDING; POLARIZABILITIES; POLARIZABLE FORCE FIELD; PROTONATED; SOLVATION PARAMETERS; THERMODYNAMICALLY STABLE;

ACIDITY; AMINO ACIDS; BINDING ENERGY; COPPER; ELECTROSTATICS; ENZYME INHIBITION; POLARIZATION; PROTEINS;

COPPER COMPOUNDS;

BACTERIAL PROTEIN; CHAPERONE; COPPER; CYSTEINE;

ARTICLE; BACILLUS SUBTILIS; BINDING SITE; CHEMISTRY; PH; QUANTUM THEORY; STATIC ELECTRICITY; THERMODYNAMICS;

BACILLUS SUBTILIS; BACTERIAL PROTEINS; BINDING SITES; COPPER; CYSTEINE; HYDROGEN-ION CONCENTRATION; MOLECULAR CHAPERONES; QUANTUM THEORY; STATIC ELECTRICITY; THERMODYNAMICS;

EID: 84859110089     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.22944     Document Type: Article

References (29)

1. See, for example: (a), L. Zhou, C. Singleton, N. E. Le Brun, Biochem. J. 2008, 413, 459
2. (b), A. Badarau, C. Dennison, J. Am. Chem. Soc. 2011, 133, 2983
3. (c), K. J. Waldon, N. J. Robinson, Nat. Rev. Microbiol. 2009, 7, 25
4. (d), N. J. Robinson, D. R. Winge, Annu. Rev. Biochem. 2010, 79, 537
5. (e), L. Banci, I. Bertini, S. Ciofi-Baffoni, T. Kozyreva, K. Zovo, P. Palumaa, Nature 2010, 465, 645-U145
6. (f), L. Banci, I. Bertini, F. Cantini, S. Ciofi-Baffoni, Cell. Mol. Life Sci. 2010, 67, 2563
7. (g), I. Bertini, G. Cavallaro, K. S. McGreevy, Coord. Chem. Rev. 2010, 254, 506.
8. C. M. MacDermaid, G. A. Kaminski, J. Phys. Chem. B 2007, 111, 9036.
9. T. H. Click, G. A. Kaminski, J. Chem. Theory Comput. 2009, 5, 2935.
10. G. A. Kaminski,. J. Phys. Chem. B 2005, 109, 5884.
11. J. W. Caldwell, P. A. Kollman, J. Am. Chem. Soc. 1995, 117, 4177.
12. L. Banci, Curr. Opin. Chem. Biol. 2003, 7, 143.
13. J.-F. Fuchs, H. Nedev, D. Poger, M. Ferrand, V. Brenner, J.-P. Dognon, S. Crouzy, J. Comput. Chem. B 2006, 27, 837.
14. D. Venkateswarlu, BMS Struct. Biol. 2010, 10. doi: 10.1186/1472-6807-10- 7.
15. A. Rodriguez-Granillo, A. Crespo, D. A. Estrin, P. Wittung-Stafshede, J. Phys. Chem. B 2010, 114, 3698.
16. S. Y. Ponomarev, T. H. Click, G. A. Kaminski, J. Phys. Chem. B 2011, 115, 10079.
17. Impact, version 3.0, Schrödinger, LLC, New York, 2004.
18. J. J. Klicic, R. A. Friesner, S.-Y. Liu, W. C. Guida, J. Phys. Chem. A 2002, 106, 1327.
19. (a), W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, M. L. Klein, J. Chem. Phys. 1983, 79, 926
20. (b), W. L. Jorgensen, D. L. Severance, J. Am. Chem. Soc. 1990, 112, 4768
21. (c), W. L. Jorgensen, D. S. Maxwell, J. Tirado-Rives, J. Am. Chem. Soc. 1996, 118, 11225.
22. (a), G. A. Kaminski, H. A. Stern, B. J. Berne, R. A. Friesner, J. Phys. Chem. A, 2004, 108, 621
23. (b), J. R. Maple, Y. X. Cao, W. G. Damm, T. A. Halgren, G. A. Kaminski, L. Y. Zhang, R. A. Friesner, J. Chem. Theory. Comput. 2005, 1, 694.
24. G. A. Kaminski, R. A. Friesner, J. Tirado-Rives, W. L. Jorgensen, J. Phys. Chem. B 2001, 105, 6474.
25. G. A. Kaminski, J. R. Maple, R. B. Murphy, D. Braden, R. A. Friesner, J. Chem. Theory Comput., 2005, 1, 248.
26. Jaguar, version 7.6; Schrodinger, LLC: New York, 2009.
27. C. P. Kelly, C. J. Cramer, D. G. Truhlar, J Phys Chem B 2006, 110, 16066.
28. J. H. Jensen, H. Li, A. D. Robertson, P. A. Molina, J. Phys. Chem. A, 2005, 109, 6634.
29. D. R. Lide, CRC Handbook of Chemistry and Physics: A Ready-Reference Book of Chemical and Physical Data; 87th ed.; CRC Press: Boca Raton, Fla., 2006.