Multiple protonation equilibria in electrostatics of protein-protein binding

Journal of Physical Chemistry B

Volumn 112, Issue 47, 2008, Pages 15074-15085

  Piłat, Zofia ^a   Antosiewicz, Jan M ^a  

^a UNIVERSITY OF WARSAW   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; BROWNIAN MOVEMENT; CONFORMATIONS; DYNAMICS; ELECTROSTATICS; FREE ENERGY; MECHANICS; MOLECULAR DYNAMICS; MONOMERS; POISSON DISTRIBUTION; POISSON EQUATION; PROTEINS; PROTONATION; QUANTUM CHEMISTRY; THERMODYNAMIC PROPERTIES;

ACCELERATED MOLECULAR DYNAMICS; BINDING FREE ENERGIES; BOLTZMANN MODELS; BROWNIAN DYNAMICS SIMULATIONS; COMPLEX STRUCTURES; COMPUTER TIMES; CONFORMATIONAL DEGREES OF FREEDOMS; ELECTROSTATIC BINDINGS; ELECTROSTATIC CONTRIBUTIONS; ENERGY LEVELS; MACROMOLECULAR CONFORMATIONS; MOLECULAR DYNAMICS ALGORITHMS; MOLECULAR DYNAMICS SIMULATIONS; NEW APPROACHES; PARTITION FUNCTIONS; PROTEIN BINDINGS; PROTEIN COMPLEXES; PROTEIN MODELS; PROTONATION DEGREES; PROTONATION STATES; SOLUTION CONDITIONS; THERMODYNAMIC CYCLES;

BINDING ENERGY;

EID: 57449090259     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp8029659     Document Type: Article

References (55)

1. Debye, P. Polar Molecules; Dover Publ.: New York, 1929.
2. Honig, B.; Nicholls, A. Science 1995, 268, 1144-1149.
3. McLaughlin, S.; Murray, D. Nature 2005, 438, 605-611.
4. Sanders, L. K.; Xian, W.; Guáqueta, C.; Strohman, M. J.; Vrasich, C. R.; Luijten, E.; Wong, G. C. L. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 15994-15999.
5. Froloff, N.; Windemuth, A.; Honig, B. Protein Sci. 1997, 6, 1293-1301.
6. Lazaridis, T. Curr. Org. Chem. 2002, 6, 1319-1332.
7. Swanson, J. M. J.; Henchman, R. H.; McCammon, J. A. Biophys. J. 2004, 86, 67-74.
8. Böttcher, C. J. F. Theory of Electric Polarization; Elsevier: Amsterdam, The Netherlands, 1973; Vol. I.
9. Sheinerman, F. B.; Norel, R.; Honig, B. Curr. Opin. Struct. Biol. 2000, 10, 153-159.
10. Tanford, C.; Roxby, R. Biochemistry 1972, 11, 2192-2198.
11. Sheinerman, F. B.; Honig, B. J. Mol. Biol. 2002, 318, 161-177.
12. Dong, F.; Vijayakumar, M.; Zhou, H.-X. Biophys. J. 2003, 85, 49-60.
13. Polticelli, F.; Ascenzi, P.; Bolognesi, M.; Honig, B. Protein Sci. 1999, 8, 2621-2629.
14. Bashford, D.; Karplus, M. Biochemistry 1990, 29, 10219-10225.
15. Yang, A. S.; Gunner, M. R.; Sampogna, R.; Sharp, K.; Honig, B. Proteins: Struct., Funct., Genet. 1993, 15, 252-265.
16. Antosiewicz, J.; McCammon, J. A.; Gilson, M. K. J. Mol. Biol. 1994, 238, 415-436.
17. Antosiewicz, J.; Briggs, J. M.; Elcock, A. E.; Gilson, M. K.; McCammon, J. A. J. Comput. Chem. 1996, 17, 1633-1644.
18. Alexov, E. G.; Gunner, M. R. Biophys. J. 1997, 74, 2075-2093.
19. Simonson, T.; Carlsson, J.; Case, D. A. J. Am. Chem. Soc. 2004, 126, 4167-4180.
20. Archontis, G.; Simonson, T. Biophys. J. 2005, 88, 3888-3904.
21. Vagedes, P.; Saenger, W.; Knapp, E. W. Biophys. J. 2002, 83, 3066-3078.
22. Mason, A. C.; Jensen, J. H. Proteins: Struct., Funct. Bioinf 2008, 77, 81-91.
23. Eberini, I.; Baptista, A. M.; Gianazza, E.; Fraternali, F.; Beringhelli, T. Proteins: Struct., Funct., Bioinf. 2004, 54, 744-758.
24. Alexov, E. Proteins: Struct. Funct, Bioinf. 2004, 56, 572-584.
25. Poland, D. Cooperative Equilibria in Physical Biochemistry; Clarendon Press: Oxford, U.K., 1978.
26. Feynman, R. P. Statistical Mechanics. A Set of Lectures; W. A. Benjamin Inc., Advanced Book Program: Reading, MA, 1972.
27. Gilson, M. K. Proteins: Struct., Funct, Genet. 1993, 15, 266-282.
28. Antosiewicz, J. M. Biopolymers 2008, 89, 262-269.
29. Antosiewicz, J.; Porschke, D. Biochemistry 1989, 28, 10072-10078.
30. Antosiewicz, J. Biophys. J. 1995, 69, 1344-1354.
31. Bernstein, F. C.; Koettzle, T. F.; Williams, G. J. B.; Meyer, E. F.; Brice, M. D.; Rodgers, J. R.; Kennard, O.; Shimanouchi, T.; Tasumi, M. J. J. Mol. Biol. 1977, 123, 557-594.
32. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
33. Warwicker, J.; Watson, H. C. J. Mol. Biol. 1982, 157, 671-679.
34. Madura, J. D.; Briggs, J. M.; Wade, R. C.; Davis, M. E.; Luty, B. A.; Ilin, A.; Antosiewicz, J.; Gilson, M. K.; Bagheri, B.; Scott. L. R.; McCammon, J. A. Comput. Phys. Commun. 1995, 91, 57-95.
35. MacKerell, A. D., Jr.; et al. J. Phys. Chem. B 1998, 102, 3586-3616.
36. Foloppe, N.; MacKerell, A. D., Jr. J. Comput. Chem. 2000, 21, 86-104.
37. Brock, K.; Talley, K.; Coley, K.; Kundrotas, P.; Alexov, E. Biophys. J. 2007, 93, 3340-3352.
38. Lee, L.; Tidor, B. Protein Sci. 2001, 10, 362-377.
39. Stites, W. E. Chem. Rev. 1997, 97, 1233-1250.
40. Gabdoulline, R. R.; Wade, R. C. J. Mol. Biol. 2001, 306, 1139-1155.
41. Mongan, J.; Case, D. A. Curr. Opin. Struct. Biol. 2005, 15, 157-163.
42. Hamelberg, D.; Mongan, J.; McCammon, J. A. J. Chem. Phys. 2004, 120, 11919-11929.
43. Takeuchi, Y.; Satow, Y.; Nakamura, K. T.; Mitsui, Y. J. Mol. Biol. 1991, 221, 309-325.
44. Buckle, M.; Schreiber, G.; Fersht, A. R. Biochemistry 1994, 33, 8878-8889.
45. Bhat, T. N.; Bentley, G. A.; Boulot, G.; I.Green, M.; Tello, D.; Dall'acqua, W.; Souchon, H.; Schwarz, F. P.; Mariuzza, R. A.; Poljak, R. J. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 1089-1093.
46. Tsukada, H.; Blow, D. M. J. Mol. Biol. 1985, 184, 703-711.
47. Jabeen, T.; Sharma, S.; Singh, N.; Singh, R. K.; Verma. A. K.; Paramasivam, M.; Srinivashan, A.; Singh, T. P. Acta Crvstallogr., Sect. D 2005, 67, 302-308.
48. Hecht, H. J.; Szardenings, M.; Collins, J.; Schomburg, D. J. Mol. Biol. 1991, 220, 711-722.
49. Bourne, Y.; Taylor, P.; Marchot, P. Cell 1995, 83, 503-512.
50. Cohen, G. H.; Silverton, E. W.; Padlan, E. A.; Dyda, F.; Wibbenmeyer, J.; Wilson, R. C.; Davies, D. R. Acta Crystallogr., Sect. D 2005, 61, 628-633.
51. Pelletier, H.; Kraut, J. Science 1992, 258, 1748-1755.
52. Breitenlechner, C. B.; Friebe, W.-G.; Brunet, E.; Werner, G.; Graul, K.; Thomas, U.; Kuenkele, K.-P.; Schaefer, W.; Gassel, M.; Bossemeyer, D.; Huber, R.; Engh, R. A.; Masjost, B. J. Med. Chem. 2005, 48, 163-170.
53. Zheng, J.; Trafny, E.; Knighton, D.; Xuong, N.-H.; Taylor, S.; Eyck, L. T.; Sowadski, J. Acta Crystallogr., Sect. D 1993, 49, 362-365.
54. Padlan, E. A.; Silverton, E. W.; Sheriff, S.; Cohen, G. H.; Smith-Gill, S. J.; Davies, D. R. Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 5938-5942.
55. Pettersen, E. F.; Goddard, T. D.; Huang, C. C.; Couch, G. S.; Greenblatt, D. M.; Meng, E. C.; Ferrin, T. E. J. Comput. Chem. 2004, 25, 1605-1612.