Understanding binding affinity: A combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin

Journal of the American Chemical Society

Volumn 125, Issue 35, 2003, Pages 10570-10579

  Talhout, Reinskje ^a   Villa, Alessandra ^b   Mark, Alan E ^b   Engberts, Jan B F N ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

CALORIMETRY; DEHYDRATION; HYDROPHOBICITY; ISOTHERMS; MOLECULAR DYNAMICS; SPECIFIC HEAT; STRUCTURAL ANALYSIS; TITRATION;

ISOTHERMAL TITRATION;

PROTEINS;

AMIDINE; BENZAMIDINIUM CHLORIDE INHIBITOR; SERINE PROTEINASE; TRYPSIN; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; CALORIMETRY; CATALYSIS; ENTHALPY; ENTROPY; HYDROPHOBICITY; MOLECULAR DYNAMICS; PROTEIN ANALYSIS; SIMULATION; STRUCTURE ANALYSIS; THERMODYNAMICS; TITRIMETRY;

BENZAMIDINES; BINDING SITES; CALORIMETRY; HYDROPHOBICITY; KINETICS; MODELS, MOLECULAR; PROTEIN CONFORMATION; THERMODYNAMICS; TITRIMETRY; TRYPSIN; TRYPSIN INHIBITORS;

EID: 0041854716     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja034676g     Document Type: Article

References (60)

1. Böhm, H.-J.; Klebe, G. Angew. Chem., Int. Ed. Engl. 1996, 35, 2588-2614.
2. Structure-Based Drug Design: Thermodynamics, Modeling and Strategy; Ladbury, J. E., Connelly, P. R., Eds.; Springer: Berlin, 1997.
3. Fersht, A. Structure and Mechanism in Protein Science; Freeman: New York, 1999.
4. Dullweber, F.; Stubbs, M. T.; Musil, D.; Stürzebecher, J.; Klebe, G. J. Mol. Biol. 2001, 313, 593-614.
5. Morgan, B. P.; Scholtz, J. M.; Ballinger, M. D.; Zipkin, I. D.; Bartlett, P. A. J. Am. Chem. Soc. 1991. 113, 297-307.
6. Proteases, Potential Role in Health and Disease; Hörl, W. H., Heidland, A., Eds.; Plenum Press: New York, 1984.
7. Proteinases in Mammalian Cells and Tissues; Barrett, A. J., Ed.; Elsevier: Amsterdam, 1977.
8. Proteinase Inhibitors; Barrett, A. J., Salvesen, G., Eds.: Elsevier: Amsterdam, 1986.
9. Mares-Guia, M.; Shaw, E. J. Biol. Chem. 1965, 240, 1579-1585.
10. Bohm, M.; Stürzebecher, J.; Klebe, G. J. Med. Chem. 1999, 42, 458-477.
11. Renatus, M.; Bode, W.; Huber, R.; Stürzebecher, J.; Stubbs, M. T. J. Med. Chem. 1998, 41, 5445-5456.
12. Marquart, M.; Walter, J.; Deisenhofer, J.; Bode, W.; Huber, R. Acta Crystallogr. 1983, B39. 480-490.
13. Bode, W.; Schwager, P. J. Mol. Biol. 1975, 98, 693-717.
14. Rasmol 2.7.2; Herbert J. Bernstein, August 2000.
15. Talhout, R.; Engberts, J. B. F. N. Eur. J. Biochem. 2001, 268, 1554-1560.
16. Exner, O. The Hammett Equation - The Present Position. In Advances in Linear Free Energy Relationships; Chapman, N. B., Shorter, J., Eds.; Plenum Press: London, 1972; pp 1-69.
17. Holdgate, G. A. Biotechniques 2001, 30, 164-184.
18. Leavitt, S.; Freire, E. Curr. Opin. Struct. Biol. 2001, 11, 560-566.
19. Applications of Calorimetry in the Biological Sciences; Ladbury, J. E., Chowdry, B. Z., Eds.; Wiley: New York, 1998.
20. Calderone, C. T.; Williams, D. H. J. Am. Chem. Soc, 2001, 123, 6262-6267.
21. Cooper, A.; Johnson, C. M.; Lakey, J. H.; Nöllmann, M. Biophys. Chem. 2001, 93, 215-230.
22. Dunitz, J. D. Chem. Biol. 1995, 2, 709-712.
23. Glock, G. Chem. Ber. 1888, 21, 2650-2659.
24. Rash, F. H.; Boatman, S.; Hauser, C. R. J. Org. Chem. 1967, 32, 372-376.
25. Moss, R. A.; Ma, W.; Merrer, D. C.; Xue, S. Tetrahedron Lett. 1995, 36, 8761-8764.
26. Wiseman, T.; Williston, S.; Brandts, J. F.; Lin, L. N. Anal. Biochem. 1989, 179, 131-137.
27. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. In Intermolecular Forces; Pullman, B., Ed.; Reidel: Dordrecht, 1981; pp 331-342.
28. van Gunsteren, W. F.; Billeter, S. R.; Eising. A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular Simulation: GROMOS96 Manual and User Guide; BIOMOS b.v.: Zürich, Groningen, 1996.
29. Schuler, L. D.; van Gunsteren, W. F. Mol. Sim. 2000, 25, 301-319.
30. Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. Comput. Phys. Commun. 1995, 91, 43-56.
31. Lindahl, E.; Hess, B.; van der Spoel, D. J. Mol. Model. 2001, 7, 306-317.
32. van der Spoel, D.; van Buuren, A. R.; Apol, E.; Meulenhoff, P. J.; Tieleman, D. P.; Sijbers, A. L. T. M.; Hess, B.; Feenstra, K. A.; Lindahl, E.; van Drunen, R.; Berendsen, H. J. C. Gromacs User Manual Version 3.0; Nijenborgh 4, 9747 AG Groningen, The Netherlands, 2001 (http://www.gromacs.org).
33. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690.
34. Miyamoto, S.; Kollman, P. A. J. Comput. Chem. 1992, 13, 952-962.
35. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. J. Comput. Chem. 1997, 18. 1463-1472.
36. Mark, A. E. In Encyclopedia of Computational Chemistry: von Ragué Schleyer, P., Ed.; Wiley: New York, 1998; pp 1070-1083.
37. Beutler, T. C.; Mark, A. E.; van Schaik, R. C.; Geber, P. R.; van Gunsteren, W. F. Chem. Phys. Lett. 1994, 222, 529-539.
38. Villa, A.; Mark, A. E. J. Comput. Chem. 2002, 23. 548-553.
39. Bishop, M.; Frinks, S. J. Chem. Phys. 1987, 87, 3675-3676.
40. Allen, M. P.; Tildesley, D. J. Computer Simulations of Liquids: Oxford Science Publications: Oxford. 1987.
41. Sangster, J. Octanol-Water Partition Coefficients: Fundamentals and Physical Chemistry; Wiley: Chichester, 1997.
42. Lee, B. Biophys. Chem. 1994, 51, 271-278.
43. Blokzijl, W.; Engberts, J. B. F. N. Angew. Chem., Int. Ed. Engl. 1993, 32, 1545-1579.
44. Graziano, G. Phys. Chem. Chem. Phys. 1999, 1, 3567-3576.
45. Southall, N. T.; Dill, K. A.; Haymet, A. D. J. J. Phys. Chem. B 2002, 106, 2812.
46. Karplus, M.; Kushick, J. N. Macromolecules 1981, 14, 325-332.
47. García, A. E. Phys. Rev. Lett. 1992, 68, 2696-2699.
48. Amedei, A.; Linssen, A. B. M.; Berendsen, H. J. C. Struct., Funct. Gen. 1993, 17, 412-425.
49. Eisenhaber, F.; Lijnzaad, P.; Argos, P.; Sander, C.; Scharf, M. J. Comput. Chem. 1995, 16, 273-284.
50. Spolar, R. S.; Livingstone, J. R.; Record, M. T. Biochemistry 1992, 31, 3947-3955.
51. Murphy, K. P.; Privalov, P. L.; Gill, S. J. Science 1990, 247, 559-561.
52. Sturtevant, J. M. Proc. Natl. Acad. Sci. U.S.A. 1977, 74, 2236-2240.
53. Spolar, R. S.; Record, M. T. Science 1994, 263, 777-784.
54. Ha, J. H.; Spolar, R. S.; Record, M. T. J. Mol. Biol. 1989, 209, 801-816.
55. Sharp, K. A.; Madan, B. J. Phys. Chem. B 1997, 101, 4343-4348.
56. Baker, B. M.; Murphy, K. P. J. Mol. Biol. 1997, 268, 557-569.
57. Antonini, E.; Ascenzi, P.; Bolognesi, M.; Gatti, G.; Guarneri, M.; Menegatti, E. J. Mol. Biol. 1983, 165, 543-558.
58. Christensen, J. J.; Hansen, L. D.; Izatt, R. M. Handbook of Proton Ionization Heats and Related Thermodynamic Quantities; Wiley: New York. 1976.
59. a = 5.
60. H+ is found, while a calculated value of -0.32 is found using the Henderson-Hasselbalch equation, indicating that this approach leads to good agreement with experiment.