Cation-π versus OH-π interactions in proteins: A density functional study

Journal of Physical Chemistry B

Volumn 104, Issue 43, 2000, Pages 10087-10091

  Sulpizi, Marialore ^a   Carloni, Paolo ^a,b,c  

^a INFM   (Italy)

^b INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY   (Italy)

^c SISSA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

AROMATIC COMPOUNDS; BONDING; DENSITY (SPECIFIC GRAVITY); DNA; ELECTROSTATICS; ENZYMES; POLARIZATION; POSITIVE IONS;

DENSITY FUNCTIONAL THEORY (DFT); HYDROGEN BONDS;

PROTEINS;

EID: 0034322574     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp000787f     Document Type: Article

References (72)

1. Burley, S. K.; Petsko, G. A. FEBS Lett. 1986, 203, 139-143.
2. Scrutton, N. S.; Raine, A. R. C. Biochem. J. 1996, 319, 1-8.
3. Shoemaker, K. R.; Fairman, K. R.; Schultz, D. A.; Robertson, A. D.; York, E. J.; Steward, J. M.; Baldwin, R. L. Biopolymers 1990, 29, 1-11.
4. Dougherty, D. A. Science 1996, 271, 163-168.
5. Ma, J. C.; Dougherty, D. A. Chem. Rev. 1997, 97, 1303-1324.
6. Stauffer, D. A.; Barrans, J. R. E.; Dougherty, D. A. Angew. Chem. Int. Ed. Engl. 1990, 29, 915-918.
7. McCurdy, A.; Jimenez, L.; Stauffer, D. A.; Dougherty, D. A. J. Am. Chem. Soc. 1992, 114, 10314-10321.
8. Shi, Z.; Buntel, C. J.; Griffin, J. H. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 7370-7374.
9. Poralla, K.; Hewelt, A.; Prestwich, G. D.; Abe, I.; Reipen, I.; Sprenger, G. Trends Biochem. Sci. 1994, 19, 157-158.
10. Abe, I.; Prestwich, G. D. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 9274-9278.
11. Poralla, K. Bioorg. Med. Chem. Lett. 1994, 4, 285-290.
12. Barak, D.; Ordentlich, A.; Segall, Y.; Velan, B.; Benschop, H.; De Jong, L.; Shafferman, A. J. Am. Chem. Soc. 1997, 119, 3157-3158.
13. Ermer, O.; Eling, A. J. Am. Chem. Soc., Perkin Trans. 1994, 2, 925.
14. Allen, F. H.; Hoy, V. J.; Howard, J. A. K.; Thalladi, V. R.; Desiraju, G. R.; Wilson, C. C. J. Am. Chem. Soc. 1996, 119, 3477.
15. (a) Suzuki, S.; Green, P. G.; Bumgarner, R. E.; Dasgupta, S.; Goddard, W. A., III; Blake, G. A. Science 1992, 257, 942.
16. (b) Rodham, D. A.; Suzuki, S.; Suenram, R. D.; Lovas, R. J.; Dasgupta, S.; Goddard, W. A., III; Blake, G. A. Nature 1993, 362, 735.
17. (c) Kashino, S.; Tomita, M.; Haisa, M. Acta Crystallogr., Sect. C 1988, 44, 780.
18. (d) Waksman, G.; Kominos, D.; Robertson, S. C.; Pant, N.; Baltimore, D.; Birge, R. B.; Cowborn, D.; Hanafusa, H.; Mayer, B. J.; Overduin, M.; Resh, M. D.; Rios, C. B.; Silverman, L.; Kurijan, J. Nature 1992, 358, 646.
19. (e) Atwood, J. L.; Hamada, F.; Robinson, K. D.; Orr, G. W.; Vincent, R. L.; Nature 1991, 349, 683.
20. Jedrzejas, M. J.; Singh S.; Brouilette, W. J.; Laver, W. G.; Air, M.; Luo, M. Biochemistry 1995, 34, 3144.
21. Ji, X.; Zhang, P.; Armstrong, R. N.; Gilliland, G. L. Biochemistry 1992, 31, 10169-10184.
22. Mecozzi, S.; West, A. P. J.; Dougherty, D. A. J. Am. Chem. Soc. 1996, 118, 2307-2308.
23. Mecozzi, S.; West, A. P. J.; Dougherty, D. A. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 10566-10571.
24. (a) Minoux, H.; Chipot, C. J. Am. Chem. Soc. 1999, 121, 10366-10372.
25. (b) Duan, G.; Smith, V. H.; Weaver, D. F. J. Phys. Chem. A 2000, 104, 4521.
26. Tarakeshwar, P.; Choi, H. S.; Lee, S. J.; Lee, J. Y.; Kim, K. S.; Ha, T. K.; Jang, J. H.; Lee, J. G.; Lee, H. J. Chem. Phys. 1999, 111, 5838-5850.
27. Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 4177-4178.
28. (a) Schneider, H. J. Angew. Chem., Int. Ed. Engl. 1991, 30, 1417-1436.
29. (b) Schneider, H. J.; Schiestel, T.; Zimmermann, P. J. Am. Chem. Soc. 1992, 114, 7698-7703.
30. Huang, H.; Chopra, R.; Verdine, G. L.; Harrison, S. C. Science 1998, 282, 1669-1675.
31. Xiao, G.; Liu, S.; Ji, X.; Johnson, W. W.; Chen, J.; Parson, F. J.; Stevens, W. W.; Gilland, G. L.; Armstrong, R. N. Biochemistry 1996, 35, 4753-4765.
32. Carloni, P.; Blochl, P.; Parrinello, M. J. Phys. Chem. 1995, 99, 1338-1348.
33. De Santis, L.; Carloni, P. Proteins: Struct. Fund. Genet. 1999, 37, 611-618.
34. (a) Roethlisberger, U.; Carloni, P.; Doklo, K.; Parrinello, M. J. Biol. Inorg. Chem., in press;
35. (b) Roethlisberger, U.; Carloni, P. Int. J. Quantum Chem. 1999, 73, 209-218.
36. (a) Segall, M. D.; Payne, M. C.; Ellis, S. W.; Tucker, G. T.; Boyes, R. N. Xenobiotica 1998, 28, 15.
37. (b) Segall, M. D.; Payne, M. C.; Ellis, S. W.; Tucker, G. T.; Boyes, R. N. Phys. Rev. E 1998, 57, 4618.
38. (c) Segall, M. D.; Payne, M. C.; Ellis, S. W.; Tucker, G. T.; Boyes, R. N. Chem. Res. Toxicol. 1998, 11, 962.
39. (d) Segall, M. D.; Payne, M. C.; Ellis, S. W.; Tucker, G. T.; Eddershaw, P. J. Xenobiotica 1999, 29, 561.
40. Alber, F.; Kuonen, O.; Scapozza, L.; Folkers, G.; Carloni, P. Proteins: Struct. Funct. Genet. 1998, 31, 453-459.
41. Bernstein, F. C.; Koetzle, T. F.; Williams, G. J. B. J. Mol. Biol. 1999, 112, 535-542.
42. Huskey, S. W.; Huskey, W. P.; Lu, A. Y. H. J. Am. Chem. Soc. 1991, 113, 2283-2290.
43. Zheng, Y. J.; Ornstein, R. L. J. Am. Chem. Soc. 1997, 119, 1523-1528.
44. Becke, A. Phys. Rev. A 1988, 38, 3098-3100.
45. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785-789.
46. Troullier, N.; Martins, J. L. Phys. Rev. B 1991, 43, 1943-2006.
47. Barnett, R. N.; Landman, U. Phys. Rev. B 1993, 48, 2081-2097.
48. Liu, S.; Ji, X.; Gilliland, G. L.; Stevens, W. J.; Armstrong, R. N. J. Am. Chem. Soc. 1993, 115, 7910-7911.
49. Pulay, P. Chem. Phys. Lett. 1980, 73, 393-398.
50. (a) Bayly, C. I.; Cieplack, P.; Cornell, W. D.; Kollman, P. A. J. Phys. Chem. 1993, 97, 10269-10280.
51. (b) Cornell, W. D.; Cieplack, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T. J. Am. Chem. Soc. 1995, 117, 5179-5197.
52. Car, R.; Parrinello, M. Phys. Rev. Lett. 1985, 55, 2471-2474.
53. Hutter, J.; Ballone, P.; Bernasconi, M.; Focher, P.; Fois, E.; Godecker, S.; Parrinello, M.; Tuckerman, M. CPMD version 3.0h; MPI für Festkörperforschung and IBM Zurich Research Laboratory, 1995-96.
54. Gu, Y.; Scheiner, S. J. Am. Chem. Soc. 1999, 121, 9411-9422.
55. Silvestrelli, P. L.; Marzari, N.; Vanderbilt, D.; Parrinello, M. Solid State Commun. 1998, 107, 7.
56. Silvestrelli, P.; Parrinello, M. Phys. Rev. Lett. 1999,82 (16), 3308-3311.
57. Marzari, N.; Vanderbilt, D. Phys. Rev. B 1997, 56, 12847.
58. Hehre, W. J.; Radom, L.; Schleyer, P. V. R.; Polple, J. A. Ab Initio Molecular Orbital Theory; Wiley: New York, 1986; p 140.
59. Alber, F.; Folkers, G.; Carloni, P. J. Phys. Chem. B 1999, 103, 6121-6126.
60. Meijer, E. J.; Sprik, M. J. Chem. Phys. 1996, 105, 8684-8689.
61. Frisch, M. J., et al. Gaussian 98, Revision A.7; Gaussian, Inc.: Pittsburgh, PA, 1995.
62. Leach, A. Molecular Modelling: Principles and Applications; Longman: Essex, U.K., 1996.
63. Hutter, J.; Carloni, P.; Parrinello, M. J. Am. Chem. Soc. 1996, 118 (8), 8710-8712.
64. Quantitative estimation of electrostatic interactions is not possible as the domain of validity of the model is limited to large distances between the two moieties.
65. Indeed, this term is a higher order in the multipolar expansion and decreases with a higher power of distance r than the dipole/dipole term (see computational section).
66. Polarity changes are calculated on the basis of the maximally localized Wannier Functions (see computational section), which by definition are not suited to describe delocalized bonds. Thus, our analysis cannot be extended to tyrosine-ring CC, CO, and OH bonds, which are partially or totally delocalized.
67. As DFT fails in reproducing dispersion attractions, our study cannot provide information on this contribution (Krystian, S.; Pulay, P. Chem. Phys. Lett. 1994, 229, 175-180;
68. Perez-Jordan, J.; Becke, A. Chem. Phys. Lett. 1995, 233, 134-137; see also ref 49).
69. In contrast, charge donation is instead not observed.
70. Electron density difference maps of CH- - -O (Gu, Y.; Scheiner, S. J. Am. Chem. Soc. 1999, 121, 9411-9422.) have shown that also this type of hydrogen bonding involves rearrangement of the charge.
71. Kraulis, P. J. MolScript v2.1, 1997.
72. Kraulis, P. J. J. Appl. Crystallogr. 1991, 24, 946-950.