Accurate theoretical prediction of vibrational frequencies in an inhomogeneous dynamic environment: A case study of a glutamate molecule in water solution and in a protein-bound form

Journal of Chemical Physics

Volumn 121, Issue 3, 2004, Pages 1516-1524

  Speranskiy, Kirill ^a   Kurnikova, Maria ^a  

^a CARNEGIE MELLON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL METHODS; COMPUTER SIMULATION; DEGREES OF FREEDOM (MECHANICS); FOURIER TRANSFORM INFRARED SPECTROSCOPY; MACROMOLECULES; MOLECULAR DYNAMICS; NATURAL FREQUENCIES; ORGANIC SOLVENTS; PROTEINS; QUANTUM THEORY;

PARTIAL HESSIAN VIBRATIONAL ANALYSIS (PHVA); ROOM TEMPERATURE; VIBRATIONAL FREQUENCIES; VIBRATIONAL SPECTROSCOPY;

MOLECULAR VIBRATIONS;

GLUTAMATE RECEPTOR; GLUTAMIC ACID; WATER;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; MUTATION;

COMPUTER SIMULATION; GLUTAMIC ACID; MODELS, MOLECULAR; MUTATION; RECEPTORS, GLUTAMATE; WATER;

EID: 3242888980     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1752887     Document Type: Article

References (44)

1. C. W. Wharton, Nat. Prod. Rep. 17, 447 (2000).
2. A. Earth and C. Zscherp, FEBS Lett. 477, 151 (2000).
3. M. Kubo, K. Odai, T. Sugimoto, and E. Ito, J. Biochem. (Tokyo) 129, 869 (2001).
4. Composite methodologies termed QM/MM, which treat a small part of a system on a quantum mechanical level while the rest is considered classically, are usually practically applicable only for simulation for very short time, usually picoseconds.
5. H. Li and J. H. Jensen, Theor. Chem. Ace. 107, 211 (2002).
6. R. Dingledine, K. Borges, D. Bowie, and S. F. Traynelis, Pharmacol. Rev. 51, 7 (1999).
7. R. C. Weast and M. M. Astle, CRC Handbook of Chemistry and Physics (CRC, Inc., Boca Raton, FL, 1982).
8. N. Armstrong and E. Gouaux, Neuron 28, 165 (2000).
9. S. Franzen, J. Am. Chem. Soc. 124, 13271 (2002).
10. C. Rovira, B. Schulze, M. Eichinger, J. D. Evanseck, and M. Parrinello, Biophys. J. 81, 435 (2001).
11. T. G. Spiro and A. A. Jarzecki, Curr. Opin. Chem. Biol. 5, 715 (2001).
12. E. S. Park, M. R. Thomas, and S. G. Boxer, J. Am. Chem. Soc. 122, 12297 (2000).
13. K. Nakamoto, Infrared and Raman Spectra of Inorganic and Coordination Compounds (Wiley, New York, 1997).
14. M. Laberge, K. A. Sharp, and J. M. Vanderkooi, Biophys. Chem. 71, 9 (1998).
15. P. W. Atkins and R. S. Friedman, Molecular Quantum Mechanics, 3rd ed. (Oxford, New York, 1997).
16. BC yielded frequency values comparable with the experimental ones. However, in many instances, especially for the molecules solvated in liquids or bound to a protein, such crude approximation is insufficient.
17. U. C. Singh, J. Comput. Chem. 5, 129 (1984).
18. B. H. Besler, J. Comput. Chem. 11, 9 (1990).
19. W. L. Jorgensen, J. Chandrasekhar, J. Madura, and M. L. Klein, J. Chem. Phys. 79, 926 (1983).
20. T. Darden, D. York, and L. Pedersen, J. Chem. Phys. 98, 10089 (1993).
21. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsterer, A. DiNola, and J. R. Haak, J. Chem. Phys. 81, 3684 (1984).
22. I. V. Kurnikov, HARLEM - biomolecular simulation program, http:// www.kurnikov.org/harlem main.html, 1999.
23. D. A. Case, D. A. Pearlman, J. W. Caldwell, et al. AMBER 6, University of California, San Francisco, 1999.
24. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. J. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, J. Am. Chem. Soc. 118, 2309 (1996).
25. A. P. Scott and L. Radom, J. Phys. Chem. 100, 16502 (1996).
26. M. J. Frisch, G. V. Trucks, H. B. Schlegel, et al., GAUSSIAN 98, Gaussian, Inc., Pittsburgh, P.A., 1998.
27. Q. Cheng, S. Thiran, D. Yernool, E. Gouaux, and V. Jayaraman, Biochemistry 41, 1602 (2002).
28. V. Jayaraman, R. Keesey, and D. R. Madden, Biochemistry 39, 8693 (2000).
29. V. Jayaraman, personal communications.
30. K. Hermansson, J. Chem. Phys. 95, 7486 (1991).
31. F. R. Tortonda, J. L. Pascual-Ahuir, E. Silla, I. Tunon, and F. J. Ramirez, J. Chem. Phys. 109, 592 (1998).
32. S. Abdali, K. J. Jalkanen, H. Bohr, S. Suhai, and R. M. Nieminen, Chem. Phys. 282, 219 (2002).
33. E. Tajkhorshid, K. J. Jalkanen, and S. Suhai, J. Phys. Chem. B 102, 5899 (1998).
34. M. Nara, H. Torii, and M. Tasumi, J. Phys. Chem. 100, 19812 (1996).
35. Q. Cui and Martin Karplus, J. Chem. Phys. 112, 1133 (2003).
36. C. Cappelli, C. O. Silva, and J. Tomasi, THEOCHEM 544, 191 (2001).
37. J. Stare, J. Mavri, G. Ambrozic, and D. Hadzi, THEOCHEM 500, 429 (2000).
38. F. J. Ramirez, I. Tunon, and E. Silla, J. Phys. Chem. B 102, 6290 (1998).
39. M. W. Wong, K. B. Wiberg, and M. Frisch, J. Chem. Phys. 95, 8991 (1991).
40. M. W. Wong, K. B. Wiberg, and M. J. Frisch, J. Am. Chem. Soc. 114, 523 (1992).
41. M. W. Wong, M. J. Frisch, and K. B. Wiberg, J. Am. Chem. Soc. 113, 4776 (1991).
42. S. Miertus, E. Scrocco, and J. Tomasi, Chem. Phys. 55, 117 (1981).
43. G. Alagona, C. Ghio, and P. Kollman, J. Am. Chem. Soc. 108, 185 (1986).
44. L. Onsager, J. Am. Chem. Soc. 58, 1486 (1936).