On the binding determinants of the glutamate agonist with the glutamate receptor ligand binding domain

Biochemistry

Volumn 44, Issue 34, 2005, Pages 11508-11517

  Speranskiy, Kirill ^a   Kurnikova, Maria ^a  

^a CARNEGIE MELLON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; FOURIER TRANSFORM INFRARED SPECTROSCOPY; MOLECULAR DYNAMICS; NEUROLOGY;

LIGANDS; MOLECULAR DYNAMICS SIMULATION; NEURAL SYSTEMS; PROTEIN-LIGAND INTERACTIONS;

PROTEINS;

CARBOXYLIC ACID; GLUTAMATE RECEPTOR; GLUTAMATE RECEPTOR AGONIST; IONOTROPIC RECEPTOR; LIGAND; MUTANT PROTEIN; WATER;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CALCULATION; HYDROGEN BOND; INFRARED SPECTROSCOPY; LIGAND BINDING; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; QUANTUM CHEMISTRY; RECEPTOR BINDING; SIMULATION; VALIDATION PROCESS; VIBRATION;

ALGORITHMS; BINDING SITES; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; EXCITATORY AMINO ACID AGONISTS; GLUTAMIC ACID; LIGANDS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN SUBUNITS; RECEPTORS, AMPA; RECEPTORS, GLUTAMATE; THERMODYNAMICS;

EID: 23944435408     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi050547w     Document Type: Article

References (50)

1. Hollmann, M., and Heinemann, S. (1994) Cloned glutamate receptors, Annu. Rev. Neurosci. 17, 31 -108.
2. Dingledine, R., Borges, K., Bowie, D., and Traynelis, S. F. (1999) The glutamate receptor ion channels, Pharmacol. Rev. 51, 7-61.
3. Laube, B., Kuhse, J., and Betz, H. (1998) Evidence for a tetrameric structure of recombinant NMDA receptors, J. Neurosci. 18, 2954-2961.
4. Rosenmund, C., Stern-Bach, Y., and Stevens, C. F. (1998) The tetrameric structure of a glutamate receptor channel, Science 280, 1596-1599.
5. Krupp, J. J., Vissel, B., Heinemann, S. F., and Westbrook, G. L. (1998) N-terminal domains in the NR2 subunit control desensitization of NMDA receptors, Neuron 20, 317-327.
6. Chen, G.-Q., and Gouaux, E. (1997) Overexpression of a glutamate receptor (GluR2) ligand binding domain in Escherichia coli: application of a novel protein folding screen, Proc. Natl. Acad. Sci. U.S.A. 94, 13431-13436.
7. Armstrong, N., and Gouaux, E. (2000) Mechanisms for activation and antagonism of an AMPA-sensitive glutamate receptor: Crystal structures of the GluR2 ligand binding core, Neuron 28, 165-181.
8. Jin, R., and Gouaux, E. (2003) Probing the function, conformational plasticity, and dimer-dimer contacts of the GluR2 ligand-binding core: Studies of 5-substituted willardiines and GluR2 S1S2 in the crystal, Biochemistry 42, 5201-5213.
9. Armstrong, N., Sun, Y., Chen, G.-Q., and Gouaux, E. (1998) Structure of a glutamate receptor ligand-binding core in complex with kainate, Nature 395, 913-917.
10. Lampinen, M., Pentikainen, O., Johnson, M. S., and Keinanen, K. (1998) AMPA receptors and bacterial periplasmic amino acid-binding proteins share the ionic mechanism of ligand recognition, EMBO J. 17, 4704-4711.
11. Kuusinen, A., Arvola, M., and Keinanen, K. (1999) Oligomerization and ligand-binding properties of the ectodomain of the α-amino-3-hydroxy-5- methyl-4-isoxazole propionic acid receptor subunit GluRD, J. Biol. Chem. 274, 28937-28943.
12. Deming, D., Cheng, Q., and Jayaraman, V. (2003) Is the isolated ligand binding domain a good model of the domain in the native receptor? J. Biol. Chem. 278, 17589-17592.
13. Abele, R., Keinanen, K., and Madden, D. R. (2000) Agonist-induced isomerization in a glutamate receptor ligand-binding domain. A kinetic and mutagenetic analysis, J. Biol. Chem. 275, 21355-21363.
14. Arinaminpathy, Y., Sansom, M. S. P., and Biggin, P. C. (2002) Molecular dynamics Simulations of the ligand binding domain of the ionotorpic glutamate receptor GluR2, Biophys. J. 82, 676-683.
15. Kubo, M., Odai, K., Sugimoto, T., and Ito, E. (2001) Quantum chemical study of agonist-receptor vibrational interactions for activation of the glutamate receptor, J. Biochem. (Tokyo). 129, 869-874.
16. Kubo, M., Shiomitsu, E., Odai, K., Sugimoto, T., Suzuki, H., and Ito, E. (2003) Quantum chemical study of ligand-receptor electrostatic interactions in molecular recognition of the glutamate receptor, J. Mol. Struct. 634, 145-157.
17. Kubo, M., Shiomitsu, E., Odai, K., Sugimoto, T., Suzuki, H., and Ito, E. (2003) Agonist-specific vibrational excitation of glutamate receptor, J. Mol. Struct. 639, 117-128.
18. Kubo, M., Shiomitsu, E., Odai, K., Sugimoto, T., Suzuki, H., and Ito, E. (2004) Picosecond dynamics of the glutamate receptor in response to agonist-induced vibrational excitation, Proteins: Struct., Funct., Genet. 54, 231-236.
19. Mendieta, J., Ramirez, G., and Gago, F. (2001) Molecular dynamics simulations of the conformational changes of the glutamate receptor ligand-binding core in the presence of glutamate and kainate, Proteins: Struct., Funct., Genet. 44, 460-469.
20. Kubo, M., and Ito, E. (2004) Structural dynamics of an ionotropic glutamate receptor, Proteins: Struct., Funct., Bioinf. 56, 411-419.
21. Herman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000) The Protein Data Bank, Nucleic Acids Res. 28, 235-242.
22. Honig, B., Sharp, K., and Yang, A. S. (1993) Macroscopic Models of aqueous-solutions - biological and chemical applications, J. Phys. Chem. 97, 1101-1109.
23. Kurnikov, I. V., Ratner, M. A., and Pacheco, A. A. (2005) Redox equilibria in hydroxylamine oxidoreductase. Electrostatic control of electron redistribution in multielectron oxidative processes, Biochemistry 44, 1856-1863.
24. Antosiewicz, J., Mccammon, J. A., and Gilson, M. K. (1994) Prediction of pH-dependent properties of proteins, J. Mol. Biol. 238, 415-436.
25. Singh, U. C. (1984) An approach to computing electrostatic charges for molecules, J. Comput. Chem. 5, 129-145.
26. Besler, B. H. (1990) Atomic charges derived from semiempirical methods, J. Comput. Chem. 11, 431-439.
27. Jin, R., Horning, M., Mayer, M., and Gouaux, E. (2002) Mechanism of activation and selectivity in a ligand-gated ion channel: Structural and functional studies of GluR2 and quisqualate, Biochemistry 41, 15635-15643.
28. Kurnikov, I. V. (2003) HARLEM, biomolecular simulation program, http://www.kurnikov.org/harlem_main.html.
29. Ryckaert, J.-P., Ciccotti, G., and Berendsen, H. J. C. (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comput. Phys. 23, 327-341.
30. Case, D. A., Pearlman, D. A., Caldwell, J. W., Cheatham III, T. E., Ross, W. S., Simmerling, C. L., Darden, T. A., Merz, K. M., Stanton, R. V., Cheng, A. L., Vincent, J. J., Crowley, M., Tsui, V., Radmer, R. J., Duan, Y., Pitera, J., Massova, I., Seibel, G. L., Singh, U. C., and Kollman, P. A. (1999). AMBER 6, University of California, San Francisco.
31. Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules, J. Am. Chem. Soc. 117, 5179-5197.
32. Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S. H., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., Donini, O., Cieplak, P., Srinivasan, J., Case, D. A., and Cheatham, T. E. (2000) Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models, Acc. Chem. Res. 33, 889-897.
33. Kalra, P., Reddy, T. V., and Jayaram, B. (2001) Free energy component analysis for drug design: A case study of HIV-I protease-inhibitor binding, J. Med. Chem. 44, 4325-4338.
34. Bryce, R. A., Hillier, I. H., and Naismith, J. H. (2001) Carbohydrate-protein recognition: molecular dynamics simulations and free energy analysis of oligosaccharide binding to concanavalin A, Biophys. J. 81, 1373-1388.
35. Hou, T., Guo, S., and Xu, X. (2002) Predictions of binding of a diverse set of ligands to gelatinase-A by a combination of molecular dynamics and continuum solvent models, J. Phys. Chem. B 106, 5527-5535.
36. Mamonov, A. B., Coalson, R. D., Nitzan, A., and Kurnikova, M. G. (2003) The role of the dielectric barrier in narrow biological channels: A novel composite approach to modeling single-channel currents, Biophys. J. 84, 3646-3661.
37. Le Grand, S. M., and Merz, J. (1993) Rapid approximation to molecular surface area via the use of Boolean logic and look-up tables, J. Comput. Chem. 14, 349-352.
38. Honig, B., and Nicholls, A. (1995) Classical electrostatics in biology and chemistry, Science 268, 1144-1149.
39. Swanson, J. M. J., Henchman, R. H., and McCammon, J. A. (2004) Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy, Biophys. J. 86, 67-74.
40. Luo, H. B., and Sharp, K. (2002) On the calculation of absolute macromolecular binding free energies, Proc. Natl. Acad. Sci. U.S.A. 99, 10399-10404.
41. Nakamoto, K. (1997) Infrared and Raman Spectra of Inorganic and Coordination Compounds, Wiley, New York.
42. Laberge, M., Sharp, K. A., and Vanderkooi, J. M. (1998) Effect of charge interactions on the carboxylate vibrational stretching frequency in c-type cytochromes investigated by continuum electrostatic calculations and FTIR spectroscopy, Biophys. Chem. 71, 9-20.
43. Speranskiy, K., and Kurnikova, M. (2004) 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, J. Chem. Phys. 121, 1516-1524.
44. Frisch, M. J., Trucks, G. V., Schlegel, H. B., Scuseria, M. A. Robb, Cheeseman, J. R., Zakrzewski, V. G., Montgomery, J. A., Stratmann, R. E., Burant, J. C., Dapprich, S., Millam, J. M., Daniels, A. D., Kudin, K. N., Strain, M. C., Farkas, O., Tomasi, J., Barone, V., Cossi, M., Cammi, R., Mennucci, B., Pomelli, C., Adamo, C., Clifford, S., Ochterski, J., Petersson, G. A., Ayala, P. Y., Cui, Q., Morokuma, K., Malick, D. K., Rabuck, A. D., Raghavachari, K., Foresman, J. B., Cioslowski, J., Ortiz, J. V., Stefanov, B. B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Gomperts, R., Martin, R. L., Fox, D. J., Keith, T., Al-Laham, M. A., Peng, C. Y., Nanayakkara, A., Gonzalez, C., Challacombe, M., Gill, P. M. W., Johnson, B. G., Chen, W., Wong, M. W., Andres, J. L., Head-Gordon, M., Replogle, E. S., and Pople, J. A. (1998) Gausssian 98, Gaussian, Inc.; Pittsburgh, PA.
45. Scott, A. P., and Radom, L. (1996) Harmonic vibrational frequencies: An evaluation of Hartree- Fock, Moller-Plesset, quadratic configuration interaction, density functional theory, and semiempirical scale factors, J. Phys. Chem. 100, 16502-16513.
46. Jayaraman, V., Keesey, R., and Madden, D. R. (2000) Ligand-protein interactions in the glutamate receptor, Biochemistry 39, 8693-8697.
47. Cheng, Q., Thiran, S., Yernool, D., Gouaux, E., and Jayaraman, V. (2002) A vibrational spectroscopic investigation of interactions of agonists with GluR0 a prokaryotic glutamate receptor, Biochemistry 41, 1602-1608.
48. Jayaraman, V. (2002) University of Texas Health Science Center, Houston, Texas, personal communication.
49. Kawamoto, S., Uchino, S., Xin, K. Q., Hattori, S., Hamajima, K., Fukushima, J., Mishina, M., and Okuda, K. (1997) Arginine-481 mutation abolishes ligand-binding of the AMPA-selective glutamate receptor channel al-subunit, Mol. Brain Res. 47, 339-344.
50. Tan, R. C., Truong, T. N., McCammon, J. A., and Sussman, J. L. (1993) Acetylcholinesterase - electrostatic steering increases the rate of ligand-binding, Biochemistry 32, 401-403.