Picosecond Dynamics of the Glutamate Receptor in Response to Agonist-Induced Vibrational Excitation

Proteins: Structure, Function and Genetics

Volumn 54, Issue 2, 2004, Pages 231-236

  Kubo, Minoru ^a,e   Shiomitsu, Eiji ^a,b   Odai, Kei ^c   Sugimoto, Tohru ^d   Suzuki, Hideo ^b   Ito, Etsuro ^a  

^a HOKKAIDO UNIVERSITY   (Japan)

^b WASEDA UNIVERSITY   (Japan)

^c North Shore College   (Japan)

^d KANTO GAKUIN UNIVERSITY   (Japan)

^e OSAKA UNIVERSITY   (Japan)

Author keywords

Conformational change; Energy transfer; Ionotropic receptor; Molecular dynamics simulation; Receptor activation

Indexed keywords

ARGININE; GLUTAMATE RECEPTOR; GUANIDINE DERIVATIVE; LYSINE;

ARTICLE; COMPUTER SIMULATION; CONFORMATIONAL TRANSITION; ENERGY TRANSFER; HYDROGEN BOND; INOTROPISM; LIGAND BINDING; MOLECULAR DYNAMICS; PRIORITY JOURNAL; RECEPTOR UPREGULATION; TIME SERIES ANALYSIS; VIBRATION;

ARGININE; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; KINETICS; LIGANDS; LYSINE; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN SUBUNITS; RECEPTORS, AMPA; STRUCTURE-ACTIVITY RELATIONSHIP; TIME FACTORS; VIBRATION;

EID: 0345827731     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10578     Document Type: Article

References (28)

1. Miller RJD. Vibrational energy relaxation and structural dynamics of heme proteins. Annu Rev Phys Chem 1991;42:581-614.
2. Kitao A, Go N. Investigating protein dynamics in collective coordinate space. Curr Opin Struct Biol 1999;9:164-169.
3. Kikuchi H, Suzuki H. Dynamical theory of photoisomerization of the rhodopsin chromophore: generation of a transient electric field during photoisomerization. J Phys Chem B 1997;101:6050-6056.
4. Sugimoto H, Ito E. A theoretical approach to the functional changes in membrane proteins by phosphorylation. J Biochem Mol Biol Biophys 1999;2:215-224.
5. Leitner DM. Vibrational energy transfer in helices. Phys Rev Lett 2001;87:188102-1-188102-4.
6. Moritsugu K, Miyashita O, Kidera A. Vibrational energy transfer in a protein molecule. Phys Rev Lett 2000;85:3970-3973.
7. Mizutani Y, Kitagawa T. Direct observation of cooling of heme upon photodissociation of carbonmonoxy myoglobin. Science 1997; 278:443-446.
8. Nakanishi S. Molecular diversity of glutamate receptors and implications for brain function. Science 1992;258:597-603.
9. Dingledine R, Borges K, Bowie D, Traynelis SF. The glutamate receptor ion channels. Pharmacol Rev 1999;51:7-61.
10. Kubo M, Odai K, Sugimoto T, Ito E. Quantum chemical study of agonist-receptor vibrational interactions for activation of the glutamate receptor. J Biochem 2001;129:869-874.
11. Kubo M, Shiomitsu E, Odai K, Sugimoto T, Suzuki H, Ito E. Agonist-specific vibrational excitation of glutamate receptor. J Mol Struct (Theochem) 2003;639:117-128.
12. Kubo M, Shiomitsu E, Odai K, Sugimoto T, Suzuki H, Ito E. Quantum chemical study of ligand-receptor electrostatic interactions in molecular recognition of the glutamate receptor. J Mol Struct (Theochem) 2003;634:145-157.
13. Odai K, Sugimoto T, Hatakeyama D, Kubo M, Ito E. A theoretical study of electronic and structural states of neurotransmitters: γ-aminobutyric acid and glutamic acid. J Biochem 2001;129:909-915.
14. Odai K, Sugimoto T, Kubo M, Ito E. Theoretical research on structures of γ-aminobutyric acid and glutamic acid in aqueous conditions. J Biochem 2003;133:335-342.
15. Armstrong N, Sun Y, Chen G-Q, Gouaux E. Structure of glutamate receptor ligand-binding core in complex with kainate. Nature 1998;395:913-917.
16. Armstrong N, Gouaux E. Mechanisms for activation and antagonism of an AMPA-sensitive glutamate receptor: crystal structures of the GluR2 ligand binding core. Neuron 2000;28:165-181.
17. Morikami K, Nakai T, Kidera A, Saito M, Nakamura H. PRESTO: a vectorized molecular mechanics program for biopolymers. Comput Chem 1992;16:243-248.
18. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
19. Evans DJ, Morriss GP. The isothermal-isobaric molecular dynamics ensemble. Phys Lett 1983;98A:433-436.
20. Hoover WG, Ladd AJC, Moran B. High-strain-rate plastic flow via non-equilibrium molecular dynamics. Phys Rev Lett 1982;48:1818-1820.
21. Kollman P, Dixon R, Cornell W, Fox T, Chipot C, Pohorille A. The development/application of a "minimalist" organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimantal data. In: van Gunsteren WF, Weiner PK, Wilkinson AJ, editors. Computer simulation of biomolecular systems. Vol. 3. Dordrecht: Kluwer/Escom; 1997. p 83-96.
22. Ding HQ, Karasawa N, Goddard WA III. Atomic level simulations on a million particles: the cell multipole method for coulomb and London nonbond interactions. J Chem Phys 1992;97:4309-4315.
23. Yamato T, Niimura N, Go N. Molecular dynamics study of femtosecond events in photoactive yellow protein after photoexcitation of the chromophore. Proteins 1998;32:268-275.
24. Ayalon G, Stern-Bach Y. Functional assembly of AMPA and kainate receptors is mediated by several discrete protein-protein interactions. Neuron 2001;31:103-113.
25. Madden DR. The structure and function of glutamate receptor ion channels. Nature Rev Neurosci 2002;3:91-101.
26. Sun Y, Olson R, Horning M, Armstrong N, Mayer M, Gouaux E. Mechanism of glutamate receptor desensitization. Nature 2002; 417:245-253.
27. Unwin N. Acetylcholine receptor channel imaged in the open state. Nature 1995;373:37-43.
28. Unwin N, Miyazawa A, Li J, Fujiyoshi Y. Activation of the nicotinic acetylcholine receptor involves a switch in conformation of the alpha subunits. J Mol Biol 2002;319:1165-1176.