Picosecond dynamics of the glutamate receptor in response to agonist-induced vibrational excitation.
Conformational changes of proteins are dominated by the excitation and relaxation processes of their vibrational states. To elucidate the mechanism of receptor activation, the conformation dynamics of receptors must be analyzed in response to agonist-induced vibrational excitation. In this study, we chose the bending vibrational mode of the guanidinium group of Arg485 of the glutamate receptor subunit GluR2 based on our previous studies, and we investigated picosecond dynamics of the glutamate receptor caused by the vibrational excitation of Arg485 via molecular dynamics simulations. The vibrational excitation energy in Arg485 in the ligand-binding site initially flowed into Lys730, and then into the J-helix at the subunit interface of the ligand-binding domain. Consequently, the atomic displacement in the subunit interface around an intersubunit hydrogen bond was evoked in about 3 ps. This atomic displacement may perturb the subunit packing of the receptor, triggering receptor activation.
Kubo
Minoru
M
Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo, Japan.
Shiomitsu
Eiji
E
Odai
Kei
K
Sugimoto
Tohru
T
Suzuki
Hideo
H
Ito
Etsuro
E
D001120:Arginine / Q000378:metabolism; D001665:Binding Sites; D018360:Crystallography, X-Ray; D007700:Kinetics; D008024:Ligands; D008239:Lysine / Q000378:metabolism; D008958:Models, Molecular; D011487:Protein Conformation; D021122:Protein Subunits / Q000737:chemistry / Q000378:metabolism; D018091:Receptors, AMPA / Q000819:agonists* / Q000737:chemistry / Q000378:metabolism*; D013329:Structure-Activity Relationship; D013997:Time Factors; D014732:Vibration
D008024:Ligands; D021122:Protein Subunits; D018091:Receptors, AMPA; D001120:Arginine; D008239:Lysine; C104722:glutamate receptor ionotropic, AMPA 2