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

Minoru Kubo, Eiji Shiomitsu, Kei Odai, Tohru Sugimoto, Hideo Suzuki, Etsuro Ito

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)231-236
Number of pages6
JournalProteins: Structure, Function and Genetics
Volume54
Issue number2
DOIs
Publication statusPublished - 2004 Feb 1
Externally publishedYes

Fingerprint

Glutamate Receptors
Chemical activation
Ligands
Excitation energy
Guanidine
Relaxation processes
Molecular Dynamics Simulation
Conformations
Molecular dynamics
Hydrogen
Hydrogen bonds
Binding Sites
Computer simulation
Proteins

Keywords

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

ASJC Scopus subject areas

  • Genetics
  • Structural Biology
  • Biochemistry

Cite this

Picosecond Dynamics of the Glutamate Receptor in Response to Agonist-Induced Vibrational Excitation. / Kubo, Minoru; Shiomitsu, Eiji; Odai, Kei; Sugimoto, Tohru; Suzuki, Hideo; Ito, Etsuro.

In: Proteins: Structure, Function and Genetics, Vol. 54, No. 2, 01.02.2004, p. 231-236.

Research output: Contribution to journalArticle

Kubo, Minoru ; Shiomitsu, Eiji ; Odai, Kei ; Sugimoto, Tohru ; Suzuki, Hideo ; Ito, Etsuro. / Picosecond Dynamics of the Glutamate Receptor in Response to Agonist-Induced Vibrational Excitation. In: Proteins: Structure, Function and Genetics. 2004 ; Vol. 54, No. 2. pp. 231-236.
@article{4c584e3b3b424bff9ddfc4851b8d629e,
title = "Picosecond Dynamics of the Glutamate Receptor in Response to Agonist-Induced Vibrational Excitation",
abstract = "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.",
keywords = "Conformational change, Energy transfer, Ionotropic receptor, Molecular dynamics simulation, Receptor activation",
author = "Minoru Kubo and Eiji Shiomitsu and Kei Odai and Tohru Sugimoto and Hideo Suzuki and Etsuro Ito",
year = "2004",
month = "2",
day = "1",
doi = "10.1002/prot.10578",
language = "English",
volume = "54",
pages = "231--236",
journal = "Proteins: Structure, Function and Genetics",
issn = "0887-3585",
publisher = "Wiley-Liss Inc.",
number = "2",

}

TY - JOUR

T1 - Picosecond Dynamics of the Glutamate Receptor in Response to Agonist-Induced Vibrational Excitation

AU - Kubo, Minoru

AU - Shiomitsu, Eiji

AU - Odai, Kei

AU - Sugimoto, Tohru

AU - Suzuki, Hideo

AU - Ito, Etsuro

PY - 2004/2/1

Y1 - 2004/2/1

N2 - 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.

AB - 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.

KW - Conformational change

KW - Energy transfer

KW - Ionotropic receptor

KW - Molecular dynamics simulation

KW - Receptor activation

UR - http://www.scopus.com/inward/record.url?scp=0345827731&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0345827731&partnerID=8YFLogxK

U2 - 10.1002/prot.10578

DO - 10.1002/prot.10578

M3 - Article

VL - 54

SP - 231

EP - 236

JO - Proteins: Structure, Function and Genetics

JF - Proteins: Structure, Function and Genetics

SN - 0887-3585

IS - 2

ER -