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Molecular modeling of ligand-receptor interactions in GABA C receptor.
- Source :
-
Journal of molecular graphics & modelling [J Mol Graph Model] 2009 Apr; Vol. 27 (7), pp. 813-21. Date of Electronic Publication: 2008 Dec 24. - Publication Year :
- 2009
-
Abstract
- A new homology model of the GABA binding site of the GABA(C) receptor was built. Natural agonist GABA and antagonist TPMPA were docked into the receptor and molecular dynamics simulation of the complexes was performed to clarify binding poses of the ligands. It was shown that orientation of the ligand is defined by salt bridges between the ligand and the arginine (Arg104) and glutamate residues (Glu194 and Glu196) of the binding site. Different behavior and binding poses for agonist and antagonist was demonstrated by molecular dynamics simulation along with differential movement of the loop C during agonist and antagonist binding. Binding orientations of the ligands revealed that main binding forces in the GABA binding site should be electrostatic ones.
- Subjects :
- Amino Acid Sequence
Arginine
Binding Sites
Computer Simulation
GABA Agonists metabolism
GABA Antagonists metabolism
Glutamic Acid
Humans
Ligands
Molecular Sequence Data
Phosphinic Acids metabolism
Protein Conformation
Pyridines metabolism
Receptors, GABA metabolism
Static Electricity
Tyrosine
gamma-Aminobutyric Acid metabolism
GABA Agonists chemistry
GABA Antagonists chemistry
Models, Molecular
Phosphinic Acids chemistry
Pyridines chemistry
Receptors, GABA chemistry
gamma-Aminobutyric Acid chemistry
Subjects
Details
- Language :
- English
- ISSN :
- 1873-4243
- Volume :
- 27
- Issue :
- 7
- Database :
- MEDLINE
- Journal :
- Journal of molecular graphics & modelling
- Publication Type :
- Academic Journal
- Accession number :
- 19167917
- Full Text :
- https://doi.org/10.1016/j.jmgm.2008.12.004