Ligand Photo-Isomerization Triggers Conformational Changes in iGluR2 Ligand Binding Domain

Tino Wolter,Thomas Steinbrecher,Marcus Elstner,Dirk Trauner

doi:10.1371/journal.pone.0092716

Abstract

Neurological glutamate receptors bind a variety of artificial ligands, both agonistic and antagonistic, in addition to glutamate. Studying their small molecule binding properties increases our understanding of the central nervous system and a variety of associated pathologies. The large, oligomeric multidomain membrane protein contains a large and flexible ligand binding domains which undergoes large conformational changes upon binding different ligands. A recent application of glutamate receptors is their activation or inhibition via photo-switchable ligands, making them key systems in the emerging field of optochemical genetics. In this work, we present a theoretical study on the binding mode and complex stability of a novel photo-switchable ligand, ATA-3, which reversibly binds to glutamate receptors ligand binding domains (LBDs). We propose two possible binding modes for this ligand based on flexible ligand docking calculations and show one of them to be analogues to the binding mode of a similar ligand, 2-BnTetAMPA. In long MD simulations, it was observed that transitions between both binding poses involve breaking and reforming the T686-E402 protein hydrogen bond. Simulating the ligand photo-isomerization process shows that the two possible configurations of the ligand azo-group have markedly different complex stabilities and equilibrium binding modes. A strong but slow protein response is observed after ligand configuration changes. This provides a microscopic foundation for the observed difference in ligand activity upon light-switching.

Highlights

Glutamate is the most important excitatory neurotransmitter of the mammalian central nervous system and its receptors play a crucial role in various neural functions [1,2]
We find that the two isomers of ATA-3 have markedly different stabilities and equilibrium binding modes to the ligand binding domains (LBDs) of the amino-3-hydroxy-5-methyl-4isoxazole-propionic acid (AMPA) receptor GluR2
For a second set, called F2, side chains close to the terminal benzyl ring of 2BnTetAMPA, which is the unswitchable ancestor of ATA-3, in the X-ray crystal structure 2P2A were selected as flexible: I712, Met708, S403, Y405, T686, E402, W767 and Y711

Summary

Introduction

Glutamate is the most important excitatory neurotransmitter of the mammalian central nervous system and its receptors play a crucial role in various neural functions [1,2]. Most of the structural studies and mechanistic models appeared before a X-ray structure of a functional iGluR2 tetramer in complex with an antagonist was published (pdb code: 3KG2) [5]. These were based on the X-ray structures of the the water-soluble ligand binding domain (LBD) dimers in complex with ligands. The comparison of the full receptor structure with the LBD dimer in complex with antagonists shows high similarity, which supports the approach to use the LBD as a model system. The water-soluble LBD dimer is obtained by replacing the first two transmembrane domains, which build the ion channel, by a linker peptide [7] (for illustration see Figure S1 in Supporting Information S1).the distance of the linker peptides have been considered as a good projection of the ionchannel opening [6]

Methods

Results

Discussion

Conclusion