Computational investigations of ionotropic glutamate receptor ligand binding and conformational change.

glutamate receptor;molecular dynamics;free energy calculations;ligand binding;conformational change;ion channels;Biophysics

Yu, AlvinAmzel, L. Mario ;

Johns Hopkins University

关键词: glutamate receptor;    molecular dynamics;    free energy calculations;    ligand binding;    conformational change;    ion channels;    Biophysics;   

Others  :  https://jscholarship.library.jhu.edu/bitstream/handle/1774.2/59139/YU-DISSERTATION-2018.pdf?sequence=1&isAllowed=y

瑞士|英语

来源: JOHNS HOPKINS DSpace Repository

【 摘 要 】

Ionotropic glutamate receptors (iGluRs) are key mediators of neuronal communication and synaptic plasticity. They are implicated in cellular mechanisms for learning and memory and can be found in the nervous systems of a diverse array of biological organisms from the complex brains in humans to the much simpler nerve nets in ctenophores. At excitatory synapses, these ligand gated ion channels sense the release of glutamate by presynaptic neurons and bind glutamate, triggering conformational change in the ligand binding domains (LBD) that opens the channel pore to allow current flow into the post synaptic neuron.Here we examine the molecular mechanisms of two processes involved in glutamate receptor activation - ligand binding and LBD domain closure. In the AMPA receptor, a glutamate receptor subtype, we present the first simulations of ligand binding in an iGluR and identified metastable binding sites, which facilitate the diffusion of ligand into the binding pocket. We also applied the string method, a chain-of-states pathway sampling method, to investigate AMPA receptor glutamate binding and found that surprisingly, the ligand may bind via at least two distinct pathways. In ctenophore glutamate receptors, early ancestors of NMDA receptors in humans, we calculated the free energy landscape of conformational change to explain puzzling changes in kinetics and thermodynamics of a particularly high affinity glycine-binding domain. These findings both further our understanding of glutamate receptor activation and have broader implications as to the physical and chemical basis for neural activity.