Computational modelling and molecular dynamics simulations of ligand-gated ion channels

Thesis

The Cys-loop ligand-gated super family of ion channels and related proteins have been studied using computational methods. Ligand-gated ion channels (LGIC) are pentameric, neurotransmitter-gated, ion selective receptors which play a key role in synaptic transmission. The nicotinic acetylcholine receptor (nAChR) is the archetypal member of the LGIC family. Found at neuronal-neuronal synapses and neuronalmuscular junctions, it is implicated in a variety of diseases and it plays a key role in nicotine addiction.

Computational techniques are used to investigate different properties of LGICs, such as ion selectivity, the location of the gate, the action of agonists, and the behaviour of the binding pocket. The aim was to apply existing computational methods and develop novel computational methodology to put forth hypotheses relating to both the general function and smaller scale behaviour of this class of membrane proteins. Binding pocket dynamics of AChBP, a high resolution crystal structure homologue of the ligand binding domain of the nAChR, shows increased stability of the binding site in the presence of a ligand. Discreet zones of persistent water molecules were identified, which are involved in bridging ligands to residues in the binding site and may play a structural role. Ensemble docking on ligand-bound and ligand-free molecular dynamics (MD) trajectories illustrates the optimization of the binding site to a bound ligand.

To overcome the lack of complete structures of LGICs, a method was developed to generate model structures of membrane proteins by combining their separate domains. A model of the a? nAChR was generated from homology models of its extracellular and transmembrane domains and the structure was used to analyze various properties such as pore profiles, electrostatics and conformational dynamics. In silico mutagenesis, together with MD and 'ensemble' docking, on the α7 nAChR investigated the role of key residues in the binding site. Residues were identified with computational techniques and verified with experimental work. This illustrates the utility of combining computational and experimental approaches.

During this work, the electron-microscopy structure of the Torpedo marmorata AChR became available. It agreed well with the previously modelled α7 nAChR model. The Torpedo AChR structure was used to make models of other LGICs. Coarse-grain MD allowed the identification of residues in the TM domain interacting with the lipid-bilayer. Born energy profiles through LGIC pores reveal that the EC domain plays a key role in ion selectivity.

Authors: Amiri, S; Amiri, Shiva

• Publication date: 2006
• DOI: 10.5287/ora-54nymxgaq
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Subjects: Ion channels; Ligands (Biochemistry); Molecular dynamics; Synapses; Models; Molecular aspects