Investigating the function of a pentameric ligand-gated ion channel with molecular simulation
<p>Pentameric ligand-gated ion channels (pLGICs) are key players in mediating fast neurotransmission. Upon neurotransmitter binding, they undergo conformational changes that lead to the opening of the channel pore, allowing ions to flow in or out of the cell. They are involved in a range of ne...
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| Other Authors: | |
| Format: | Thesis |
| Language: | English |
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2019
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| _version_ | 1797112747702353920 |
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| author | Dämgen, MA |
| author2 | Biggin, P |
| author_facet | Biggin, P Dämgen, MA |
| author_sort | Dämgen, MA |
| collection | OXFORD |
| description | <p>Pentameric ligand-gated ion channels (pLGICs) are key players in mediating fast neurotransmission. Upon neurotransmitter binding, they undergo conformational changes that lead to the opening of the channel pore, allowing ions to flow in or out of the cell. They are involved in a range of neurological diseases which makes them important drug targets. The glycine receptor (GlyR) is a chloride-selective member of this receptor family, which is an excellent model system, because structures in key functional states are available and it has been extensively characterized experimentally. This thesis therefore seeks to investigate the function of the GlyR as a representative of the pLGIC superfamily with molecular dynamics (MD) simulations with four focal points.</p>
<p>1. Recent work has questioned the physiological relevance of the open state structure of the GlyR, since it rapidly collapses in MD simulations. I show that the collapse can be avoided by a careful equilibration protocol that reconciles the more problematic regions of the original density map and gives a stable open state that shows frequent selective chloride permeation. The stability can be explained by the 90 leucine gate residues being locked into so far unreported hydrophobic pockets that are functionally conserved across pLGICs.</p>
<p>2. pLGICs are known to be sensitive to their lipid environment, yet it is still poorly understood how lipids modulate receptor function. By embedding this receptor in a realistic model of a neuronal membrane and performing coarse-grained molecular dynamics simulations, I find that the lipid environment as well as the lipid-protein interaction strength are dependent on the receptor state, suggesting that lipids play a crucial role in stabilizing either the active or inactive state. Cholesterol can bind to the binding site of the positive allosteric modulator ivermectin, indicating that intrinsic membrane lipids might have positive modulatory function.</p>
<p>3. A molecular level of understanding of partial agonism in pLGICs has remained elusive thus far. Using atomistic MD simulations, I characterize the binding modes and determine the binding free energies of the full agonist glycine and several partial agonists. All agonists stabilize loop C, which covers the binding site like a lid, in a closed conformation, but the interactions in the binding site are less optimal for partial agonists than for glycine.</p>
<p>4. The atomistic details of the gating mechanism of pLGICs are still not fully understood. Via a combination of targeted MD and Markov state modelling, I reconstruct the equilibrium distribution and underlying kinetics of the gating process. The analysis reveals that the closed-to-open transition involves an intermediate shut state.</p> |
| first_indexed | 2024-03-07T08:28:18Z |
| format | Thesis |
| id | oxford-uuid:d8a41d1b-67ac-453f-8abe-8c98380e4c95 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T08:28:18Z |
| publishDate | 2019 |
| record_format | dspace |
| spelling | oxford-uuid:d8a41d1b-67ac-453f-8abe-8c98380e4c952024-02-27T08:31:23ZInvestigating the function of a pentameric ligand-gated ion channel with molecular simulationThesishttp://purl.org/coar/resource_type/c_db06uuid:d8a41d1b-67ac-453f-8abe-8c98380e4c95EnglishHyrax Deposit2019Dämgen, MABiggin, P<p>Pentameric ligand-gated ion channels (pLGICs) are key players in mediating fast neurotransmission. Upon neurotransmitter binding, they undergo conformational changes that lead to the opening of the channel pore, allowing ions to flow in or out of the cell. They are involved in a range of neurological diseases which makes them important drug targets. The glycine receptor (GlyR) is a chloride-selective member of this receptor family, which is an excellent model system, because structures in key functional states are available and it has been extensively characterized experimentally. This thesis therefore seeks to investigate the function of the GlyR as a representative of the pLGIC superfamily with molecular dynamics (MD) simulations with four focal points.</p> <p>1. Recent work has questioned the physiological relevance of the open state structure of the GlyR, since it rapidly collapses in MD simulations. I show that the collapse can be avoided by a careful equilibration protocol that reconciles the more problematic regions of the original density map and gives a stable open state that shows frequent selective chloride permeation. The stability can be explained by the 90 leucine gate residues being locked into so far unreported hydrophobic pockets that are functionally conserved across pLGICs.</p> <p>2. pLGICs are known to be sensitive to their lipid environment, yet it is still poorly understood how lipids modulate receptor function. By embedding this receptor in a realistic model of a neuronal membrane and performing coarse-grained molecular dynamics simulations, I find that the lipid environment as well as the lipid-protein interaction strength are dependent on the receptor state, suggesting that lipids play a crucial role in stabilizing either the active or inactive state. Cholesterol can bind to the binding site of the positive allosteric modulator ivermectin, indicating that intrinsic membrane lipids might have positive modulatory function.</p> <p>3. A molecular level of understanding of partial agonism in pLGICs has remained elusive thus far. Using atomistic MD simulations, I characterize the binding modes and determine the binding free energies of the full agonist glycine and several partial agonists. All agonists stabilize loop C, which covers the binding site like a lid, in a closed conformation, but the interactions in the binding site are less optimal for partial agonists than for glycine.</p> <p>4. The atomistic details of the gating mechanism of pLGICs are still not fully understood. Via a combination of targeted MD and Markov state modelling, I reconstruct the equilibrium distribution and underlying kinetics of the gating process. The analysis reveals that the closed-to-open transition involves an intermediate shut state.</p> |
| spellingShingle | Dämgen, MA Investigating the function of a pentameric ligand-gated ion channel with molecular simulation |
| title | Investigating the function of a pentameric ligand-gated ion channel with molecular simulation |
| title_full | Investigating the function of a pentameric ligand-gated ion channel with molecular simulation |
| title_fullStr | Investigating the function of a pentameric ligand-gated ion channel with molecular simulation |
| title_full_unstemmed | Investigating the function of a pentameric ligand-gated ion channel with molecular simulation |
| title_short | Investigating the function of a pentameric ligand-gated ion channel with molecular simulation |
| title_sort | investigating the function of a pentameric ligand gated ion channel with molecular simulation |
| work_keys_str_mv | AT damgenma investigatingthefunctionofapentamericligandgatedionchannelwithmolecularsimulation |