| Summary: | <p>Electrical signalling is key to a vast number of biological processes within the nervous system. For this to occur, specific types of transmembrane proteins, named voltage-gated ion channels, are utilised. In voltage-gated sodium (Nav) channels, recent advances in structural biology are beginning to solve structures in complex with so-called “auxiliary” β subunits. These transmembrane proteins are multifunctional and interact with the main α subunit of the Nav channel, in addition to having a cell adhesion function through their extracellular immunoglobulin (Ig) domain. In Nav1.5, β3 has been found to cross-link subunits within the membrane, as well as form trimers and higher order oligomers.</p>
<p>In this thesis, both atomistic and coarse grained (CG) molecular dynamics (MD) simulations are performed to gain an insight into the behaviour of the α subunit, the α - β subunit relationship, and β subunit dynamics in isolation.</p>
<p>Firstly, atomistic simulations are used to investigate a splice variant of Nav1.5. Two single point mutations that were responsible for a shift in voltage-gating characteristics were investigated and found to most likely disrupt gating through interruption of voltage-sensing arginine residues.</p>
<p>Secondly, a large number of simulations are performed to explore Nav β1 and β3 subunit behaviour in a simple membrane composition. Results showed large differences between β1 and β3, with the latter exhibiting increased fluctuations in Ig domain orientation. These differences are attributed to key charged residues that influence Ig domain interaction with the membrane surface. Protein - lipid interactions suggest that a conserved glutamic acid residue is important in transmembrane domain location, rather than being involved in observed oligomerisation.</p>
<p>Finally, the use of CG simulations examines the dependency of both α and β subunit clustering with various lipids in a complex membrane composition. Protein clustering of both subunits was primarily mediated by glycosphingolipids present in the upper leaflet. The β subunit orientations adopted three states, one of which agreed well with an atomistic trimer model of the β3 Ig domain. Large-scale simulations explored a large (≈ 2 million particle) system within which multiple protein binding events occurred. Conformations present between α and β subunits agreed with experimental results from atomic force microscopy and increase our understanding of Nav subunit interaction.</p>
<p>Overall, the in silico multiscale approach adopted in this thesis aims to characterise Nav channel subunit behaviour in a variety of contexts. These simulations demonstrate the predictive power of MD in characterising channel function away from the pore, as well as informing potential future strategies against various channelopathies.</p>
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