| Summary: | <p>Ion channels are integral membrane proteins that facilitate the permeation of ions through lipid bilayers. By means of a molecular mechanism known as hydrophobic gating, these proteins can close their conduction pathway to ion flow without the need for steric occlusion. Hydrophobic gates pose a challenge in the analysis of novel ion channel structures, as they cannot be detected by measuring the physical dimensions of a channel pore. This thesis therefore presents the Channel Annotation Package (CHAP), an open-source software tool for the functional annotation of ion channel structures based on molecular dynamics (MD) simulation and capable of reliably indentifying hydrophobic gates. The cation-selective 5-HT<sub>3</sub> receptor and the anion-selective glycine receptor served as test cases to demonstrate the utility of CHAP. The functional status of several recent structures of these two channels was determined through MD simulation and hydrophobic gates were identified in both receptors. Furthermore, a high-throughput survey of ion channel structures enabled by CHAP revealed that hydrophobic gates occur in ~20% of the ion channel structural proteome. Next-generation polarisable force fields were used to explore the importance of electronic polarisation in MD simulations of ion channels. Water molecules passing a hydrophobic gate experienced a significant reduction of their dipole moment, mirroring the behaviour of water in a liquid-vapour phase transition. Polarisable ions interacted more strongly with uncharged protein residues than simulations employing traditional additive force fields suggest. Incorporating polarisation effects will thus be an important aspect of future computational studies of ion channel structure and function. The impact of a transmembrane potential on the hydrophobic gate in the 5-HT<sub>3</sub> receptor was studied through atomistic MD simulations. Electrowetting occured only at supraphysiological voltages, while at lower field strengths pore de-wetting effectively prevented ion permeation. The hydration response of the channel could be quantitatively described by a thermodynamic model that includes the influence of the charged amino acid residues of the channel protein. Electric field effects are unlikely to play an important role for hydrophobic gating in biological ion channels, but may potentially be exploited in the design of gated artificial nanopores.</p>
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