Elucidating the structure and spatial organisation of mechanosensitive ion channels using simulations and spectroscopy

[Truncated abstract] This thesis presents an investigation into ways to combine data from Electron Paramagnetic Resonance (EPR) and Fluorescence Resonance Energy Transfer (FRET) spectroscopy with simulations to investigate the structure and spatial organisation of mechanosensitive (MS) ion channels. These ion channels convert a mechanical force into an electrical or chemical signal and are involved in physiological processes such as hearing, touch sensation and tissue growth. The understanding of the function of MS ion channels is greatly facilitated by the availability of structural information at the molecular level. While Xray crystallography has proved challenging for membrane proteins and only provides a static picture, techniques such as EPR and FRET spectroscopy can be used to study the structural rearrangements of proteins that underlie ion channel function. However, the interpretation and analysis of data from FRET spectroscopy is complicated by a number of common assumptions and approximations. The first part of this thesis consists of a series of studies that demonstrate how simulations can be used to aid in the interpretation and analysis of FRET experiments. Molecular Dynamics (MD) simulations are another way to study the dynamics and function ion channels as they allow structural rearrangements to be observed at high temporal and spatial resolution. The main limitation of this method is that standard MD simulations are usually restricted to 100’s of ns, a time-scale that is significantly shorter than that of the physiological function of most ion channels. The second part of this thesis presents a study that combines data from EPR and FRET spectroscopy with coarse grained simulations to overcome the limitations of standard MD simulations...
Thesis (Ph.D.)--University of Western Australia, 2012