In-silico Investigation of Ion-Pumping Rotary A- and V-type ATPases: Structural and Dynamical Aspects

Advances in Molecular Biosciences have revolutionised the way we perceive and pursue current biological research. Dynamic, complex biomacromolecules constitute the essential components of Cells. Particularly proteins have been characterised as the workhorse molecules of life. Either as single chains or complexes of associated units, proteins participate in every biological process with a specific structural and/or functional role. Ion-pumping rotary ATPases is a large family of important membrane-bound protein nanomachines. In the current work we investigate structural and dynamical aspects of the A- and V-type rotary ATPases, related to functional dynamics, and propose a multiscale computational framework for their in-silico biophysical characterisation and the interpretation of low-resolution experimental data from electron microscopy in Chapter 3. For the first time we present results from explicit-solvent atomistic molecular dynamics simulations of the prokaryotic A-type peripheral stator stalk and central rotor axle, both being critical subunits involved in the mechanical coupling of the rotary ATPases in Chapter 4. Our simulation data reveal the presence of flexibility heterogeneity and demonstrate the dynamic nature of the peripheral stator stalk as a source of intact ATPase particle conformational variability. In Chapter 5 we show the presence of structural plasticity in the eukaryotic peripheral stator stalk of the V-ATPase and discuss possible implications for V-ATPase regulation. Overall, the wealth of information accessed with molecular-dynamics simulations allows the exploitation of atomistic information within the multiscale framework of Chapter 3 to be applied for the mechanical characterisation of rotary ATPases in future studies. In particular, atomistic data could serve as high-resolution information for future parameterisation of simplified coarse-grain models for all ATPase subunits and the construction of molecular models for the intact ATPases. We anticipate that our approach will contribute to elucidating the molecular origin of rotary ATPases’ conformational flexibility and its implications for the holoenzyme’s function and kinetic efficiency.