Phd in THEORETICAL AND APPLIED MECHANICS

Thesis title: Fluid behaviour in biological confinement: gating of the hERG potassium channel via Molecular Dynamics simulations and network analysis

The boundary between biological cells and the external environment is represented by a lipid membrane that does not allow the passage of polar molecules such as ions and water. However, their orchestrated movements are fundamental for the function of vital organs. For this reason, there are transmembrane proteins called as “ion channels” that forming pores on the cells allow the ion to flow through these impermeable membranes. Normally, an ion channel has three functional states: the open state that is permeable to ions, the closed state where they can not pass, and the inactivated state that is structurally similar to the open state but functionally closed. The mechanisms by which an ion channel switches from the open to the closed state and vice versa are defined as “activation” and “deactivation” respectively, while the transition from the open to the inactivated state is defined as “inactivation”. All these transitions define the so-called “gating” mechanism. The main features of the biological channels are the selectivity, the sensing and the regulation of their gating mechanism. The characterization of these properties gives the possibility to extract the basic principles to design bioinspired artificial channels that can be used, for example, to study various molecules in confined spaces and in real time by current measurements. The biomimetic channels are becoming the focus of attention for bionanotechnology because they offer greater flexibility in terms of shape and size, robustness and surface properties boosting, in this way, their fields of application. In this context, we studied the human ether-à-go-go–related gene channel (hERG, KCNH2, or Kv11.1) that is a voltage-gated potassium channel involved in the heart contraction. hERG malfunctions are associated with severe pathologies such as long QT syndrome type 2 (LQTS2) that can be due to loss-of-function mutations (congenital LQTS2) or channel blockage induced by unspecific interactions with medications (acquired LQTS2). These conditions have been described to promote arrhythmia and sudden cardiac death. Based on the protein architecture, hERG is a member of the non-domain-swapped channel family where the sensor of the channel is always connected covalently to the pore of the same subunit. The gating mechanism of these channels is still not completely characterized. Due to its importance in human health, we decided to focus on hERG gating addressing the problem with a theoretical approach based on Molecular Dynamics simulations. Using a network analysis, we microscopically identified the kinematic chain of residues that couple the sensor of the channel to the pore. In general, our results could provide the basis for studying the coupling mechanisms between sensors and pores in ion channels to explain the origin of inherited and induced channelopathies such as LQTS2.