UC Davis

Ion channels are integral membrane proteins facilitating permeation of ions through aqueous pores across cell membranes. They are essential to numerous physiological processes such as nerve impulses and heartbeats and are key therapeutic targets due to their involvement in various diseases. This dissertation employs advanced computational techniques to investigate the structure and function of ion channels, specifically focusing on the human (denoted by the prefix “h”) voltage-gated sodium channel hNaV1.7, voltage-gated potassium channel hERG, and small-conductance calcium-activated potassium channel hSK2, which are critical therapeutic targets for pain management and the treatment of cardiac arrhythmias. A brief overview of ion channels and lipid membranes as well as their experimental and computational studies is provided in Chapters 1 and 2, followed by three specific ion channel related stories in Chapters 3 through 5 and finishing with closing remarks and future outlook in Chapter 6.The first story focuses on the human voltage-gated sodium channel hNaV1.7, a prime target for pain therapy due to its predominant expression in peripheral nociceptive neurons. We explored the interaction between the hNaV1.7 channel’s voltage sensing domains (VSDs) II and IV in different conformational states and the tarantula venom peptide protoxin-II, a potent and selective inhibitor of the channel. Our computational models revealed that protoxin-II exhibits state-specific binding modes to different states of the channel’s VSDs, illuminating the molecular basis of its inhibitory effects through enhanced hNaV1.7 channel deactivation and inactivation. Additionally, we identified key channel’s residues involved in the toxin binding and their energetic contributions. These findings are crucial for the rational design of novel pain therapeutics with improved selectivity and potency. The second story shifts focus to the human voltage-gated potassium channel hKV11.1, also known as hERG (human Ether-à-go-go-Related Gene), a vital component of cardiac repolarization and a notorious drug anti-target. This makes the hERG channel a primary target for assessing the safety of new drugs due to association of its inhibition with drug-induced arrhythmias. Utilizing AlphaFold2, a state-of-the-art deep learning tool trained to predict protein structures from amino acid sequences, we modeled the elusive inactivated and closed conformations of the hERG channel not available experimentally. Molecular dynamics and drug docking simulations validated these models, aligning closely with existing experimental data. Drug docking simulations revealed state-specific drug interactions, underscoring the critical importance of the inactivated state for drug binding and the potential for drug entrapment in the closed state. Analysis of interaction networks across different conformational states of the hERG channel provided insights into potential molecular mechanisms underlying state transitions. These findings are pivotal not only for understanding the functioning of this crucial channel but also for predicting drug-induced arrhythmias from drug chemical structures and thus developing cardiac-safe medications. The third story explores the regulation of the human small-conductance calcium-activated potassium channel hSK2 by phosphatidylinositol 4,5-bisphosphate (PIP2) lipid in cardiac cells, aiming to enhance therapeutic strategies for cardiac arrhythmias like atrial fibrillation. Using optogenetic constructs to deplete PIP2, our collaborative study demonstrated that PIP2 depletion reduces hSK2 current in both cultured Chinese hamster ovary (CHO) cells and rabbit ventricular myocytes, underscoring PIP2's crucial role in hSK2 channel activation. Homology modeling and molecular dynamics simulations revealed the dynamic binding sites and mechanisms of PIP2 interaction with hSK2 channels, identifying key residues like R395 and E398 involved in channel activation by PIP2. This detailed analysis provides insights into the molecular mechanisms regulating cardiac excitability, offering potential targets for new anti-arrhythmic therapies. In summary, this doctoral dissertation delves into the intricate world of membrane proteins, in particular, ion channels, exploring their structural and functional intricacies including their interactions with the lipid bilayer environment, pharmacological agents, and toxin peptides. By employing cutting-edge computational approaches, we provided novel insights and strategies that hold promise for accelerating drug discovery and advancing precision medicine, ultimately aiming to develop more targeted and effective therapies for cardiac and neurological disorders.