Quantum Calculations of Electron Tunneling in Respiratory Complex III

The complexities of ligand/receptor interactions: Exploring the role of molecular vibrations and quantum tunnelling

Molecular vibrations and quantum tunneling may link ligand binding to the function of pharmacological receptors. The well-established lock-and-key model explains a ligand's binding and recognition by a receptor; however, a general mechanism by which receptors translate binding into activation, inactivation, or modulation remains elusive. The Vibration Theory of Olfaction was proposed in the 1930s to explain this subset of receptor-mediated phenomena by correlating odorant molecular vibrations to smell, but a mechanism was lacking. In the 1990s, inelastic electron tunneling was proposed as a plausible mechanism for translating molecular vibration to odorant physiology. More recently, studies of ligands' vibrational spectra and the use of deuterated ligand analogs have provided helpful information to study this admittedly controversial hypothesis in metabotropic receptors other than olfactory receptors. In the present work, based in part on published experiments from our laboratory using planarians as an experimental organism, I will present a rationale and possible experimental approach for extending this idea to ligand-gated ion channels.

Respiratory Complex III: A Bioengine with a Ligand-Triggered Electron-Tunneling Gating Mechanism

Respiratory complex III (a.k.a., the bc1 complex) plays a key role in the electron transport chain in aerobic cells. The bc1 complex exhibits multiple unique electron tunneling (ET) processes, such as ET-bifurcation at the Qo site and movement of the Rieske domain. Moreover, we previously discovered that electron tunneling in the low potential arm of the bc1 complex is regulated by a key phenylalanine residue (Phe90). The main goal of the current work is to study the dynamics of the key Phe90 residue in the electron tunneling reaction between heme bL and heme bH as a function of the occupancy of the Qo and Qi binding sites in the bc1 complex. We simulated the molecular dynamics of four model systems of respiratory complex III with different ligands bound at the Qo and Qi binding sites. In addition, we calculated the electron tunneling rate constants between heme bL and heme bH along the simulated molecular dynamics trajectories. The binding of aromatic ligands at the Qo site induces a conformational cascade that properly positions the Phe90 residue, reducing the through-space ET distance from ∼7 to ∼5.5 Å and thus enhancing the electron transfer rate between the heme bL and the heme bH redox pair. Also, the binding of aromatic ligands at the Qi site induces conformational changes that stabilize the Phe90 conformational variation from ∼1.5 to ∼0.5 Å. Hence, our molecular dynamics simulation results show an on-demand two-step conformational connection between the occupancy of the Qo and Qi binding sites and the conformational dynamics of the Phe90 residue. Additionally, our dynamic electron tunneling results confirm our previously reported findings that the Phe90 residue acts as an electron-tunneling gate or switch, controlling the electron transfer rate between the heme bL and heme bH redox systems.

Medical hypothesis: Neurodegenerative diseases arise from oxidative damage to electron tunneling proteins in mitochondria

Mitochondria likely arose from serial endosymbiosis by early eukaryotic cells and control electron flow to molecular oxygen to facilitate energy transformation. Mitochondria translate between the quantum and macroscopic worlds and utilize quantum tunneling of electrons to reduce activation energy barriers to electron flow. Electron tunneling has been extensively characterized in Complex I of the electron transport chain. Age-related increases in oxidative damage to these electron tunneling systems may account for decreased energy storage found in aged and neurodegenerative disease tissues, such as those from sufferers of amyotrophic lateral sclerosis (ALS), Alzheimer's disease (AD) and Parkinson's disease (PD). This hypothesis is testable. If correct, this hypothesis supports pre-symptomatic, mitochondrially-directed oxygen free radical scavenging therapies.

Redox-Driven Proton Pumps of the Respiratory Chain

In aerobic cells, the proton gradient that drives ATP synthesis is created by three different proton pumps-membrane enzymes of the respiratory electron transport chain known as complex I, III, and IV. Despite the striking dissimilarity of structures and apparent differences in molecular mechanisms of proton pumping, all three enzymes have much in common and employ the same universal physical principles of converting redox energy to proton pumping. In this study, we describe a simple mathematical model that illustrates the general principles of redox-driven proton pumps and discuss their implementation in complex I, III, and IV of the respiratory chain.

Fragment-orbital tunneling currents and electronic couplings for analysis of molecular charge-transfer systems

In theoretical charge-transfer research, calculation of the electronic coupling element is crucial for examining the degree of the electronic donor-acceptor interaction. The tunneling current (TC), representing the magnitudes and directions of electron flow, provides a way of evaluating electronic couplings, along with the ability of visualizing how electrons flow in systems. Here, we applied the TC theory to π-conjugated organic dimer systems, in the form of our fragment-orbital tunneling current (FOTC) method, which uses the frontier molecular-orbitals of system fragments as diabatic states. For a comprehensive test of FOTC, we assessed how reasonable the computed electronic couplings and the corresponding TC densities are for the hole- and electron-transfer databases HAB11 and HAB7. FOTC gave 12.5% mean relative unsigned error with regard to the high-level ab initio reference. The shown performance is comparable with that of fragment-orbital density functional theory, which gave the same error by 20.6% or 13.9% depending on the formulation. In the test of a set of nucleobase π stacks, we showed that the original TC expression is also applicable to nondegenerate cases under the condition that the overlap between the charge distributions of diabatic states is small enough to offset the energy difference. Lastly, we carried out visual analysis on the FOTC densities of thiophene dimers with different intermolecular alignments. The result depicts an intimate topological connection between the system geometry and electron flow. Our work provides quantitative and qualitative grounds for FOTC, showing it to be a versatile tool in characterization of molecular charge-transfer systems.

Novel Inhibitors for a Novel Binding Site in Respiratory Complex III

A new binding site and potential novel inhibitors of the respiratory complex III are described. The site is located at the opposite side of the enzyme with respect to ubiquinol binding site (Qo site), and distinctly different from both Qo and Qi sites (hence designated as Non-Q binding site, NQ). NQ site binding pocket extends up close to Phe90 residue, an internal switch (LH switch) that regulates electron transfer between heme bL and heme bH of the low potential redox chain. Docking studies and molecular dynamics simulations of different molecules to the NQ site revealed potential ligands which exhibit a novel inhibitory effect for bc1 complex by switching the LH switch to "off" conformation, thereby shutting down electron transfer in the low potential redox chain. Moreover, the novel inhibitors have lower binding affinity for both Qo and Qi sites, and hence do not interfere with binding of the natural ligands to those sites. The inhibitory activity of those novel ligands in bc1 complex is suggested to promote the production of reactive oxygen species (ROS) at the Qo site. Hence those ligands are potential candidates for designing new "mitocan" drugs.