Concerted Two-Electron Reduction of Ubiquinone in Respiratory Complex I

Mitochondrial complex I ROS production and redox signaling in hypoxia

Mitochondria are a main source of cellular energy. Oxidative phosphorylation (OXPHOS) is the major process of aerobic respiration. Enzyme complexes of the electron transport chain (ETC) pump protons to generate a protonmotive force (Δp) that drives OXPHOS. Complex I is an electron entry point into the ETC. Complex I oxidizes nicotinamide adenine dinucleotide (NADH) and transfers electrons to ubiquinone in a reaction coupled with proton pumping. Complex I also produces reactive oxygen species (ROS) under various conditions. The enzymatic activities of complex I can be regulated by metabolic conditions and serves as a regulatory node of the ETC. Complex I ROS plays diverse roles in cell metabolism ranging from physiologic to pathologic conditions. Progress in our understanding indicates that ROS release from complex I serves important signaling functions. Increasing evidence suggests that complex I ROS is important in signaling a mismatch in energy production and demand. In this article, we review the role of ROS from complex I in sensing acute hypoxia.

Single protonation of the reduced quinone in respiratory complex I drives four-proton pumping

Complex I is a key proton-pumping enzyme in bacterial and mitochondrial respiratory electron transport chains. Using quantum chemistry and electrostatic calculations, we have examined the pKa of the reduced quinone QH-/QH2 in the catalytic cavity of complex I. We find that pKa (QH-/QH2) is very high, above 20. This means that the energy of a single protonation reaction of the doubly reduced quinone (i.e. the reduced semiquinone QH-) is sufficient to drive four protons across the membrane with a potential of 180 mV. Based on these calculations, we propose a possible scheme of redox-linked proton pumping by complex I. The model explains how the energy of the protonation reaction can be divided equally among four pumping units of the pump, and how a single proton can drive translocation of four additional protons in multiple pumping blocks.

Extracellular electron uptake for CO2 fixation by Rhodopseudomonas palustris during electro-cultivation in darkness

As a vital part of the global carbon cycle, photosynthesis helps in fixing CO₂ to produce diverse biomass. However, over-reliance on optical density results in inadequate photosynthesis under limited light sources. The coupling of extracellular respiration and photosynthetic chain via the quinone pool provides a possibility for electrically driven photosynthesis in darkness, which is not well understood. In this study, CO₂ fixation of photosynthetic bacteria Rhodopseudomonas palustris was enhanced in the dark via extracellular electron uptake from the electrode at -0.4 V. The copy number of R. palustris increased by 35 folds during 28 days of operation, accompanied by the increase of ATP content, NADH/NAD⁺, and NADPH/NADP⁺ of cells. Especially, the activity of Rubisco, the key enzyme of the Calvin cycle, increased by 28 % during electro-cultivation. Accordingly, the electrochemical activity of R. palustris was found to increase, which might be attributed to the structural modification of protein-like substances due to the enhanced proton-coupled electron transfer (PCET) process in electro-cultivation, which was further confirmed by in situ Fourier transform infrared spectroscopy and kinetic isotope effect tests. This study indicated that extracellular respiration could be electrostimulated via PCET to maintain photosynthesis in R. palustris in the dark.

Mechanical Allosteric Couplings of Redox-Induced Conformational Changes in Respiratory Complex I

We apply linear response theory to calculate mechanical allosteric couplings in respiratory complex I between the iron sulfur cluster N2, located in the catalytic cavity, and the membrane part of the enzyme, separated from it by more than 50 Å. According to our hypothesis, the redox reaction of ubiquinone in the catalytic cavity of the enzyme generates an unbalanced charge that via repulsion of the charged redox center N2 produces local mechanical stress that transmits into the membrane part of the enzyme where it induces proton pumping. Using coarse-grained simulations of the enzyme, we calculated mechanistic allosteric couplings that reveal the pathways of the mechanical transmission of the stress along the enzyme. The results shed light on the recent experimental studies where a stabilization of the enzyme with an introduced disulfide bridge resulted in the abolishing of proton pumping. Simulation of the disulfide bond action indicates a dramatic change of the mechanistic coupling pathways in line with experimental findings.

Quinone binding in respiratory complex I: Going through the eye of a needle. The squeeze-in mechanism of passing the narrow entrance of the quinone site

At the joint between the membrane and hydrophilic arms of the enzyme, the structure of the respiratory complex I reveals a tunnel-like Q-chamber for ubiquinone binding and reduction. The narrow entrance of the quinone chamber located in ND1 subunit forms a bottleneck (eye of a needle) which in all resolved structures was shown to be too small for a bulky quinone to pass through, and it was suggested that a conformational change is required to open the channel. The closed bottleneck appears to be a well-established feature of all structures reported so-far, both for the so-called open and closed states of the enzyme, with no indication of a stable open state of the bottleneck. We propose a squeeze-in mechanism of the bottleneck passage, where dynamic thermal conformational fluctuations allow quinone to get in and out. Here, using molecular dynamics simulations of the bacterial enzyme, we have identified collective conformational changes that open the quinone chamber bottleneck. The model predicts a significant reduction—due to a need for a rare opening of the bottleneck—of the effective bi-molecular rate constant, in line with the available kinetic data. We discuss possible reasons for such a tight control of the quinone passage into the binding chamber and mechanistic consequences for the quinone two-electron reduction.

Respiratory complex I: Bottleneck at the entrance of quinone site requires conformational change for its opening

The structure of the entire respiratory complex I is now known at reasonably high resolution for many species - bacteria, yeast, and several mammals, including human. The structure reveals an almost 30 angstrom tunnel-like chamber for ubiquinone binding in the core part of the enzyme, at the joint between the membrane and hydrophilic arms of the enzyme. Here we characterize the geometric bottleneck forming the entrance of the quinone reaction chamber. Computer simulations of quinone/quinol passage through the bottleneck suggest that in all structures available, from bacterial to human, this bottleneck is too narrow for the quinone or quinol to pass and that a conformational change is required to open the channel. Moreover, the bottleneck is too narrow even for isoprenoid tail free passage. The closed structure can be an artifact of the crystallization packing forces, low temperature, or other unnatural conditions occurring in the structural data acquisition procedure that affect this flexible part of the enzyme. Two of the helices forming the bottleneck are in direct contact with the subunit (ND3) that was recently demonstrated to be involved in conformational changes during the redox proton pumping cycle, which indicates flexibility of that part of the enzyme. We conclude that the published structures are all locked in the unfunctional states and do not represent correctly the functional enzyme; we discuss possible ways to open the structure in the context of possible mechanisms of the enzyme.

Kinetics and Efficiency of Energy-Transducing Enzymes

Complexes I to IV, with the exception of Complex II, are redox-driven proton pumps that convert redox energy of oxygen reduction to proton gradient across the mitochondrial or bacterial membrane; in turn, the created electrochemical gradient drives the adenosine triphosphate synthesis in the cells by utilizing complex V of the chain. Here we address a general question of the efficiency of such enzymes, considering them as molecular machines that couple endergonic and exergonic reactions and converting one form of free energy into another. One well-known example of the efficiency is given by Carnot's theorem for heat engines. Here we extend the concept to respiratory enzymes and specifically focus on the proton pumping by Complex I of the respiratory chain, nicotinamide adenine dinucleotide dehydrogenase. To discuss the efficiency issues, we develop a model of enzyme kinetics, which generalizes the Michaelis-Menten model. Our model includes several substrates and products and, in general, can be considered as Generalized Michaelis-Menten Kinetic model. The model might be useful for describing complex enzyme kinetics, regardless of the efficiency issues that are addressed in this paper.