Lateral diffusion of redox components in the mitochondrial inner membrane is unaffected by inner membrane folding and matrix density

Amazing structure of respirasome: unveiling the secrets of cell respiration

Respirasome, a huge molecular machine that carries out cellular respiration, has gained growing attention since its discovery, because respiration is the most indispensable biological process in almost all living creatures. The concept of respirasome has renewed our understanding of the respiratory chain organization, and most recently, the structure of respirasome solved by Yang's group from Tsinghua University (Gu et al. Nature 237(7622):639-643, 2016) firstly presented the detailed interactions within this huge molecular machine, and provided important information for drug design and screening. However, the study of cellular respiration went through a long history. Here, we briefly showed the detoured history of respiratory chain investigation, and then described the amazing structure of respirasome.

Determination of protein mobility in mitochondrial membranes of living cells

Molecular mobility in membranes of intracellular organelles is poorly understood, due to the lack of experimental tools applicable for a great diversity of shapes and sizes such organelles can acquire. Determinations of diffusion within the plasma membrane or cytosol are based mostly on the assumption of an infinite flat space, not valid for curved membranes of smaller organelles. Here we extend the application of FRAP to mitochondria of living cells by application of numerical analysis to data collected from a small region inside a single organelle. The spatiotemporal pattern of light pulses generated by the laser scanning microscope during the measurement is reconstructed in silico and consequently the values of diffusion parameters best suited to the particular organelle are found. The mobility of the outer membrane proteins hFis and Tom7, as well as oxidative phosphorylation complexes COX and F(1)F(0) ATPase located in the inner membrane is analyzed in detail. Several alternative models of diffusivity applied to these proteins provide insight into the mechanisms determining the rate of motion in each of the membranes. Tom7 and hFis move along the mitochondrial axis in the outer membrane with similar diffusion coefficients (D=0.7μm(2)/s and 0.6μm(2)/s respectively) and equal immobile fraction (7%). The notably slower motion of the inner membrane proteins is best represented by a dual-component model with approximately equal partitioning of the fractions (F(1)F(0) ATPase: 0.4μm(2)/s and 0.0005μm(2)/s; COX: 0.3μm(2)/s and 0.007μm(2)/s). The mobility patterns specific for the membranes of this organelle are unambiguously distinguishable from those of the plasma membrane or artificial lipid environments: The parameters of mitochondrial proteins indicate a distinct set of factors responsible for their diffusion characteristics.

Subunits of mitochondrial complex I exist as part of matrix- and membrane-associated subcomplexes in living cells

Mitochondrial complex I (CI) is a large assembly of 45 different subunits, and defects in its biogenesis are the most frequent cause of mitochondrial disorders. In vitro evidence suggests a stepwise assembly process involving pre-assembled modules. However, whether these modules also exist in vivo is as yet unresolved. To answer this question, we here applied submitochondrial fluorescence recovery after photobleaching to HEK293 cells expressing 6 GFP-tagged subunits selected on the basis of current CI assembly models. We established that each subunit was partially present in a virtually immobile fraction, possibly representing the holo-enzyme. Four subunits (NDUFV1, NDUFV2, NDUFA2, and NDUFA12) were also present as highly mobile matrix-soluble monomers, whereas, in sharp contrast, the other two subunits (NDUFB6 and NDUFS3) were additionally present in a slowly mobile fraction. In the case of the integral membrane protein NDUFB6, this fraction most likely represented one or more membrane-bound subassemblies, whereas biochemical evidence suggested that for the NDUFS3 protein this fraction most probably corresponded to a matrix-soluble subassembly. Our results provide first time evidence for the existence of CI subassemblies in mitochondria of living cells.

FRAP beam-size analysis to measure palmitoylation-dependent membrane association dynamics and microdomain partitioning of Ras proteins

Motions of membrane-associated proteins within and between membranes are essential for many cellular functions. We describe the application of fluorescence recovery after photobleaching (FRAP) beam-size analysis to investigate the role of palmitoylation in the membrane targeting and membrane association dynamics of H-Ras. The method described distinguishes between FRAP by lateral diffusion and by cytoplasmic exchange, and enables to obtain an estimate of the membrane affinity in live cells. These studies show distinct roles for the two palmitoylation sites (Cys181 and Cys184) on H-Ras, with different effects on membrane affinity and microlocalization.

Kinetics of bimolecular reactions in model bilayers and biological membranes. A critical review

The quantitative study of the probability of molecular encounters giving rise to a reaction in membranes is a challenging discipline. Model systems, model in the sense that they use model bilayers and model reactants, have been widely used for this purpose, but the methodologies employed for the analysis of the results obtained in experiments, and for experimental design, are so disparate that a concerned experimentalist has difficulty in deciding about the value of each approach. This review intends to examine the several approaches that can be found in the literature showing, when feasible, the weakness, strengths and limits of application of each of them. There is not, so far, a full experimental validation of the most promising theories for the analysis of reactions in two dimensions, what leaves open a large field for new research. The major challenge resides in the time range in which the processes take place, but the possibilities of the existing techniques for these studies are far from exhausted. We review also the attempts of several authors to quantitatively analyze the kinetics of reactions in biological membranes. Especially in this field, the recently developed microspectroscopies enclose a still unexplored potential.

Respiratory chain supercomplexes in plant mitochondria

Supercomplexes are defined associations of protein complexes, which are important for several cellular functions. This "quintenary" organization level of protein structure recently was also described for the respiratory chain of plant mitochondria. Except succinate dehydrogenase (complex II), all complexes of the oxidative phosphorylation (OXPOS) system (complexes I, III, IV and V) were found to form part of supercomplexes. Compositions of these supramolecular structures were systematically investigated using digitonin solubilizations of mitochondrial fractions and two-dimensional Blue-native (BN) polyacrylamide gel electrophoresis. The most abundant supercomplex of plant mitochondria includes complexes I and III at a 1:2 ratio (I1 + III2 supercomplex). Furthermore, some supercomplexes of lower abundance could be described, which have I2 + III4, V2, III2 + IV(1-2), and I1 + III2 + IV(1-4) compositions. Supercomplexes consisting of complexes I plus III plus IV were proposed to be called "respirasome", because they autonomously can carry out respiration in the presence of ubiquinone and cytochrome c. Plant specific alternative oxidoreductases of the respiratory chain were not associated with supercomplexes under all experimental conditions tested. However, formation of supercomplexes possibly indirectly regulates alternative respiratory pathways in plant mitochondria on the basis of electron channeling. In this review, procedures to characterize the supermolecular organization of the plant respiratory chain and results concerning supercomplex structure and function are summarized and discussed.

Kinetics of the quinone binding reaction at the QB site of reaction centers from the purple bacteria Rhodobacter sphaeroides reconstituted in liposomes

Transmembrane proton translocation in the photosynthetic membranes of the purple bacterium Rhodobacter sphaeroides is driven by light and performed by two transmembrane complexes; the photosynthetic reaction center and the ubiquinol-cytochrome c oxidoreductase complex, coupled by two mobile electron carriers; the cytochrome and the quinone. This paper focuses on the kinetics and thermodynamics of the interaction between the lipophylic electron carrier ubiquinone-10 and the photosynthetic enzyme reconstituted in liposomes. The collected data were simulated with an existing recognized kinetic scheme and the kinetic constants of the uptake (7.2 x 107 M(-1) x s(-1)) and release (40 s(-1)) processes of the ligand were inferred. The results obtained for the quinone release kinetic constant are comparable to the rate of the charge recombination reaction from the state D(+)QA(-). Values for the kinetic constants are discussed as part of the overall photocycle, suggesting that its bottleneck may not be the quinone uptake reaction in agreement with a previous report.

Energy metabolism during insect flight: biochemical design and physiological performance

Flying insects achieve the highest known mass-specific rates of O(2) consumption in the animal kingdom. Because the flight muscles account for >90% of the organismal O(2) uptake, accurate estimates of metabolic flux rates (J) in the muscles can be made. In steady state, these are equal to the net forward flux rates (v) at individual steps and can be compared with flux capacities (V(max)) measured in vitro. In flying honeybees, hexokinase and phosphofructokinase, both nonequilibrium reactions in glycolysis, operate at large fractions of their maximum capacities (i.e., they operate at high v/V(max)). Phosphoglucoisomerase is a reversible reaction that operates near equilibrium. Despite V(max) values more than 20-fold greater than the net forward flux rates during flight, a close match is found between the V(max) required in vivo (estimated using the Haldane relationship) to maintain near equilibrium and this net forward flux rate and the V(max) measured in vitro under simulated physiological conditions. Rates of organismal O(2) consumption and difference spectroscopy were used to estimate electron transfer rates per molecule of respiratory chain enzyme during flight. These are much higher than those estimated in mammalian muscles. Current evidence indicates that metabolic enzymes in honeybees do not display higher catalytic efficiencies than the homologous enzymes in mammals, and the high electron transfer rates do not appear to be the result of higher enzyme densities per unit cristae surface area. A number of possible mechanistic explanations for the higher rates of electron transfer are proposed.

Dynamics of the mitochondrial reticulum in live cells using Fourier imaging correlation spectroscopy and digital video microscopy

We report detailed studies of the dynamics of the mitochondrial reticulum in live cells using two independent experimental techniques: Fourier imaging correlation spectroscopy and digital video fluorescence microscopy. When both methods are used to study the same system, it is possible to directly compare measurements of preaveraged statistical dynamical quantities with their microscopic counterparts. This approach allows the underlying mechanism of the observed rates to be determined. Our results indicate that the dynamics of the reticulum structure is composed of two independent contributions, each important on very different time and length scales. During short time intervals (1-15 sec), local regions of the reticulum primarily undergo constrained thermally activated motion. During long time intervals (>15 sec), local regions of the reticulum undergo long-range "jump" motions that are associated with the action of cytoskeletal filaments. Although the frequency of the jumps depend on the physiological state of the cells, the average jump distance ( approximately 0.8 microm) is unaffected by metabolic activity. During short time intervals, the dynamics appear to be spatially heterogeneous, whereas the cumulative effect of the infrequent jumps leads to the appearance of diffusive motion in the limit of long time intervals.

The sorting of mitochondrial DNA and mitochondrial proteins in zygotes: preferential transmission of mitochondrial DNA to the medial bud

Green fluorescent protein (GFP) was used to tag proteins of the mitochondrial matrix, inner, and outer membranes to examine their sorting patterns relative to mtDNA in zygotes of synchronously mated yeast cells in rho+ x rho0 crosses. When transiently expressed in one of the haploid parents, each of the marker proteins distributes throughout the fused mitochondrial reticulum of the zygote before equilibration of mtDNA, although the membrane markers equilibrate slower than the matrix marker. A GFP-tagged form of Abf2p, a mtDNA binding protein required for faithful transmission of rho+ mtDNA in vegetatively growing cells, colocalizes with mtDNA in situ. In zygotes of a rho+ x rho+ cross, in which there is little mixing of parental mtDNAs, Abf2p-GFP prelabeled in one parent rapidly equilibrates to most or all of the mtDNA, showing that the mtDNA compartment is accessible to exchange of proteins. In rho+ x rho0 crosses, mtDNA is preferentially transmitted to the medial diploid bud, whereas mitochondrial GFP marker proteins distribute throughout the zygote and the bud. In zygotes lacking Abf2p, mtDNA sorting is delayed and preferential sorting is reduced. These findings argue for the existence of a segregation apparatus that directs mtDNA to the emerging bud.

Carbocyanine dyes with long alkyl side-chains: broad spectrum inhibitors of mitochondrial electron transport chain activity

Certain indocarbocyanine, thiacarbocyanine, and oxacarbocyanine dyes possessing short alkyl side-chains (one to five carbons) are potent inhibitors of mammalian mitochondrial NADH-ubiquinone reductase (EC 1.6.99.3) activity (Anderson et al., Biochem Pharmacol 41: 677-684, 1991; Anderson et al., Biochem Pharmacol 45: 691-696, 1993; Anderson et al., Biochem Pharmacol 45: 2115-2122, 1993), and act similarly to rotenone. This study examines the inhibitory capacities of twelve other carbocyanine dyes (six indocarbocyanines, four oxacarbocyanines, and two thiacarbocyanines) possessing long alkyl side-chains (seven to eighteen carbons with both saturated and unsaturated side-chains) on mitochondrial NADH, succinate and cytochrome c oxidase activities. Three of the indocarbocyanines inhibited electron transport chain activity, while three were non-inhibitory. Two of the oxacarbocyanines also inhibited electron transport chain activity, while the other two were without effect. Both the thiacarbocyanines were non-inhibitory. In contrast to previous studies, the long alkyl side-chain carbocyanines exhibited a broad spectrum of inhibition of respiratory chain activity, affecting either oxidation of all three substrates or of NADH and cytochrome c, rather than specific inhibition of mitochondrial NADH-ubiquinone reductase activity, indicating that there could be multiple binding sites for these compounds. The five inhibitory long side-chain carbocyanines also inhibited reduction of ferricyanide and coenzyme Q1 by NADH, using submitochondrial particles, but not when tested with purified complex I, indicating that the mitochondrial inner membrane was an integral component in their inhibitory capacity. No general correlation of side-chain length or degree of unsaturation and inhibitory capacity was discernible.

Comparisons of the relative effects of polyhydroxyl compounds on local versus long-range motions in the mitochondrial inner membrane. Fluorescence recovery after photobleaching, fluorescence lifetime, and fluorescence anisotropy studies

This laboratory has been interested in understanding the relationship between molecular motion and electron transport rates in the mitochondrial inner membrane. We have previously noted a sucrose-induced decrease in both multicomponent electron transport rates and lateral diffusion of redox components. The decreases in lateral diffusion and the related mobile fraction of redox components were greater than expected from hydrodynamic theory. In this report we sought to understand how the presence of increasing aqueous concentrations of polyhydroxyl agents affect short-range motions in different regions of the inner membrane bilayer, frequently expressed in terms of 'viscosity' and order, compared to lateral diffusion. Fluorescence recovery after photobleaching was used to monitor long-range phospholipid and integral protein diffusion. Multifrequency fluorescence lifetime and steady-state fluorescence anisotropy techniques were used to monitor local dynamics of diphenylhexatriene (DPH) and trimethylaminodiphenylhexatriene (TMA-DPH). Light scattering corrections were found to be essential for inner membrane measurements by the latter two techniques. DPH and TMA-DPH each exhibited two-lifetime components. Generally, increasing the aqueous concentration of polyhydroxyl agents decreased the average DPH lifetime and increased the average TMA-DPH lifetime. In general, under the same conditions fluorescence anisotropies increased. Our results indicated that changes in the rotational diffusion coefficient, microviscosity and order were being induced at both the phospholipid headgroup and in the acyl chain regions of the membrane bilayer. Our results suggest that these changes may be due in part to induced changes in the interaction and distribution of water with membranes. Long-range lateral diffusion was found to be significantly retarded by increasing concentrations of polyhydroxyl agents. We conclude that the discrepancies between bulk viscosity predicted decreases in long-range diffusion may result, in part, from the aforementioned membrane/water interactions. We also note an apparent qualitative relationship between long-range lateral diffusion reported diffusion coefficient with local TMA-DPH reported rotational diffusion coefficient and apparent microviscosities.