Multidimensional diffusion modes and collision frequencies of cytochrome c with its redox partners

Structures of Tetrahymena thermophila respiratory megacomplexes on the tubular mitochondrial cristae

Tetrahymena thermophila, a classic ciliate model organism, has been shown to possess tubular mitochondrial cristae and highly divergent electron transport chain involving four transmembrane protein complexes (I-IV). Here we report cryo-EM structures of its ~8 MDa megacomplex IV₂+ (I + III₂+ II)₂, as well as a ~ 10.6 MDa megacomplex (IV₂ + I + III₂+ II)₂ at lower resolution. In megacomplex IV₂+ (I + III₂+ II)₂, each CIV₂ protomer associates one copy of supercomplex I + III₂ and one copy of CII, forming a half ring-shaped architecture that adapts to the membrane curvature of mitochondrial cristae. Megacomplex (IV₂+ I + III₂+ II)₂ defines the relative position between neighbouring half rings and maintains the proximity between CIV₂ and CIII₂ cytochrome c binding sites. Our findings expand the current understanding of divergence in eukaryotic electron transport chain organization and how it is related to mitochondrial morphology.

Structure and Mechanism of Respiratory III-IV Supercomplexes in Bioenergetic Membranes

In the final steps of energy conservation in aerobic organisms, free energy from electron transfer through the respiratory chain is transduced into a proton electrochemical gradient across a membrane. In mitochondria and many bacteria, reduction of the dioxygen electron acceptor is catalyzed by cytochrome c oxidase (complex IV), which receives electrons from cytochrome bc1 (complex III), via membrane-bound or water-soluble cytochrome c. These complexes function independently, but in many organisms they associate to form supercomplexes. Here, we review the structural features and the functional significance of the nonobligate III2IV1/2 Saccharomyces cerevisiae mitochondrial supercomplex as well as the obligate III2IV2 supercomplex from actinobacteria. The analysis is centered around the Q-cycle of complex III, proton uptake by CytcO, as well as mechanistic and structural solutions to the electronic link between complexes III and IV.

The proton pumping mechanism of the bc1 complex

The bc₁ complex is a proton pump of the mitochondrial electron transport chain which transfers electrons from ubiquinol to cytochrome c. It operates via the modified Q cycle in which the two electrons from oxidation of ubiquinol at the Q_o center are bifurcated such that the first electron is passed to Cytc via an iron sulfur center and c₁ whereas the second electron is passed across the membrane by b_L and b_H to reduce ubiquinone at the Q_i center. Proton pumping occurs because oxidation of ubiquinol at the Q_o center releases protons to the P-side and reduction of ubiquinone at the Q_i center takes up protons from the N-side. However, the mechanisms which prevent the thermodynamically more favorable short circuit reactions and so ensure precise bifurcation and proton pumping are not known. Here we use statistical thermodynamics to show that reaction steps that originate from high energy states cannot support high flux even when they have large rate constants. We show how the chemistry of ubiquinol oxidation and the structure of the Q_o site can result in free energy profiles that naturally suppress flux through the short circuit pathways while allowing high rates of bifurcation. These predictions are confirmed through in-silico simulations using a Markov state model.

Kinetic advantage of forming respiratory supercomplexes

Components of respiratory chains in mitochondria and some aerobic bacteria assemble into larger, multiprotein membrane-bound supercomplexes. Here, we address the functional significance of supercomplexes composed of respiratory-chain complexes III and IV. Complex III catalyzes oxidation of quinol and reduction of water-soluble cytochrome c (cyt c), while complex IV catalyzes oxidation of the reduced cyt c and reduction of dioxygen to water. We focus on two questions: (i) under which conditions does diffusion of cyt c become rate limiting for electron transfer between these two complexes? (ii) is there a kinetic advantage of forming a supercomplex composed of complexes III and IV? To answer these questions, we use a theoretical approach and assume that cyt c diffuses in the water phase while complexes III and IV either diffuse independently in the two dimensions of the membrane or form supercomplexes. The analysis shows that the electron flux between complexes III and IV is determined by the equilibration time of cyt c within the volume of the intermembrane space, rather than the cyt c diffusion time constant. Assuming realistic relative concentrations of membrane-bound components and cyt c and that all components diffuse independently, the data indicate that electron transfer between complexes III and IV can become rate limiting. Hence, there is a kinetic advantage of bringing complexes III and IV together in the membrane to form supercomplexes.

Peripheral membrane associations of matrix metalloproteinases

Water soluble matrix metalloproteinases (MMPs) have been regarded as diffusing freely in the extracellular matrix. Yet multiple MMPs are also observed at cell surfaces. Their membrane-proximal activities include sheddase activities, collagenolysis, bacterial killing, and intracellular trafficking reaching as far as the nucleus. The catalytic domains of MMP-7 and MMP-12 bind bilayers peripherally, each in two different orientations, by presenting positive charges and a few hydrophobic groups to the surface. Related peripheral membrane associations are predicted for other soluble MMPs. The peripheral membrane associations may support pericellular proteolysis and endocytosis. The isolated soluble domains of MT1-MMP can also associate with membranes. NMR assays suggest transient association of the hemopexin-like domains of MT1-MMP and MMP-12 with lipid bilayers. Peripheral association of soluble MMP domains with bilayers or heparin sulfate proteoglycans probably concentrates them near the membrane. This could increase the probability of forming complexes with membrane-associated proteins, such as those targeted for proteolysis. This article is part of a Special Issue entitled: Matrix Metalloproteinases edited by Rafael Fridman.

A cell is more than the sum of its (dilute) parts: A brief history of quinary structure

Most knowledge of protein structure and function is derived from experiments performed with purified protein resuspended in dilute, buffered solutions. However, proteins function in the crowded, complex cellular environment. Although the first four levels of protein structure provide important information, a complete understanding requires consideration of quinary structure. Quinary structure comprises the transient interactions between macromolecules that provides organization and compartmentalization inside cells. We review the history of quinary structure in the context of several metabolic pathways, and the technological advances that have yielded recent insight into protein behavior in living cells. The evidence demonstrates that protein behavior in isolated solutions deviates from behavior in the physiological environment.

Ambidextrous binding of cell and membrane bilayers by soluble matrix metalloproteinase-12

Matrix metalloproteinases (MMPs) regulate tissue remodelling, inflammation and disease progression. Some soluble MMPs are inexplicably active near cell surfaces. Here we demonstrate the binding of MMP-12 directly to bilayers and cellular membranes using paramagnetic NMR and fluorescence. Opposing sides of the catalytic domain engage spin-labelled membrane mimics. Loops project from the β-sheet interface to contact the phospholipid bilayer with basic and hydrophobic residues. The distal membrane interface comprises loops on the other side of the catalytic cleft. Both interfaces mediate MMP-12 association with vesicles and cell membranes. MMP-12 binds plasma membranes and is internalized to hydrophobic perinuclear features, the nuclear membrane and inside the nucleus within minutes. While binding of TIMP-2 to MMP-12 hinders membrane interactions beside the active site, TIMP-2-inhibited MMP-12 binds vesicles and cells, suggesting compensatory rotation of its membrane approaches. MMP-12 association with diverse cell membranes may target its activities to modulate innate immune responses and inflammation.

Lytic and non-lytic permeabilization of cardiolipin-containing lipid bilayers induced by cytochrome C

The release of cytochrome c (cyt c) from mitochondria is an important early step during cellular apoptosis, however the precise mechanism by which the outer mitochondrial membrane becomes permeable to these proteins is as yet unclear. Inspired by our previous observation of cyt c crossing the membrane barrier of giant unilamellar vesicle model systems, we investigate the interaction of cyt c with cardiolipin (CL)-containing membranes using the innovative droplet bilayer system that permits electrochemical measurements with simultaneous microscopy observation. We find that cyt c can permeabilize CL-containing membranes by induction of lipid pores in a dose-dependent manner, with membrane lysis eventually observed at relatively high (µM) cyt c concentrations due to widespread pore formation in the membrane destabilizing its bilayer structure. Surprisingly, as cyt c concentration is further increased, we find a regime with exceptionally high permeability where a stable membrane barrier is still maintained between droplet compartments. This unusual non-lytic state has a long lifetime (>20 h) and can be reversibly formed by mechanically separating the droplets before reforming the contact area between them. The transitions between behavioural regimes are electrostatically driven, demonstrated by their suppression with increasing ionic concentrations and their dependence on CL composition. While membrane permeability could also be induced by cationic PAMAM dendrimers, the non-lytic, highly permeable membrane state could not be reproduced using these synthetic polymers, indicating that details in the structure of cyt c beyond simply possessing a cationic net charge are important for the emergence of this unconventional membrane state. These unexpected findings may hold significance for the mechanism by which cyt c escapes into the cytosol of cells during apoptosis.

Limitations for current production in Geobacter sulfurreducens biofilms

Devices that exploit electricity produced by electroactive bacteria such as Geobacter sulfurreducens have not yet been demonstrated beyond the laboratory scale. The current densities are far from the maximum that the bacteria can produce because fundamental properties such as the mechanism of extracellular electron transport and factors limiting cell respiration remain unclear. In this work, a strategy for the investigation of electroactive biofilms is presented. Numerical modeling of the response of G. sulfurreducens biofilms cultured on a rotating disk electrode has allowed for the discrimination of different limiting steps in the process of current production within a biofilm. The model outputs reveal that extracellular electron transport limits the respiration rate of the cells furthest from the electrode to the extent that cell division is not possible. The mathematical model also demonstrates that recent findings such as the existence of a redox gradient in actively respiring biofilms can be explained by an electron hopping mechanism but not when considering metallic-like conductivities.

Age-related decline in mitochondrial bioenergetics: does supercomplex destabilization determine lower oxidative capacity and higher superoxide production?

Mitochondrial decay plays a central role in the aging process. Although certainly multifactorial in nature, defective operation of the electron transport chain (ETC) constitutes a key mechanism involved in the age-associated loss of mitochondrial energy metabolism. Primarily, mitochondrial dysfunction affects the aging animal by limiting bioenergetic reserve capacity and/or increasing oxidative stress via enhanced electron leakage from the ETC. Even though the important aging characteristics of mitochondrial decay are known, the molecular events underlying inefficient electron flux that ultimately leads to higher superoxide appearance and impaired respiration are not completely understood. This review focuses on the potential role(s) that age-associated destabilization of the macromolecular organization of the ETC (i.e. supercomplexes) may be important for development of the mitochondrial aging phenotype, particularly in post-mitotic tissues.

Measurement of the mitochondrial membrane potential and pH gradient from the redox poise of the hemes of the bc1 complex

The redox potentials of the hemes of the mitochondrial bc(1) complex are dependent on the proton-motive force due to the energy transduction. This allows the membrane potential and pH gradient components to be calculated from the oxidation state of the hemes measured with multi-wavelength cell spectroscopy. Oxidation states were measured in living RAW 264.7 cells under varying electron flux and membrane potential obtained by a combination of oligomycin and titration with a proton ionophore. A stochastic model of bc(1) turnover was used to confirm that the membrane potential and redox potential of the ubiquinone pool could be measured from the redox poise of the b-hemes under physiological conditions assuming the redox couples are in equilibrium. The pH gradient was then calculated from the difference in redox potentials of cytochrome c and ubiquinone pool using the stochastic model to evaluate the ΔG of the bc(1) complex. The technique allows absolute quantification of the membrane potential, pH gradient, and proton-motive force without the need for genetic manipulation or exogenous compounds.

Gyroid nanoporous membranes with tunable permeability

Understanding the relevant permeability properties of ultrafiltration membranes is facilitated by using materials and procedures that allow a high degree of control on morphology and chemical composition. Here we present the first study on diffusion permeability through gyroid nanoporous cross-linked 1,2-polybutadiene (1,2-PB) membranes with uniform pores that, if needed, can be rendered hydrophilic. The gyroid porosity has the advantage of isotropic percolation with no need for structure prealignment. Closed (skin) or opened (nonskin) outer surface can be simply realized by altering the interface energy in the process of membrane fabrication. The morphology of the membranes' outer surface was investigated by scanning electron microscopy, contact angle, and X-ray photoelectron spectroscopy. The effective diffusion coefficient of glucose decreases from nonskin, to one-sided skin to two-sided skin membranes, much faster than expected by a naive resistance-in-series model; the flux through the two-sided skin membranes even increases with the membrane thickness. We propose a model that captures the physics behind the observed phenomena, as confirmed by flow visualization experiments. The chemistry of 1,2-PB nanoporous membranes can be controlled, for example, by hydrophilic patterning of the originally hydrophobic membranes, which allows for different active porosity toward aqueous solutions and, therefore, different permeability. The membrane selectivity is evaluated by comparing the effective diffusion coefficients of a series of antibiotics, proteins, and other biomolecules; solute permeation is discussed in terms of hindered diffusion. The combination of uniform bulk morphology, isotropically percolating porosity, controlled surface chemistry, and tunable permeability is distinctive for the presented gyroid nanoporous membranes.

Elucidating cytochrome C release from mitochondria: insights from an in silico three-dimensional model

Mitochondrial regulation of apoptosis depends on the programmed release of proapoptotic proteins such as cytochrome c (Cyt c) through the outer mitochondrial membrane (OMM). Although a few key processes involved in this release have been identified, including the liberation of inner membrane-bound Cyt c and formation of diffusible pores on the OMM, other details like the transport of Cyt c within complex mitochondrial compartments, e.g., the cristae and crista junctions, are not yet fully understood (to our knowledge). In particular, a remodeling of the inner mitochondrial membrane accompanying apoptosis seen in a few studies, in which crista junctions widen, has been hypothesized to be a necessary step in the Cyt c release. Using a three-dimensional spatial modeling of mitochondrial crista and the crista junction, model simulations and analysis illustrated how the interplay among solubilization of Cyt c, fast diffusion of Cyt c, and OMM permeabilization gives rise to the observed experimental release profile. Importantly, the widening of the crista junction was found to have a negligible effect on the transport of free Cyt c from cristae. Finally, model simulations showed that increasing the fraction of free/loosely-bound Cyt c can sensitize the cell to apoptotic stimuli in a threshold manner, which may explain increased sensitivity to cell death associated with aging.

Electrostatic docking of a supramolecular host-guest assembly to cytochrome c probed by bidirectional photoinduced electron transfer

A water-soluble octacarboxyhemicarcerand was used as a shuttle to transport redox-active substrates across the aqueous medium and deliver them to the target protein. The results show that weak multivalent interactions and conformational flexibility can be exploited to reversibly bind complex supramolecular assemblies to biological molecules. Hydrophobic electron donors and acceptors were encapsulated within the hemicarcerand, and photoinduced electron transfer (ET) between the Zn-substituted cytochrome c (MW = 12.3 kD) and the host-guest complexes (MW = 2.2 kD) was used to probe the association between the negatively charged hemicarceplex and the positively charged protein. The behavior of the resulting ternary protein-hemicarcerand-guest assembly was investigated in two binding limits: (1) when K(encaps) ≫ K(assoc), the hemicarcerand transports the ligand to the protein while protecting it from the aqueous medium; and (2) when K(assoc) > K(encaps), the hemicarcerand-protein complex is formed first, and the hemicarcerand acts as an artificial receptor site that intercepts ligands from solution and positions them close to the active site of the metalloenzyme. In both cases, ET mediated by the protein-bound hemicarcerand is much faster than that due to diffusional encounters with the respective free donor or acceptor in solution. The measured ET rates suggest that the dominant binding region of the host-guest complex on the surface of the protein is consistent with the docking area of the native redox partner of cytochrome c. The strong association with the protein is attributed to the flexible conformation and adaptable charge distribution of the hemicarcerand, which allow for surface-matching with the cytochrome.

Structural and functional organization of the mitochondrial respiratory chain: a dynamic super-assembly

The structural organization of the mitochondrial oxidative phosphorylation (OXPHOS) system has received large attention in the past and most investigations led to the conclusion that the respiratory enzymatic complexes are randomly dispersed in the lipid bilayer of the inner membrane and functionally connected by fast diffusion of smaller redox components, Coenzyme Q and cytochrome c. More recent investigations by native gel electrophoresis, however, have shown the existence of supramolecular associations of the respiratory complexes, confirmed by electron microscopy analysis and single particle image processing. Flux control analysis has demonstrated that Complexes I and III in mammalian mitochondria and Complexes I, III, and IV in plant mitochondria kinetically behave as single units with control coefficients approaching unity for each single component, suggesting the existence of substrate channelling within the supercomplexes. The reasons why the presence of substrate channelling for Coenzyme Q and cytochrome c was overlooked in the past are analytically discussed. The review also discusses the forces and the conditions responsible for the formation of the supramolecular units. The function of the supercomplexes appears not to be restricted to kinetic advantages in electron transfer: we discuss evidence on their role in the stability and assembly of the individual complexes and in preventing excess oxygen radical formation. Finally, there is increasing evidence that disruption of the supercomplex organization leads to functional derangements responsible for pathological changes.

Association of cytochrome c with membrane-bound cytochrome c oxidase proceeds parallel to the membrane rather than in bulk solution

Electron transfer between the water-soluble cytochrome c and the integral membrane protein cytochrome c oxidase (COX) is the terminal reaction in the respiratory chain. The first step in this reaction is the diffusional association of cytochrome c toward COX, and it is still not completely clear whether cytochrome c diffuses in the bulk solution while encountering COX, or whether it prefers to diffuse laterally on the membrane surface. This is a rather crucial question, since in the latter case the association would be strongly dependent on the lipid composition and the presence of additional membrane proteins. We applied Brownian dynamics simulations to investigate the effect of an atomistically modeled dipalmitoyl phosphatidylcholine membrane on the association behavior of cytochrome c toward COX from Paracoccus denitrificans. We studied the negatively charged, physiological electron-transfer partner of COX, cytochrome c(552), and the positively charged horse-heart cytochrome c. As expected, both cytochrome c species prefer diffusion in bulk solution while associating toward COX embedded in a membrane, where the partial charges of the lipids were switched off, and the corresponding optimal association pathways largely overlap with the association toward fully solvated COX. Remarkably, after switching on the lipid partial charges, both cytochrome c species were strongly attracted by the inhomogeneous charge distribution caused by the zwitterionic lipid headgroups. This effect is particularly enhanced for horse-heart cytochrome c and is stronger at lower ionic strength. We therefore conclude that in the presence of a polar or even a charged membrane, cytochrome c diffuses laterally rather than in three dimensions.

Toward a chemical mechanism of proton pumping by the B-type cytochrome c oxidases: application of density functional theory to cytochrome ba3 of Thermus thermophilus

A mechanism for proton pumping by the B-type cytochrome c oxidases is presented in which one proton is pumped in conjunction with the weakly exergonic, two-electron reduction of Fe-bound O 2 to the Fe-Cu bridging peroxodianion and three protons are pumped in conjunction with the highly exergonic, two-electron reduction of Fe(III)- (-)O-O (-)-Cu(II) to form water and the active oxidized enzyme, Fe(III)- (-)OH,Cu(II). The scheme is based on the active-site structure of cytochrome ba 3 from Thermus thermophilus, which is considered to be both necessary and sufficient for coupled O 2 reduction and proton pumping when appropriate gates are in place (not included in the model). Fourteen detailed structures obtained from density functional theory (DFT) geometry optimization are presented that are reasonably thought to occur during the four-electron reduction of O 2. Each proton-pumping step takes place when a proton resides on the imidazole ring of I-His376 and the large active-site cluster has a net charge of +1 due to an uncompensated, positive charge formally associated with Cu B. Four types of DFT were applied to determine the energy of each intermediate, and standard thermochemical approaches were used to obtain the reaction free energies for each step in the catalytic cycle. This application of DFT generally conforms with previously suggested criteria for a valid model (Siegbahn, P. E. M.; Blomberg, M. A. R. Chem. Rev. 2000, 100, 421-437) and shows how the chemistry of O 2 reduction in the heme a 3 -Cu B dinuclear center can be harnessed to generate an electrochemical proton gradient across the lipid bilayer.

Functional biomimetic models for the active site in the respiratory enzyme cytochrome c oxidase

A functional analog of the active site in the respiratory enzyme, cytochrome c oxidase (CcO) reproduces every feature in CcO's active site: a myoglobin-like heme (heme a3), a distal tridentate imidazole copper complex (Cu(B)), a phenol (Tyr244), and a proximal imidazole. When covalently attached to a liquid-crystalline SAM film on an Au electrode, this functional model continuously catalyzes the selective four-electron reduction of dioxygen at physiological potential and pH, under rate-limiting electron flux (as occurs in CcO).

Cytochrome c-mediated oxidation of hydroethidine and mito-hydroethidine in mitochondria: identification of homo- and heterodimers

Here we report that ferricytochrome c (cyt c(3+)) induces oxidation of hydroethidine (HE) and mitochondria-targeted hydroethidine (Mito-HE or MitoSOX Red) forming highly characteristic homo- and heterodimeric products. Using an HPLC-electrochemical (EC) method, several products were detected from cyt c(3+)-catalyzed oxidation of HE and Mito-HE and characterized by mass spectrometry and NMR techniques as follows: homodimers (HE-HE, E(+)-E(+), Mito-HE-Mito-HE, and Mito-E(+)-Mito-E(+)) and heterodimers (HE-E(+) and Mito-HE-Mito-E(+)), as well as the monomeric ethidium (E(+)) and mito-ethidium (Mito-E(+)). Similar products were detected when HE and Mito-HE were incubated with mitochondria. In contrast, mitochondria depleted of cyt c(3+) were much less effective in oxidizing HE or Mito-HE to corresponding dimeric products. Unlike E(+) or Mito-E(+), the dimeric analogs (E(+)-E(+) and Mito-E(+)-Mito-E(+)) were not fluorescent. Superoxide (O(2)(*-)) or Fremy's salt reacts with Mito-HE to form a product, 2-hydroxy-mito-ethidium (2-OH-Mito-E(+)) that was detected by HPLC. We conclude that HPLC-EC but not the confocal and fluorescence microscopy is a viable technique for measuring superoxide and cyt c(3+)-dependent oxidation products of HE and Mito-HE in cells. Superoxide detection using HE and Mito-HE could be severely compromised due to their propensity to undergo oxidation.

Kinetics of integrated electron transfer in the mitochondrial respiratory chain: random collisions vs. solid state electron channeling

Recent evidence, mainly based on native electrophoresis, has suggested that the mitochondrial respiratory chain is organized in the form of supercomplexes, due to the aggregation of the main respiratory chain enzymatic complexes. This evidence strongly contrasts the previously accepted model, the Random Diffusion Model, largely based on kinetic studies, stating that the complexes are randomly distributed in the lipid bilayer of the inner membrane and functionally connected by lateral diffusion of small redox molecules, i.e., coenzyme Q and cytochrome c. This review critically examines the experimental evidence, both structural and functional, pertaining to the two models and attempts to provide an updated view of the organization of the respiratory chain and of its kinetic consequences. The conclusion that structural respiratory assemblies exist is overwhelming, whereas the expected functional consequence of substrate channeling between the assembled enzymes is controversial. Examination of the available evidence suggests that, although the supercomplexes are structurally stable, their kinetic competence in substrate channeling is more labile and may depend on the system under investigation and the assay conditions.

The role of the mitochondrial apoptosis induced channel MAC in cytochrome c release

Permeabilization of the mitochondrial outer membrane is a crucial event during apoptosis. It allows the release of proapoptotic factors, like cytochrome c, from the intermembrane space, and represents the commitment step in apoptosis. The mitochondrial apoptosis-induced channel, MAC, is a high-conductance channel that forms during early apoptosis and is the putative cytochrome c release channel. Unlike activation of the permeability transition pore, MAC formation occurs without loss of outer membrane integrity and depolarization. The single channel behavior and pharmacology of reconstituted MAC has been characterized with patch-clamp techniques. Furthermore, MAC's activity is compared to that detected in mitochondria inside the cells at the time cytochrome c is released. Finally, the regulation of MAC by the Bcl-2 family proteins and insights concerning its molecular composition are also discussed.

Coverage-dependent changes of cytochrome c transverse location in phospholipid membranes revealed by FRET

The method of fluorescence resonance energy transfer (FRET) has been employed to monitor cytochrome c interaction with bilayer phospholipid membranes. Liposomes composed of phosphatidylcholine and varying amounts of anionic lipid cardiolipin (CL) were used as model membranes. Trace amount of fluorescent lipid derivative, anthrylvinyl-phosphatidylcholine was incorporated into the membranes to serve energy donor for heme moiety of cytochrome c. Energy transfer efficiency was measured at different lipid and protein concentrations to obtain extensive set of data, which were further analyzed globally in terms of adequate models of protein adsorption and energy transfer on the membrane surface. It has been found that the cytochrome c association with membranes containing 10 mol% CL can be described in terms of equilibrium binding model (yielding dissociation constant Kd = 0.2-0.4 microM and stoichiometry n = 11-13 lipid molecules per protein binding site) combined with FRET model assuming uniform acceptor distribution with the distance of 3.5-3.6 nm between the bilayer midplane and heme moiety of cytochrome c. However, increasing the CL content to 20 or 40 mol% (at low ionic strength) resulted in a different behavior of FRET profiles, inconsistent with the concepts of equilibrium adsorption of cytochrome c at the membrane surface and/or uniform acceptor distribution. To explain this fact, several possibilities are analyzed, including cytochrome c-induced formation of non-bilayer structures and clusters of charged lipids, or changes in the depth of cytochrome c penetration into the bilayer depending on the protein surface density. Additional control experiments have shown that only the latter process can explain the peculiar concentration dependences of FRET at high CL content.

Supercomplex organization of the mitochondrial respiratory chain and the role of the Coenzyme Q pool: pathophysiological implications

In this review we examine early and recent evidence for an aggregated organization of the mitochondrial respiratory chain. Blue Native Electrophoresis suggests that in several types of mitochondria Complexes I, III and IV are aggregated as fixed supramolecular units having stoichiometric proportions of each individual complex. Kinetic evidence by flux control analysis agrees with this view, however the presence of Complex IV in bovine mitochondria cannot be demonstrated, presumably due to high levels of free Complex. Since most Coenzyme Q appears to be largely free in the lipid bilayer of the inner membrane, binding of Coenzyme Q molecules to the Complex I-III aggregate is forced by its dissociation equilibrium; furthermore free Coenzyme Q is required for succinate-supported respiration and reverse electron transfer. The advantage of the supercomplex organization is in a more efficient electron transfer by channelling of the redox intermediates and in the requirement of a supramolecular structure for the correct assembly of the individual complexes. Preliminary evidence suggests that dilution of the membrane proteins with extra phospholipids and lipid peroxidation may disrupt the supercomplex organization. This finding has pathophysiological implications, in view of the role of oxidative stress in the pathogenesis of many diseases.

Effects of cytochromecon the mitochondrial apoptosis-induced channel MAC

Recent studies indicate that cytochrome c is released early in apoptosis without loss of integrity of the mitochondrial outer membrane in some cell types. The high-conductance mitochondrial apoptosis-induced channel (MAC) forms in the outer membrane early in apoptosis of FL5.12 cells. Physiological (micromolar) levels of cytochrome c alter MAC activity, and these effects are referred to as types 1 and 2. Type 1 effects are consistent with a partitioning of cytochrome c into the pore of MAC and include a modest decrease in conductance that is dose and voltage dependent, reversible, and has an increase in noise. Type 2 effects may correspond to “plugging” of the pore or destabilization of the open state. Type 2 effects are a dose-dependent, voltage-independent, and irreversible decrease in conductance. MAC is a heterogeneous channel with variable conductance. Cytochrome c affects MAC in a pore size-dependent manner, with maximal effects of cytochrome c on MAC with conductance of 1.9–5.4 nS. The effects of cytochrome c, RNase A, and high salt on MAC indicate that size, rather than charge, is crucial. The effects of dextran molecules of various sizes indicate that the pore diameter of MAC is slightly larger than that of 17-kDa dextran, which should be sufficient to allow the passage of 12-kDa cytochrome c. These findings are consistent with the notion that MAC is the pore through which cytochrome c is released from mitochondria during apoptosis.

Inhibition of mitochondrial protein synthesis results in increased endothelial cell susceptibility to nitric oxide-induced apoptosis

Mutations in mitochondrial DNA, affecting the activity of respiratory complexes, have been implicated in many chronic degenerative diseases. Mitochondrial proteins coded for by both the mitochondrial and nuclear genes are known to have important signaling roles in apoptosis. However, the impact of the inhibition of mitochondrial protein synthesis on apoptosis is largely unknown. This inhibition is particularly important in NO-dependent cytotoxicity, which is believed to have a significant mitochondrial component and depend on other factors such as glycolysis. In this study we have examined whether the inhibition of mitochondrial protein synthesis by chloramphenicol increases the susceptibility of endothelial cells to undergo NO-dependent apoptosis in glucose-free media. Bovine aortic endothelial cells were treated with chloramphenicol, which resulted in a decreased ratio of mitochondrial complex IV to cytochrome c and increased oxidant production in the cell. Inhibition of mitochondrial protein synthesis was associated with a greater susceptibility of the cells to apoptosis induced by NO in glucose-free medium.

Mitochondrial dysfunction in cardiac disease: ischemia--reperfusion, aging, and heart failure

Mitochondria contribute to cardiac dysfunction and myocyte injury via a loss of metabolic capacity and by the production and release of toxic products. This article discusses aspects of mitochondrial structure and metabolism that are pertinent to the role of mitochondria in cardiac disease. Generalized mechanisms of mitochondrial-derived myocyte injury are also discussed, as are the strengths and weaknesses of experimental models used to study the contribution of mitochondria to cardiac injury. Finally, the involvement of mitochondria in the pathogenesis of specific cardiac disease states (ischemia, reperfusion, aging, ischemic preconditioning, and cardiomyopathy) is addressed.

Aging decreases electron transport complex III activity in heart interfibrillar mitochondria by alteration of the cytochrome c binding site

Aging alters cardiac physiology and structure and enhances damage during ischemia and reperfusion. Aging selectively decreases the rate of oxidative phosphorylation in the interfibrillar population of cardiac mitochondria (IFM) located among the myofibers, whereas subsarcolemmal mitochondria (SSM) located beneath the plasma membrane remain unaffected. Aging decreased the rate of oxidative phosphorylation using durohydroquinone, an electron donor to complex III, in IFM only. Complex III activity was decreased in IFM, but not SSM. Aging did not alter the content of catalytic centers of complex III (cytochromes b and c(1)and iron-sulfur protein). Complex III activity measured at physiologic ionic strength in IFM from aging hearts was decreased by 49% compared to IFM from adults, whereas activity measured at low ionic strength was unchanged, localizing the aging defect to the cytochrome c binding site of complex III. Subunits VIII and X of the cytochrome c binding site were present in complex III with the aging defect, indicating that loss of subunits did not occur. Study of aging damage to complex III will help clarify the contribution of altered electron transport in IFM to increased oxidant production during aging, formation of the aging cardiac phenotype, and the relationship of aging defects to increased damage following ischemia.

The interaction of ferrocytochrome c with long-chain fatty acids and their CoA and carnitine esters

Non-covalent modification of cytochrome c may have implications for electron transport and energy metabolism. We examined the interaction of various fatty acids (FAs), their coenzyme A and carnitine esters, and fatty alcohols with horse heart ferrocytochrome c. A comparison of FAs indicated a minimum chain length of 14 carbons was required for significant effect on the ferroheme chromophore and major changes in electronic spectra. Coenzyme A and carnitine esters interacted less strongly than FAs whereas long-chain alcohols did not interact with the protein. We found a single, saturable FA binding site with Kd (oleate) of 23.1 µM (by stopped-flow kinetics), 30 µM (by radiochemical binding assay), and 29 µM (by spectrophotometric assay). The binding stoichiometry was 1:1. We present evidence from electronic spectra, and proton NMR (nuclear magnetic resonance) that the S–Fe coordination (methionine 80) was disrupted by ligand binding. From molecular modeling we identify a putative binding channel flanked by lysines 72 and 73.Key words: cytochrome c, fatty acids, acyl-CoA, acyl-carnitine.

Identification of the site where the electron transfer chain of plant mitochondria is stimulated by electrostatic charge screening

Modular kinetic analysis was used to determine the sites in plant mitochondria where charge-screening stimulates the rate of electron transfer from external NAD(P)H to oxygen. In mitochondria isolated from potato (Solanum tuberosum L.) tuber callus, stimulation of the rate of oxygen uptake was accompanied by a decrease in the steady-state reduction level of coenzyme Q, and by a small decrease in the steady-state reduction level of cytochrome c. Modular kinetic analysis around coenzyme Q revealed that stimulation of the rate was due to stimulation of quinol oxidation via the cytochrome pathway (cytochrome bc1, cytochrome c and cytochrome c oxidase). It was not a consequence of any effect on quinone reduction (by external NADH or NADPH dehydrogenase). This explains the salt-induced decrease in the steady-state reduction level of coenzyme Q. Analysis around cytochrome c revealed that stimulation by salts was due to a dual effect on the respiratory chain. The kinetic curves for the oxidation and reduction pathways of cytochrome c revealed that they were both activated by salt, the simultaneity explaining the small variation observed in the steady-state reduction level of cytochrome c. A simple kinetic core model is used to show that changes in the rate of dissociation of cytochrome c from the membrane can explain the observed kinetic changes in both cytochrome c reduction and cytochrome c oxidation. The stimulation is proposed to be the result of an increase in the rate constant of cytochrome c dissociation from the membrane induced by cation screening. We conclude that this type of modular kinetic analysis is a powerful tool to identify and quantitatively characterize multiple-site effects on the mitochondrial respiratory chain.

The mitochondrial permeability transition is required for tumor necrosis factor alpha-mediated apoptosis and cytochrome c release

This study assesses the controversial role of the mitochondrial permeability transition (MPT) in apoptosis. In primary rat hepatocytes expressing an IkappaB superrepressor, tumor necrosis factor alpha (TNFalpha) induced apoptosis as shown by nuclear morphology, DNA ladder formation, and caspase 3 activation. Confocal microscopy showed that TNFalpha induced onset of the MPT and mitochondrial depolarization beginning 9 h after TNFalpha treatment. Initially, depolarization and the MPT occurred in only a subset of mitochondria; however, by 12 h after TNFalpha treatment, virtually all mitochondria were affected. Cyclosporin A (CsA), an inhibitor of the MPT, blocked TNFalpha-mediated apoptosis and cytochrome c release. Caspase 3 activation, cytochrome c release, and apoptotic nuclear morphological changes were induced after onset of the MPT and were prevented by CsA. Depolarization and onset of the MPT were blocked in hepatocytes expressing DeltaFADD, a dominant negative mutant of Fas-associated protein with death domain (FADD), or crmA, a natural serpin inhibitor of caspases. In contrast, Asp-Glu-Val-Asp-cho, an inhibitor of caspase 3, did not block depolarization or onset of the MPT induced by TNFalpha, although it inhibited cell death completely. In conclusion, the MPT is an essential component in the signaling pathway for TNFalpha-induced apoptosis in hepatocytes which is required for both cytochrome c release and cell death and functions downstream of FADD and crmA but upstream of caspase 3.

The respiratory chain in yeast behaves as a single functional unit

Inhibitor titrations using antimycin have been used to study the pool behavior of ubiquinone and cytochrome c in the respiratory chain of the yeast Saccharomyces cerevisiae. If present in a homogeneous pool, these carriers should be able to diffuse freely through or along the membrane respectively and accept and subsequently donate electrons to an infinite number of the respective respiratory complex. However, we show that under physiological conditions neither ubiquinone nor cytochrome c exhibits pool behavior, implying that the respiratory chain in yeast is one functional unit. Pool behavior can be introduced for both small carriers by adding chaotropic agents to the reaction medium. We conclude that these agents disrupt the interaction between the respiratory complexes, thereby causing them to become randomly arranged in the membrane. In such a situation, ubiquinone and cytochrome c become mobile carriers, shuttling between the large respiratory complexes. Furthermore, we conclude from the respiratory activities found for different substrates that the respiratory units in yeast vary in composition with respect to the ubiquinone reducing enzyme. All units contain the cytochrome chain, supplemented with either succinate dehydrogenase or the internal or the external NADH dehydrogenase. This implies that when only one substrate is available, only a certain fraction of the cytochrome chain is used in respiration. The molecular organization of the respiratory chain in yeast is compared with that of higher eukaryotes and to the electron transfer systems of photosynthetic membranes. Differences between the organization of the respiratory chain of yeast and that of higher eukaryotes are discussed in terms of the ability of yeast to radically alter its metabolism in response to change of the available carbon source.

Electron transfer between cytochrome c and cytochrome c peroxidase

The reaction between cytochrome c (CC) and cytochrome c peroxidase (CcP) is a very attractive system for investigating the fundamental mechanism of biological electron transfer. The resting ferric state of CcP is oxidized by hydrogen peroxide to compound I (CMPI) containing an oxyferryl heme and an indolyl radical cation on Trp-191. CMPI is sequentially reduced to CMPII and then to the resting state CcP by two molecules of CC. In this review we discuss the use of a new ruthenium photoreduction technique and other rapid kinetic techniques to address the following important questions: (1) What is the initial electron acceptor in CMPI? (2) What are the true rates of electron transfer from CC to the radical cation and to the oxyferryl heme? (3) What are the binding domains and pathways for electron transfer from CC to the radical cation and the oxyferryl heme? (4) What is the mechanism for the complete reaction under physiological conditions?

Persistence of cytochrome c binding to membranes at physiological mitochondrial intermembrane space ionic strength

We have shown that cytochrome c (cyt c) diffuses primarily in three dimensions in the intermembrane space (IMS) of intact mitochondria at physiological ionic strength (I). Recently, we found that a small percentage (11.2 +/- 2.1%) of endogenous cyt c remains bound to inner mitochondrial membranes (IMM) at high, physiological I (I = 150 mM), even after extensive washing with solutions at physiological I, overnight dialysis, changes in medium osmolarity, or further purification of IMM at high I using self-generating Percoll gradients. Measurements of heme c/heme a ratios, and electron transport (ET) reactions in which cyt c participates, confirmed the presence of a low amount of this I-resistant, membrane-bound form of cyt c (MB-cyt c), that had one third of the ET activity of electrostatically-bound cyt c (EB-cyt c), and which could not account for maximal ET rates. The amount of MB-cyt c was significantly increased above endogenous MB-cyt c by exposing KCl-washed IMM to increasing concentrations of exogenous cyt c. Also, subjecting large unilamellar vesicles (LUV) to successive cycles of cyt c binding/high I KCl-washes gave progressive increases in MB-cyt c. These protocols allowed in vitro characterization of MB-cyt c. The I at which binding takes place affects the affinity of cyt c for membranes, and oxidized cyt c had a greater intrinsic affinity for IMM or SUV than reduced cyt c. MB-cyt c appears to be bound partially by hydrophobic interactions since MB-cyt c was detected on negatively charged (asolectin) LUV and also on neutral, zwitterionic (phosphatidylcholine) LUV at high I. Consistent with the concentration-dependent changes in MB-cyt c, decreasing the IMS-volume of intact mitochondria (i.e., increasing th endogenous IMS-cyt c concentration) by metabolic or osmotic means increased the amount of MB-cyt c. After cyt c was delivered into the IMS by liposome-mediated low pH-induced fusion, resonance energy transfer showed a time-dependent cyt c-membrane proximity which was consistent with slow exchange of soluble IMS-entrapped cyt c molecules with a population bound to membranes at I = 150 mM. We conclude that, even though the majority of functional IMS-cyt c diffuses in three dimensions, a small portion remains firmly bound on the surface of the IMM under I conditions that are physiological for intact mitochondria. The occurrence of MB-cyt c may reflect an intrinsic conformational flexibility in cyt c, that allows a degree of membrane penetration and the formation of hydrophobic interactions which stabilize the membrane-bound form. The persistence of cyt c-membrane interactions under physiological I conditions indicates that cyt c-mediated ET in the IMS involves both fast (3D-diffusion) and slow (2D-diffusion) pathways for electron transfer.

Lipid specificity for membrane mediated partial unfolding of cytochrome c

In this study we investigated the lipid specificity for destabilization of the native structure of horse heart cytochrome c by model membranes. From (i) the enhanced release of deuterium from deuterium-labelled cytochrome c and (ii) the increased proteolytic digestion of the protein in the presence of anionic lipids, it was concluded that these lipids are able to destabilize the native structure of cytochrome c. Changes in the absorbance at 695 nm indicated that the destabilization was accompanied by a diminished ligation of Met-80 to the heme. Beef heart cardiolipin was found to be more effective than DOPS, DOPG or DOPA, while no protein destabilization was observed in the presence of the zwitterionic lipid DOPC or, surprisingly, in the presence of E. coli cardiolipin. Experiments with mitoplasts showed that the protein can also be destabilized in its native structure by a biological membrane.

Design of a ruthenium-cytochrome c derivative to measure electron transfer to the initial acceptor in cytochrome c oxidase

A ruthenium-labeled cytochrome c derivative was prepared to meet two design criteria: the ruthenium group must transfer an electron rapidly to the heme group, but not alter the interaction with cytochrome c oxidase. Site-directed mutagenesis was used to replace His39 on the backside of yeast C102T iso-1-cytochrome c with a cysteine residue, and the single sulfhydryl group was labeled with (4-bromomethyl-4' methylbipyridine) (bis-bipyridine)ruthenium(II) to form Ru-39-cytochrome c (cyt c). There is an efficient pathway for electron transfer from the ruthenium group to the heme group of Ru-39-cyt c comprising 13 covalent bonds and one hydrogen bond. Electron transfer from the excited state Ru(II*) to ferric heme c occurred with a rate constant of (6.0 +/- 2.0) x 10(5) s-1, followed by electron transfer from ferrous heme c to Ru(III) with a rate constant of (1.0 +/- 0.2) x 10(6) s-1. Laser excitation of a complex between Ru-39-cyt c and beef cytochrome c oxidase in low ionic strength buffer (5 mM phosphate, pH7) resulted in electron transfer from photoreduced heme c to CuA with a rate constant of (6 +/- 2) x 10(4) s-1, followed by electron transfer from CuA to heme a with a rate constant of (1.8 +/- 0.3) x 10(4) s-1. Increasing the ionic strength to 100 mM leads to bimolecular kinetics as the complex is dissociated. The second-order rate constant is (2.5 +/- 0.4) x 10(7) M-1s-1 at 230 mM ionic strength, nearly the same as that of wild-type iso-1-cytochrome c.

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.

The interaction of horse heart cytochrome c with phospholipid bilayers. Structural and dynamic effects

The interaction of cytochrome c with phospholipid bilayers is reviewed. Special emphasis is given to the structural and dynamic perturbations induced, either in the membrane lipid component or protein itself, by the lipid-protein interaction. The lipid-induced perturbations in the structure of cytochrome c involve: i) conformational changes in and around the heme crevice, converting the heme iron to a high-spin state: and ii) a destabilisation/loosening of the overall tertiary and secondary structure. This highly mobile, partially unfolded intermediate of cytochrome c has a remarkable resemblance to partially folded membrane-bound intermediates of the precursor protein. The functional implications of lipid-protein intermediates for (apo) cytochrome c in (protein-translocation) electron-transfer are discussed.

Motional dynamics of functional cytochrome c delivered by low pH fusion into the intermembrane space of intact mitochondria

We have investigated the motional dynamics of cytochrome c in the intact, functional rat liver mitochondrion. To do this, functional, FITC-cytochrome c (fluorescein isothiocyanate monoderivatized cytochrome c) was incorporated into the intermembrane space (IMS) of intact mitochondria through encapsulation of cytochrome c into asolectin liposomes followed by low pH-induced fusion of the liposomes with the outer membranes of the mitochondria. A cytochrome c controlled enrichment of between 15%-50% (1800-7200 molecules incorporated per mitochondrion) was obtained. All cytochrome c incorporated, regardless of the quantity, participated in the function of electron transport, indicative of a functional, independent random diffusant. Resonance energy transfer was determined from the IMS-entrapped functional FITC-cytochrome c to octadecylrhodamine B incorporated into the mitochondrial membranes. Resonance energy transfer from FITC-cytochrome c to octadecylrhodamine B in isolated inner or outer mitochondrial membranes (IMM and OMM, respectively) was also measured. We found substantial differences in the effects of ionic strength (I) on the proximity of cytochrome c to isolated IMM and OMM. Interactions with isolated IMM were very dynamic, i.e., very I-dependent, and cytochrome c binding to IMM was significant only at very low I. I-dependent interactions of cytochrome c with isolated OMM were less I-dependent than those for the IMM. However, FITC-cytochrome c was essentially released from IMM and OMM at physiological I. The proximity of FITC-cytochrome c to each mitochondrial membrane after its incorporation into the IMS of intact mitochondria in the condensed configuration was estimated at different external, bulk I using: (a) resonance energy transfer from IMS-entrapped FITC-cytochrome c to octadecylrhodamine B-label evenly distributed in both mitochondrial membranes; and (b) resonance energy transfer from IMS-entrapped FITC-cytochrome c to octadecylrhodamine B-label concentrated in the OMM. Resonance energy transfer showed that the average distance between cytochrome c and the two IMS-membrane surfaces increased with increasing IMS-I, approaching a maximal measurable distance of 85 A at 150 mM I. This result is consistent with a dissociation of FITC-cytochrome c and both membranes of intact mitochondria at physiological I, i.e., when the activity of cytochrome c in electron transport is highest. Our findings reveal a primarily three-dimensional diffusion mode for IMS-cytochrome c during its function in electron transport in intact mitochondria at physiological I, and offer further evidence that mitochondrial electron transport is a process driven by random collisions between its independently diffusing electron transferring, redox components.

Patches, posts and fences: proteins and plasma membrane domains

Recent findings have indicated the presence of micrometre-scale protein-based domains in the membranes of several cell types. What are the implications of this organization for membrane function? Here, Michael Edidin describes the formation of protein-based domains, and discusses their possible effects on protein interactions within the bilayer.

The ionic strength of the intermembrane space of intact mitochondria is not affected by the pH or volume of the intermembrane space

Ionic strength affects the electron transport activity of cytochrome c through its electrostatic interactions with redox partners and membrane lipids. We previously reported (Cortese, J.D., Voglino, A.L. and Hackenbrock, C.R. (1991) J. Cell Biol. 113, 1331-1340) that the ionic strength (I) of the intermembrane space (IMS-I) in isolated, intact condensed mitochondria is similar to the external, bulk I, over a wide range of bulk I. We now consider the possible effects of IMS-pH and IMS-volume, both variable parameters of mitochondrial function in situ, on IMS-I. IMS-pH and IMS-I were measured with pH- and I-sensitive fluorescent probes (highly fluorescent FITC-dextran for IMS-pH and FITC-BSA for IMS-I). These probes were delivered into the IMS of intact mitochondria via probe encapsulation into asolectin vesicles, followed by low pH-induced fusion of the vesicles with the outer membranes of intact mitochondria. IMS-pH was found to be 0.4-0.5 units lower than bulk pH over the pH range 6.0-8.5 for mitochondria with a large IMS-volume separating the two mitochondrial membranes (condensed configuration), and 0-0.2 units lower for mitochondria with a small IMS-volume and membranes closely opposed (orthodox configuration). This small pH difference between IMS-pM and bulk pH did not influence the similarity between IMS-I and bulk I. When the IMS-volume was osmotically decreased, bringing the two mitochondrial membranes in close proximity as in the orthodox configuration, IMS-I followed the bulk I above 10 mM but did not respond to changes in bulk I below 10 mM. The lack of response of the IMS-I below 10 mM indicates that the close proximity of the two mitochondrial membranes excludes ions only at low, nonphysiological I. Since the similarity of IMS-I and bulk I is unaffected by either IMS-pH or IMS-volume above a bulk I of 10 mM, at cytosolic physiological I (i.e., 100-150 mM) cytochrome c can be expected to be a free, three-dimensional diffusant in the IMS irrespective of the pH or volume of the IMS.

A water-lipid interface induces a highly dynamic folded state in apocytochrome c and cytochrome c, which may represent a common folding intermediate

In this study, we have used CD and NMR techniques to investigate the secondary structure of (apo-) cytochrome c both in solution and when associated with micelles. In aqueous solution, the holoprotein cytochrome c is tightly folded at secondary and tertiary levels and differs strongly from its random-coiled precursor. However, in the presence of 12-PN/12-Pglycol (9:1) micelles, we observed a remarkable resemblance between the CD spectra of these partially helical proteins. The water-lipid interface induces a secondary folding of apocytochrome c, whereas cytochrome c is suggested to partially lose its tertiary structure. The exchange of all amide protons and, using deuterium-labeled proteins, of all amide deuterons with the solvent was monitored by NMR. A rapid exchange rate was observed, indicating that these folding states are highly dynamic. Saturation-transfer NMR of micelle-associated apocytochrome c showed that the exchange takes place at the (sub-) second time scale. The holoprotein in the presence of micelles was found to have two distinct exchange rates: (1) a fast rate, comparable to that found for the micelle-associated precursor and 4.5 times slower than that of the random-coiled apocytochrome c, and (2) a slow rate which is 75 times slower than the precursor in solution. Urea denaturation studies showed the micelle-bound proteins to have a low helix stability, which explains the inability of the lipid-induced secondary structure to prevent its labile protons from rapid exchange. The uniqueness of this lipid-induced highly dynamic folding state of (apo-) cytochrome c is demonstrated by comparison with amphiphilic polypeptides like melittin, and its implications for membrane translocation and functioning are discussed.