Relating the multi-functionality of cytochrome c to membrane binding and structural conversion

Probing the Interactions of Cytochrome c with Anionic Phospholipid Nanodiscs Using Millisecond Hydrogen-Deuterium Exchange Mass Spectrometry

The interplay between the anionic phospholipid cardiolipin (CL) and cytochrome c (cyt c) holds significance in the early stages of apoptosis. Despite identification of up to four potential sites of interaction between cytochrome c and cardiolipin bearing membranes, the exact mode of interaction remains unexplained, especially given that some of the putative binding surfaces are mutually exclusive. In this study, we utilize millisecond time-resolved electrospray ionization hydrogen-deuterium exchange mass spectrometry (TRESI-HDX-MS) to investigate conformational and dynamic changes in cytochrome c in the presence of various phospholipids (DMPC, POPG, and CL) incorporated into nanodiscs. We observe that, among the proposed binding sites, the adjacent "L"- and "A"-sites exhibited a decrease in deuterium exchange, while the "N" site remained unperturbed, suggesting a specific orientation of cytochrome c with respect to cell membranes upon binding. We also demonstrate that negatively charged phospholipids with physical differences (i.e., POPG and CL) exhibit essentially the same interaction with cytochrome c, supporting the utility of POPG nanodiscs as a model for cytochrome c-membrane interactions.

Order-to-Disorder and Disorder-to-Order Transitions of Proteins upon Binding to Phospholipid Membranes: Common Ground and Dissimilarities

Cytochrome c is one of the most prominent representatives of peripheral membrane proteins. Besides functioning as an electron transfer carrier in the mitochondrial respiratory chain, it can acquire peroxidase capability, promote the self-assembly of α-synuclein, and function as a scavenger of superoxide. An understanding of its function requires knowledge of how the protein interacts with the inner membrane of mitochondria. The first part of this article provides an overview of a variety of experiments that were aimed at exploring the details of cytochrome c binding to anionic lipid liposomes, which serve as a model system for the inner membrane. While cytochrome c binding involves a conformational change from a folded into a partially disordered state, α-synuclein is intrinsically disordered in solution and subjected to a partial coil -> helix transition on membranes. Depending on the solution conditions and the surface density of α-synuclein, the protein facilitates the self-assembly into oligomers and fibrils. As for cytochrome c, results of binding experiments are discussed. In addition, the article analyzes experiments that explored α-synuclein aggregation. Similarities and differences between cytochrome c and α-synuclein binding are highlighted. Finally, the article presents a brief account of the interplay between cytochrome c and α-synuclein and its biological relevance.

Significance of the Double Bond in the Acyl Chain of Cardiolipin Revealed by the Partial Unfolding Dynamics of Cytochrome c Using Femtosecond Transient Absorption Spectroscopy

Cytochrome c (Cyt c) released from the mitochondrion acts as a trigger for the onset of apoptosis in which a double bond of cardiolipin (CL) is oxidized upon interaction with Cyt c. To understand the interaction dynamics of Cyt c with the double bond of CL, CLs having acyl chains with a systematic increase in the number of double bonds, 0 (18:0 CL), 1 (18:1 CL), and 2 (18,2 CL), were complexed with Cyt c, and their excited-state dynamics were studied using femtosecond time-resolved pump-probe spectroscopy. Steady-state and femtosecond transient absorption spectra revealed a systematic increase in the partial unfolding of Cyt c with an increase in double bonds in CL, as observed by the enhanced fluorescence intensity and lifetime of tryptophan due to variations in the resonance energy transfer and extended global conformational relaxation time constants. These studies reflect the significance of occurrence of global conformational changes of Cyt c by structural modification near the double bond of CL in the Cyt c-CL complex, which could be prerequisites for the apoptosis.

Probing the versatility of cytochrome c by spectroscopic means: A Laudatio on resonance Raman spectroscopy

Over the last 50 years resonance Raman spectroscopy has become an invaluable tool for the exploration of chromophores in biological macromolecules. Among them, heme proteins and metal complexes have attracted considerable attention. This interest results from the fact that resonance Raman spectroscopy probes the vibrational dynamics of these chromophores without direct interference from the surrounding. However, the indirect influence via through-bond and through-space chromophore-protein interactions can be conveniently probed and analyzed. This review article illustrates this point by focusing on class 1 cytochrome c, a comparatively simple heme protein generally known as electron carrier in mitochondria. The article demonstrates how through selective excitation of resonance Raman active modes information about the ligation, the redox state and the spin state of the heme iron can be obtained from band positions in the Raman spectra. The investigation of intensities and depolarization ratios emerged as tools for the analysis of in-plane and out-of-plane deformations of the heme macrocycle. The article further shows how resonance Raman spectroscopy was used to characterize partially unfolded states of oxidized cytochrome c. Finally, it describes its use for exploring structural changes due to the protein's binding to anionic surfaces like cardiolipin containing membranes.

Human cytochrome C natural variants: Studying the membrane binding properties of G41S and Y48H by fluorescence energy transfer and molecular dynamics

Cytochrome C (cyt C), the protein involved in oxidative phosphorylation, plays several other crucial roles necessary for both cell life and death. Studying natural variants of cyt C offers the possibility to better characterize the structure-to-function relationship that modulates the different activities of this protein. Naturally mutations in human cyt C (G41S and Y48H) occur in the protein central Ω-loop and cause thrombocytopenia 4. In this study, we have investigated the binding of such variants and of wild type (wt) cyt C to synthetic cardiolipin-containing vesicles. The mutants have a lower propensity in membrane binding, displaying higher dissociation constants with respect to the wt protein. Compressibility measurements reveal that both variants are more flexible than the wt, suggesting that the native central Ω-loop is important for the interaction with membranes. Such hypothesis is supported by molecular dynamics simulations. A minimal distance analysis indicates that in the presence of cardiolipin the central Ω-loop of the mutants is no more in contact with the membrane, as it happens instead in the case of wt cyt C. Such finding might provide a hint for the reduced membrane binding capacity of the variants and their enhanced peroxidase activity in vivo.

The Increase in the Peroxidase Activity of the Cytochrome C with Substitutions in the Universal Binding Site Is Associated with Changes in the Ability to Interact with External Ligands

Cytochrome c (CytC), a one-electron carrier, transfers electrons from complex bc1 to cytochrome c oxidase (CcO) in the electron-transport chain. Electrostatic interaction with the partners, complex bc1 and CcO, is ensured by a lysine cluster near the heme forming the Universal Binding Site (UBS). We constructed three mutant variants of mitochondrial CytC with one (2Mut), four (5Mut), and five (8Mut) Lys->Glu substitutions in the UBS and some compensating Glu->Lys substitutions at the periphery of the UBS for charge compensation. All mutants showed a 4-6 times increased peroxidase activity and accelerated binding of cyanide to the ferric heme of CytC. In contrast, decomposition of the cyanide complex with ferrous CytC, as monitored by magnetic circular dichroism spectroscopy, was slower in mutants compared to WT. Molecular dynamic simulations revealed the increase in the fluctuations of Cα atoms of individual residues of mutant CytC compared to WT, especially in the Ω-loop (70-85), which can cause destabilization of the Fe…S(Met80) coordination link, facilitation of the binding of exogenous ligands cyanide and peroxide, and an increase in peroxidase activity. It was found that only one substitution K72E is enough to induce all these changes, indicating the significance of K72 and the Ω-loop (70-85) for the structure and physiology of mitochondrial CytC. In this work, we also propose using a ferro-ferricyanide buffer as a substrate to monitor the peroxidase activity of CytC. This new approach allows us to determine the rate of peroxidase activity at moderate (200 µM) concentrations of H2O2 and avoid complications of radical formation during the reaction.

Effects of removal of the axial methionine heme ligand on the binding of S. cerevisiae iso-1 cytochrome c to cardiolipin

The cleavage of the axial S(Met) - Fe bond in cytochrome c (cytc) upon binding to cardiolipin (CL), a glycerophospholipid of the inner mitochondrial membrane, is one of the key molecular changes that impart cytc with (lipo)peroxidase activity essential to its pro-apoptotic function. In this work, UV - VIS, CD, MCD and fluorescence spectroscopies were used to address the role of the Fe - M80 bond in controlling the cytc-CL interaction, by studying the binding of the Met80Ala (M80A) variant of S. cerevisiae iso-1 cytc (ycc) to CL liposomes in comparison with the wt protein [Paradisi et al. J. Biol. Inorg. Chem. 25 (2020) 467-487]. The results show that the integrity of the six-coordinate heme center along with the distal heme site containing the Met80 ligand is a not requisite for cytc binding to CL. Indeed, deletion of the Fe - S(Met80) bond has a little impact on the mechanism of ycc-CL interaction, although it results in an increased heme accessibility to solvent and a reduced structural stability of the protein. In particular, M80A features a slightly tighter binding to CL at low CL/cytc ratios compared to wt ycc, possibly due to the lift of some constraints to the insertion of the CL acyl chains into the protein hydrophobic core. M80A binding to CL maintains the dependence on the CL-to-cytc mixing scheme displayed by the wt species.

Anomalous peroxidase activity of cytochrome c is the primary pathogenic target in Barth syndrome

Barth syndrome (BTHS) is a life-threatening genetic disorder with unknown pathogenicity caused by mutations in TAFAZZIN (TAZ) that affect remodeling of mitochondrial cardiolipin (CL). TAZ deficiency leads to accumulation of mono-lyso-CL (MLCL), which forms a peroxidase complex with cytochrome c (cyt c) capable of oxidizing polyunsaturated fatty acid-containing lipids. We hypothesized that accumulation of MLCL facilitates formation of anomalous MLCL-cyt c peroxidase complexes and peroxidation of polyunsaturated fatty acid phospholipids as the primary BTHS pathogenic mechanism. Using genetic, biochemical/biophysical, redox lipidomic and computational approaches, we reveal mechanisms of peroxidase-competent MLCL-cyt c complexation and increased phospholipid peroxidation in different TAZ-deficient cells and animal models and in pre-transplant biopsies from hearts of patients with BTHS. A specific mitochondria-targeted anti-peroxidase agent inhibited MLCL-cyt c peroxidase activity, prevented phospholipid peroxidation, improved mitochondrial respiration of TAZ-deficient C2C12 myoblasts and restored exercise endurance in a BTHS Drosophila model. Targeting MLCL-cyt c peroxidase offers therapeutic approaches to BTHS treatment.

Ligand-Based Regulation of Dynamics and Reactivity of Hemoproteins

Hemoproteins include several heme-binding proteins with distinct structure and function. The presence of the heme group confers specific reactivity and spectroscopic properties to hemoproteins. In this review, we provide an overview of five families of hemoproteins in terms of dynamics and reactivity. First, we describe how ligands modulate cooperativity and reactivity in globins, such as myoglobin and hemoglobin. Second, we move on to another family of hemoproteins devoted to electron transport, such as cytochromes. Later, we consider heme-based reactivity in hemopexin, the main heme-scavenging protein. Then, we focus on heme-albumin, a chronosteric hemoprotein with peculiar spectroscopic and enzymatic properties. Eventually, we analyze the reactivity and dynamics of the most recently discovered family of hemoproteins, i.e., nitrobindins.

Effect of Cytochrome C on the Conductance of Asolectin Membranes and the Occurrence of Through Pores at Different pHs

The study of the electrical parameters of asolectin bilayer lipid membranes in the presence of cytochrome c (cyt c) at various concentrations showed that an increase in the concentration of cyt c leads to an increase in the membrane conductance and the appearance of through pores. The studied membranes did not contain cardiolipin, which is commonly used in studying the effect of cyt c on membrane permeability. In the presence of cyt c, discrete current fluctuations were recorded. The occurrence of these fluctuations may be associated with the formation of through pores. The diameter of these pores was ~0.8 nm, which is smaller than the size of the cyt c globule (~3 nm). Measurements carried out at pH values from 6.4 to 8.4 showed that the concentration dependence of the membrane conductance increases with increasing pH. To assess the binding of cyt c to the bilayer, we measured the concentration and pH dependences of the difference in surface potentials induced by the unilateral addition of cyt c. The amount of bound cyt c at the same concentrations decreased with increasing pH, which did not correspond to the conductance trend. An analysis of conductance traces leads to the conclusion that an increase in the integral conductance of membranes is associated with an increase in the lifetime of pores. The formation of "long-lived" pores, of which the residence time in the open state is longer than in the closed state, was achieved at various combinations of pHs and cyt c concentrations: the higher the pH, the lower the concentration at which the long-lived pores appeared and, accordingly, a higher conductance was observed. The increase in conductance and the formation of transmembrane pores are not due to the electrostatic interaction between cyt c and the membrane. We hypothesize that an increase in pH leads to a weakening of hydrogen bonds between lipid heads, which allows cyt c molecules to penetrate into the membrane. This disrupts the order of the bilayer and leads to the occurrence of through pores.

Assessing the Functional and Structural Stability of the Met80Ala Mutant of Cytochrome c in Dimethylsulfoxide

The Met80Ala variant of yeast cytochrome c is known to possess electrocatalytic properties that are absent in the wild type form and that make it a promising candidate for biocatalysis and biosensing. The versatility of an enzyme is enhanced by the stability in mixed aqueous/organic solvents that would allow poorly water-soluble substrates to be targeted. In this work, we have evaluated the effect of dimethylsulfoxide (DMSO) on the functionality of the Met80Ala cytochrome c mutant, by investigating the thermodynamics and kinetics of electron transfer in mixed water/DMSO solutions up to 50% DMSO v/v. In parallel, we have monitored spectroscopically the retention of the main structural features in the same medium, focusing on both the overall protein structure and the heme center. We found that the organic solvent exerts only minor effects on the redox and structural properties of the mutant mostly as a result of the modification of the dielectric constant of the solvent. This would warrant proper functionality of this variant also under these potentially hostile experimental conditions, that differ from the physiological milieu of cytochrome c.

PB1F2 from Influenza A Virus Regulates the Interaction between Cytochrome C and Cardiolipin

PB1F2 is a membrane associated protein encoded by the influenza virus gene in the host. Similar to endogenous pro-apoptotic proteins, it acts on the mitochondria of the host immune cells, inducing apoptosis of the cells. The PB1F2 protein has been demonstrated to facilitate the release of cytochrome c in addition to impairing the integrity of the inner mitochondrial membrane. This investigation focused on how the protein PB1F2 interacted with cardiolipin and cytochrome c. The regulation of PB1F2 on the binding of cytochrome c to cardiolipin in two kinds of in vitro membrane mimics was investigated by biophysical techniques. PB1F2 aids in the dissociation of cytochrome c-cardiolipin complexes in liposomes and nanodiscs. The results provide novel explanations and evidence for how PB1F2 functions as a viral virulence factor by inducing immune cell death.

Cytochrome c Interaction with Cardiolipin Plays a Key Role in Cell Apoptosis: Implications for Human Diseases

In the cell cytochrome, c performs different functions depending on the environment in which it acts; therefore, it has been classified as a multifunction protein. When anchored to the outer side of the inner mitochondrial membrane, native cytochrome c acts as a Schweitzer-StennerSchweitzer-Stenner that transfers electrons from cytochrome c reductase to cytochrome c oxidase in the respiratory chain. On the other hand, to interact with cardiolipin (one of the phospholipids making up the mitochondrial membrane) and form the cytochrome c/cardiolipin complex in the apoptotic process, the protein reorganizes its structure into a non-native state characterized by different asymmetry. The formation of the cytochrome c/cardiolipin complex is a fundamental step of the apoptotic pathway, since the structural rearrangement induces peroxidase activity in cytochrome c, the subsequent permeabilization of the membrane, and the release of the free protein into the cytoplasm, where cytochrome c activates the apoptotic process. Apoptosis is closely related to the pathogenesis of neoplastic, neurodegenerative and cardiovascular diseases; in this contest, the biosynthesis and remodeling of cardiolipin are crucial for the regulation of the apoptotic process. Since the role of cytochrome c as a promoter of apoptosis strictly depends on the non-native conformation(s) that the protein acquires when bound to the cardiolipin and such event leads to cytochrome c traslocation into the cytosol, the structural and functional properties of the cytochrome c/cardiolipin complex in cell fate will be the focus of the present review.

Calcium-induced release of cytochrome c from cardiolipin nanodisks: Implications for apoptosis

Miniature bilayer membranes comprised of phospholipid and an apolipoprotein scaffold, termed nanodisks (ND), have been used in binding studies. When ND formulated with cardiolipin (CL), but not phosphatidylcholine, were incubated with cytochrome c, FPLC gel filtration chromatography provided evidence of a stable binding interaction. Incubation of CL ND with CaCl₂ resulted in a concentration-dependent increase in sample turbidity caused by ND particle disruption. Prior incubation of CL ND with cytochrome c increased CL ND sensitivity to CaCl₂-induced effects. Centrifugation of CaCl₂-treated CL ND samples yielded pellet and supernatant fractions. Whereas the ND scaffold protein, apolipophorin III, was recovered in the pellet fraction along with CL, the majority of the cytochrome c pool was in the supernatant fraction. Moreover, when cytochrome c CL ND were incubated with CaCl₂ at concentrations below the threshold to induce ND particle disruption, FPLC analysis showed that cytochrome c was released. Pre-incubation of CL ND with CaCl₂ under conditions that do not disrupt ND particle integrity prevented cytochrome c binding to CL ND. Thus, competition between Ca²⁺ and cytochrome c for a common binding site on CL modulates cytochrome c binding and likely plays a role in its dissociation from CL-rich cristae membranes in response to apoptotic stimuli.

Modulating the pro-apoptotic activity of cytochrome c at a biomimetic electrified interface

Programmed cell death via apoptosis is a natural defence against excessive cell division, crucial for fetal development to maintenance of homeostasis and elimination of precancerous and senescent cells. Here, we demonstrate an electrified liquid biointerface that replicates the molecular machinery of the inner mitochondrial membrane at the onset of apoptosis. By mimicking in vivo cytochrome c (Cyt c) interactions with cell membranes, our platform allows us to modulate the conformational plasticity of the protein by simply varying the electrochemical environment at an aqueous-organic interface. We observe interfacial electron transfer between an organic electron donor decamethylferrocene and O₂, electrocatalyzed by Cyt c. This interfacial reaction requires partial Cyt c unfolding, mimicking Cyt c in vivo peroxidase activity. As proof of concept, we use our electrified liquid biointerface to identify drug molecules, such as bifonazole, that can potentially down-regulate Cyt c and protect against uncontrolled neuronal cell death in neurodegenerative disorders.

How to Turn an Electron Transfer Protein into a Redox Enzyme for Biosensing

Cytochrome c is a small globular protein whose main physiological role is to shuttle electrons within the mitochondrial electron transport chain. This protein has been widely investigated, especially as a paradigmatic system for understanding the fundamental aspects of biological electron transfer and protein folding. Nevertheless, cytochrome c can also be endowed with a non-native catalytic activity and be immobilized on an electrode surface for the development of third generation biosensors. Here, an overview is offered of the most significant examples of such a functional transformation, carried out by either point mutation(s) or controlled unfolding. The latter can be induced chemically or upon protein immobilization on hydrophobic self-assembled monolayers. We critically discuss the potential held by these systems as core constituents of amperometric biosensors, along with the issues that need to be addressed to optimize their applicability and response.

Activation of Cytochrome C Peroxidase Function Through Coordinated Foldon Loop Dynamics upon Interaction with Anionic Lipids

Cardiolipin (CL) is a mitochondrial anionic lipid that plays important roles in the regulation and signaling of mitochondrial apoptosis. CL peroxidation catalyzed by the assembly of CL-cytochrome c (cyt c) complexes at the inner mitochondrial membrane is a critical checkpoint. The structural changes in the protein, associated with peroxidase activation by CL and different anionic lipids, are not known at a molecular level. To better understand these peripheral protein-lipid interactions, we compare how phosphatidylglycerol (PG) and CL lipids trigger cyt c peroxidase activation, and correlate functional differences to structural and motional changes in membrane-associated cyt c. Structural and motional studies of the bound protein are enabled by magic angle spinning solid state NMR spectroscopy, while lipid peroxidase activity is assayed by mass spectrometry. PG binding results in a surface-bound state that preserves a nativelike fold, which nonetheless allows for significant peroxidase activity, though at a lower level than binding its native substrate CL. Lipid-specific differences in peroxidase activation are found to correlate to corresponding differences in lipid-induced protein mobility, affecting specific protein segments. The dynamics of omega loops C and D are upregulated by CL binding, in a way that is remarkably controlled by the protein:lipid stoichiometry. In contrast to complete chemical denaturation, membrane-induced protein destabilization reflects a destabilization of select cyt c foldons, while the energetically most stable helices are preserved. Our studies illuminate the interplay of protein and lipid dynamics in the creation of lipid peroxidase-active proteolipid complexes implicated in early stages of mitochondrial apoptosis.

Electroanalysis of Biomolecules: Rational Selection of Sensor Construction

Methods of electrochemical analysis of biological objects based on the reaction of electro-oxidation/electro-reduction of molecules are presented. Polymer nanocomposite materials that modify electrodes to increase sensitivity of electrochemical events on the surface of electrodes are described. Examples of applications electrochemical biosensors constructed with nanocomposite material for detection of biological molecules are presented, advantages and drawbacks of different applications are discussed.

Anion-Specific Effects on the Alkaline State of Cytochrome c

Specific effects of anions on the structure, thermal stability, and peroxidase activity of native (state III) and alkaline (state IV) cytochrome c (cyt c) have been studied by the UV-VIS absorbance spectroscopy, intrinsic tryptophan fluorescence, and circular dichroism. Thermal and isothermal denaturation monitored by the tryptophan fluorescence and circular dichroism, respectively, implied lower stability of cyt c state IV in comparison with the state III. The pK_a value of alkaline isomerization of cyt c depended on the present salts, i.e., kosmotropic anions increased and chaotropic anions decreased pK_a (Hofmeister effect on protein stability). The peroxidase activity of cyt c in the state III, measured by oxidation of guaiacol, showed clear dependence on the salt position in the Hofmeister series, while cyt c in the alkaline state lacked the peroxidase activity regardless of the type of anions present in the solution. The alkaline isomerization of cyt c in the presence of 8 M urea, measured by Trp59 fluorescence, implied an existence of a high-affinity non-native ligand for the heme iron even in a partially denatured protein conformation. The conformation of the cyt c alkaline state in 8 M urea was considerably modulated by the specific effect of anions. Based on the Trp59 fluorescence quenching upon titration to alkaline pH in 8 M urea and molecular dynamics simulation, we hypothesize that the Lys79 conformer is most likely the predominant alkaline conformer of cyt c. The high affinity of the sixth ligand for the heme iron is likely a reason of the lack of peroxidase activity of cyt c in the alkaline state.

The effect of cardiolipin side chain composition on cytochrome c protein conformation and peroxidase activity

Skeletal muscle, a highly active tissue, makes up 40% of the total body weight. This tissue relies on mitochondria for ATP production, calcium homeostasis, and programed cell death. Mitochondrial phospholipid composition, namely, cardiolipin (CL), influences the functional efficiency of mitochondrial proteins, specifically cytochrome c. The interaction of CL with cytochrome c in the presence of free radicals induces structural and functional changes promoting peroxidase activity and cytochrome c release, a key event in the initiation of apoptosis. The CL acyl chain degree of saturation has been implicated in the cytochrome c to cytochrome c peroxidase transition in liposomal models. However, mitochondrial membranes are composed of differing CL acyl chain composition. Currently, it is unclear how differing CL acyl chain composition utilizing liposomes will influence the cytochrome c form and function as a peroxidase. Thus, this study examined the role of CL acyl chain saturation within liposomes broadly reflecting the relative CL composition of mitochondrial membranes from healthy and dystrophic mouse muscle on cytochrome c conformation and function. Despite no differences in protein conformation or function between healthy and dystrophic liposomes, cytochrome c's affinity to CL increased with greater unsaturation. These findings suggest that increasing CL acyl chain saturation, as implicated in muscle wasting diseases, may not influence cytochrome c transformation and function as a peroxidase but may alter its interaction with CL, potentially impacting further downstream effects.

The Puzzling Problem of Cardiolipin Membrane-Cytochrome c Interactions: A Combined Infrared and Fluorescence Study

The interaction of cytochrome c (cyt c) with natural and synthetic membranes is known to be a complex phenomenon, involving both protein and lipid conformational changes. In this paper, we combined infrared and fluorescence spectroscopy to study the structural transformation occurring to the lipid network of cardiolipin-containing large unilamellar vesicles (LUVs). The data, collected at increasing protein/lipid ratio, demonstrate the existence of a multi-phase process, which is characterized by: (i) the interaction of cyt c with the lipid polar heads; (ii) the lipid anchorage of the protein on the membrane surface; and (iii) a long-distance order/disorder transition of the cardiolipin acyl chains. Such effects have been quantitatively interpreted introducing specific order parameters and discussed in the frame of the models on cyt c activity reported in literature.

Adsorbing surface strongly influences the pseudoperoxidase and nitrite reductase activity of electrode-bound yeast cytochrome c. The effect of hydrophobic immobilization

The Met80Ala and Met80Ala/Tyr67Ala variants of S. cerevisiae iso-1 cytochrome c (ycc) and their adducts with cardiolipin immobilized onto a gold electrode coated with a hydrophobic self-assembled monolayer (SAM) of decane-1-thiol were studied through cyclic voltammetry and surface-enhanced resonance Raman spectroscopy (SERRS). The electroactive species - containing a six-coordinate His/His axially ligated heme and a five-coordinate His/- heme stable in the oxidized and reduced state, respectively - and the pseudoperoxidase activity match those found previously for the wt species and are only slightly affected by CL binding. Most importantly, the reduced His/- ligated form of these variants is able to catalytically reduce the nitrite ion, while electrode-immobilized wt ycc and other His/Met heme ligated variants under a variety of conditions are not. Besides the pseudoperoxidase and nitrite reductase functions, which are the most physiologically relevant abilities of these constructs, also axial heme ligation and the equilibria between conformers are strongly affected by the nature - hydrophobic vs. electrostatic - of the non-covalent interactions determining protein immobilization. Also affected are the catalytic activity changes induced by a given mutation as well as those due to partial unfolding due to CL binding. It follows that under the same solution conditions the structural and functional properties of immobilized ycc are surface-specific and therefore cannot be transferred from an immobilized system to another involving different interfacial protein-SAM interactions.

Wheel and Deal in the Mitochondrial Inner Membranes: The Tale of Cytochrome c and Cardiolipin

Cardiolipin oxidation and degradation by different factors under severe cell stress serve as a trigger for genetically encoded cell death programs. In this context, the interplay between cardiolipin and another mitochondrial factor—cytochrome c—is a key process in the early stages of apoptosis, and it is a matter of intense research. Cytochrome c interacts with lipid membranes by electrostatic interactions, hydrogen bonds, and hydrophobic effects. Experimental conditions (including pH, lipid composition, and post-translational modifications) determine which specific amino acid residues are involved in the interaction and influence the heme iron coordination state. In fact, up to four binding sites (A, C, N, and L), driven by different interactions, have been reported. Nevertheless, key aspects of the mechanism for cardiolipin oxidation by the hemeprotein are well established. First, cytochrome c acts as a pseudoperoxidase, a process orchestrated by tyrosine residues which are crucial for peroxygenase activity and sensitivity towards oxidation caused by protein self-degradation. Second, flexibility of two weakest folding units of the hemeprotein correlates with its peroxidase activity and the stability of the iron coordination sphere. Third, the diversity of the mode of interaction parallels a broad diversity in the specific reaction pathway. Thus, current knowledge has already enabled the design of novel drugs designed to successfully inhibit cardiolipin oxidation.

Met80 and Tyr67 affect the chemical unfolding of yeast cytochromec: comparing the solutionvs.immobilized state

The motional regime affects the unfolding propensity and axial heme coordination of the Met80Ala and Met80Ala/Tyr67Ala variants of yeast iso-1 cytochromec.

A Heme Propionate Staples the Structure of Cytochrome c for Methionine Ligation to the Heme Iron

Ligand-switch reactions at the heme iron are common in biological systems, but their mechanisms and the features of the polypeptide fold that support dual ligation are not well understood. In cytochrome c (cyt c), two low-stability loops (Ω-loop C and Ω-loop D) are connected by the heme propionate HP6. At alkaline pH, the native Met80 ligand from Ω-loop D switches to a Lys residue from the same loop. Deprotonation of an as yet unknown group triggers the alkaline transition. We have created the two cyt c variants T49V/K79G and T78V/K79G with altered connections of these two loops to HP6. Electronic absorption, NMR, and EPR studies demonstrate that at pH 7.4 ferric forms of these variants are Lys-ligated, whereas ferrous forms maintain the native Met80 ligation. Measurements of protein stability, cyclic voltammetry, pH-jump and gated electron-transfer kinetics have revealed that these Thr to Val substitutions greatly affect the alkaline transition in both ferric and ferrous proteins. The substitutions modify the stability of the Met-ligated species and reduction potentials of the heme iron. The kinetics of ligand-switch processes are also altered, and analyses of these effects implicate redox-dependent differences in metal-ligand interactions and the role of the protein dynamics, including cross-talk between the two Ω-loops. With the two destabilized variants, it is possible to map energy levels for the Met- and Lys-ligated species in both ferric and ferrous proteins and assess the role of the protein scaffold in redox-dependent preferences for these two ligands. The estimated shift in the heme iron reduction potential upon deprotonation of the "trigger" group is consistent with those associated with deprotonation of an HP, suggesting that HP6, on its own or as a part of a hydrogen-bonded cluster, is a likely "trigger" for the Met to Lys ligand switch.

Surface-Binding to Cardiolipin Nanodomains Triggers Cytochrome c Pro-apoptotic Peroxidase Activity via Localized Dynamics

The peroxidation of cardiolipins by reactive oxygen species, which is regulated and enhanced by cytochrome c (cyt c), is a critical signaling event in mitochondrial apoptosis. We probe the molecular underpinnings of this mitochondrial death signal through structural and functional studies of horse heart cyt c binding to mixed-lipid membranes containing cardiolipin with mono- and polyunsaturated acyl chains. Lipidomics reveal the selective oxidation of polyunsaturated fatty acid (PUFA) cardiolipin (CL), while multidimensional solid-state NMR probes the structure and dynamics of the membrane and the peripherally bound protein. The hydrophilic milieu at the membrane interface stabilizes a native-like fold, but also leads to localized flexibility at the membrane-interacting protein face. PUFA CL acts as both a preferred substrate and a dynamic regulator by affecting the dynamics of the cyt c N70-I85 Ω loop, which covers the heme cavity.

pH-Induced Switch between Different Modes of Cytochrome c Binding to Cardiolipin-Containing Liposomes

Fluorescence, visible circular dichroism (CD), absorption, and resonance Raman spectroscopy techniques were combined to explore structural changes of ferricytochrome c upon its binding to cardiolipin-containing liposomes (20% 1,1',1,2'-tetraoleyolcardiolipin and 1,2-deoleyol-sn-glycero-3-phosphocholine) at acidic pH (6.5). According to the earlier work of Kawai [J. Biol. Chem.2005, 280, 34709-347171],cytochrome c binding at this pH is governed by interactions between the phosphate head groups of cardiolipin and amino acid side chains of the so-called L-site, which contains the charged residues K22, K25, K27, and potentially H26 and H33. We found that L-site binding causes a conformational transition that involves a change of the protein's ligation and spin state. In this paper, we report spectroscopic responses to an increasing number of cardiolipin-containing liposomes at pH 6.5 in the absence and presence of NaCl. The latter was found to mostly inhibit protein binding already with 50 mM concentration. The inhibition effect can be quantitatively reproduced by applying the electrostatic theory of Heimburg [Biophys. J.1995, 68, 536-546]. A comparison with corresponding spectroscopic response data obtained at pH 7.4 reveals major differences in that the latter indicates hydrophobic binding, followed by an electrostatically driven conformational change. Visible CD data suggest that structural changes in the heme pocket of liposome-bound ferricytochrome c resemble to some extent those in the denatured protein in urea at neutral and acidic pH. The measured noncoincidence between absorption and CD Soret band of cytochrome c in the presence of a large access of cardiolipin is caused by the electric field at the membrane surface. The very fact that its contribution to the internal electric field in the heme pocket is detectable by spectroscopic means suggests some penetration of the protein into membrane surface.

Changes in the mitochondrial proteome in human hepatocytes in response to alpha-amanitin hepatotoxicity

Amanitin-induced apoptosis is proposed to have a significant effect on the pathogenesis of liver damage. However, few reports have focused on proteome changes induced by α-amanitin (α-AMA). Here, we evaluated changes in mitochondrial proteins of hepatocytes in response to 2 μM α-AMA, a concentration at which α-AMA-induced cell damage could be rescued at cellular level by common clinical drugs. We found 56 proteins were differentially expressed in an α-AMA-treated group. Among them, 38 proteins were downregulated and 18 were upregulated. Downregulated functional proteins included importer TOMM40, respiratory chain component cytochrome C, and metabolic enzymes of citrate acid cycle such as malate dehydrogenase, which localize on the mitochondrial outer membrane, inner membrane and matrix respectively. Immunoblot analysis showed that α-AMA decreased mitochondrial import receptor subunit TOMM40 and cytochrome c accompanied by an increase in the cytosol although their total protein levels were not affected significantly. The mitochondrial membrane potential was also destroyed by α-AMA and was restored by the clinical drug silibinin. Immunofluorescence suggested that mitochondrial morphology did not change. Taken together, our results provide further insights into the toxic mechanism of α-AMA on hepatocytes.