High affinity binding of Bcl-xL to cytochrome c: Possible relevance for interception of translocated cytochrome c in apoptosis

Diverse functions of cytochrome c in cell death and disease

The redox-active protein cytochrome c is a highly positively charged hemoglobin that regulates cell fate decisions of life and death. Under normal physiological conditions, cytochrome c is localized in the mitochondrial intermembrane space, and its distribution can extend to the cytosol, nucleus, and extracellular space under specific pathological or stress-induced conditions. In the mitochondria, cytochrome c acts as an electron carrier in the electron transport chain, facilitating adenosine triphosphate synthesis, regulating cardiolipin peroxidation, and influencing reactive oxygen species dynamics. Upon cellular stress, it can be released into the cytosol, where it interacts with apoptotic peptidase activator 1 (APAF1) to form the apoptosome, initiating caspase-dependent apoptotic cell death. Additionally, following exposure to pro-apoptotic compounds, cytochrome c contributes to the survival of drug-tolerant persister cells. When translocated to the nucleus, it can induce chromatin condensation and disrupt nucleosome assembly. Upon its release into the extracellular space, cytochrome c may act as an immune mediator during cell death processes, highlighting its multifaceted role in cellular biology. In this review, we explore the diverse structural and functional aspects of cytochrome c in physiological and pathological responses. We summarize how posttranslational modifications of cytochrome c (e.g., phosphorylation, acetylation, tyrosine nitration, and oxidation), binding proteins (e.g., HIGD1A, CHCHD2, ITPR1, and nucleophosmin), and mutations (e.g., G41S, Y48H, and A51V) affect its function. Furthermore, we provide an overview of the latest advanced technologies utilized for detecting cytochrome c, along with potential therapeutic approaches related to this protein. These strategies hold tremendous promise in personalized health care, presenting opportunities for targeted interventions in a wide range of conditions, including neurodegenerative disorders, cardiovascular diseases, and cancer.

Simultaneous quantification of Cyt c interactions with HSP27 and Bcl-xL using molecularly imprinted polymers (MIPs) coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based targeted proteomics

Cytochrome c (Cyt c) plays an important role in cell apoptosis. However, it could be functionally compromised by interaction with anti-apoptosis proteins, known as protein-protein interactions (PPIs). Among the proteins potentially interacting with Cyt c, both HSP27 and Bcl-xL serve as pivotal anti-apoptosis proteins. Because multiple PPIs, especially those involve the same protein, could affect each other, their simultaneous and quantitative detection is highly needed. In this study, a combined approach of molecularly imprinted polymers (MIPs) and LC-MS/MS-based targeted proteomics was developed for simultaneous quantification of Cyt c-HSP27 and Cyt c-Bcl-xL interactions. Surrogate peptides of Cyt c, HSP27 and Bcl-xL were first selected and used for the corresponding proteins quantification in targeted proteomics analysis. For MIPs, epitope approach was employed and a short peptide of Cyt c was selected as template for protein complexes recognition and enrichment. The characteristics of the synthesized MIPs including adsorption capacity, kinetics and efficiency were then evaluated. After validation, this combined assay was applied to quantitative analysis of total Cyt c including Cyt c in mitochondria and cytosol, total HSP27, total Bcl-xL and Cyt c-HSP27 and Cyt c-Bcl-xL protein complexes in breast cells. The result was also compared with that using Co-IP/Western Blotting. SIGNIFICANCE: Protein-protein interactions (PPIs) are essential for many cellular processes and the changes of PPIs are often associated with cellular dysfunction. More importantly, each protein typically has more than one interaction partner and multiple PPIs, especially those involve the same protein, could affect each other. The selectivity of these interactions determines the activities of proteins and further the developmental potential of the cell. Thus, simultaneous and quantitative detection of multiple PPIs is highly needed in biological research and related disciplines. However, it is still challenging to even qualitatively or semi-quantitatively analyze multiple PPIs because of the limitations of current experimental techniques for interaction detection. In this study, molecularly imprinted polymers (MIPs) epitope approach was combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) targeted proteomics for the simultaneous and quantitative detection of Cyt c-HSP27 and Cyt c-Bcl-xL interactions in breast cancer. Given high sensitivity, high selectivity and wide dynamic range of LC-MS/MS, MIPs approach was employed here to separate and enrich protein complexes prior to targeted proteomics analysis.

X-ray structure of bovine heart cytochrome c at high ionic strength

Bovine heart cytochrome c (bCyt c) is an extensively studied hemoprotein of only 104 residues. Due to the existence of isoforms generated by non-enzymatic deaminidation, crystallization of bCyt c is difficult and involves extensive purification and the use of microseeding or the presence of an electric field. Taking advantage of the capacity of cytochrome c (cyt c) to bind anions on its protein surface, the commercially available bCyt c was crystallized without extra purifications, using ammonium sulfate as precipitant and nitrate ions as additives. The structure of the ferric bCyt c in a new crystal form is described and compared with that previously solved at low ionic strength and with those of human and horse cyt c. The overall structure of bCyt c is conserved, while the side chains of several residues that play a role in the interactions of cyt c with its partners have different rotamers in the two structures. The effect of the presence of nitrate ions on the structure of the protein is then evaluated and compared with that observed in the case of ferrous and ferric horse heart cyt c.

Cloning, Escherichia coli expression, purification, characterization, and enzyme assay of the ribosomal protein S4 from wheat seedlings (Triticum vulgare)

S4 is a paradigm of ribosomal proteins involved in multifarious activities both within and outside the ribosome. For a detailed biochemical and structural investigations of eukaryotic S4, the wheat S4 gene has been cloned and expressed in Escherichia coli, and the protein purified to a high degree of homogeneity. The 285-residue recombinant protein containing an N-terminal His(6) tag along with fourteen additional residues derived from the cloning vector is characterized by a molecular mass of 31981.24 Da. The actual sequence of 265 amino acids having a molecular mass of 29931 Da completely defines the primary structure of wheat S4. Homology modeling shows a bi-lobed protein topology arising from folding of the polypeptide into two domains, consistent with the fold topology of prokaryotic S4. The purified protein is stable and folded since it can be reversibly unfolded in guanidinium hydrochloride, and is capable of hydrolyzing cysteine protease-specific peptide-based fluorescence substrates, including Ac-DEVD-AFC (N-acetyl-Asp-Glu-Val-Asp-7-amino-4-trifluoromethylcoumarin) and Z-FR-AMC (N-CBZ-Phe-Arg-aminomethylcoumarin).

The anti-apoptotic Bcl-x(L) protein, a new piece in the puzzle of cytochrome c interactome

A structural model of the adduct between human cytochrome c and the human anti-apoptotic protein Bcl-x_L, which defines the protein-protein interaction surface, was obtained from solution NMR chemical shift perturbation data. The atomic level information reveals key intermolecular contacts identifying new potentially druggable areas on cytochrome c and Bcl-x_L. Involvement of residues on cytochrome c other than those in its complexes with electron transfer partners is apparent. Key differences in the contact area also exist between the Bcl-x_L adduct with the Bak peptide and that with cytochrome c. The present model provides insights to the mechanism by which cytochrome c translocated to cytosol can be intercepted, so that the apoptosome is not assembled.

Synthetic and natural polyanions induce cytochrome c release from mitochondria in vitro and in situ

A synthetic polyanion composed of styrene, maleic anhydride, and methacrylic acid (molar ratio 56:37:7) significantly inhibited the respiration of isolated rat liver mitochondria in a time-dependent fashion that correlated with 1) collapse of the mitochondrial membrane potential and 2) high amplitude mitochondrial swelling. The process is apparently Ca(2+) dependent. Since it is blocked by cyclosporin A, the process is ascribed to induction of the mitochondrial permeability transition. In mitoplasts, i.e., mitochondria lacking their outer membranes, the polyanion rapidly blocked respiration. After incubation of rat liver mitochondria with the polyanion, cytochrome c was released into the incubation medium. In solution, the polyanion modified by conjugation with fluorescein formed a complex with cytochrome c. Addition of the polyanion to cytochrome c-loaded phosphatidylcholine/cardiolipin liposomes induced the release of the protein from liposomal membrane evidently due to coordinated interplay of Coulomb and hydrophobic interactions of the polymer with cytochrome c. We conclude that binding of the polyanion to cytochrome c renders it inactive in the respiratory chain due to exclusion from its native binding sites. Apparently, the polyanion interacts with cytochrome c in mitochondria and releases it to the medium through breakage of the outer membrane as a result of severe swelling. Similar properties were demonstrated for the natural polyanion, tobacco mosaic virus RNA. An electron microscopy study confirmed that both polyanions caused mitochondrial swelling. Exposure of cerebellar astroglial cells in culture to the synthetic polyanion resulted in cell death, which was associated with nuclear fragmentation.

Amyloid fibrillation of human Apaf-1 CARD

The idea of establishing the amyloid-like fibrillation tendency of pro- and antisurvival proteins of human apoptotic pathways is relevant for delineating the conditions that lead to aberrant differentiation, development, and tissue homeostasis. As the first step in this direction, we report here that the caspase recruitment domain (CARD) of recombinant human apoptotic protease activating factor-1 (Apaf-1) can be induced to undergo amyloid-like fibrillation. The study was initiated with a set of biophysical investigations into the possibility and in vitro conditions for fibril growth. By scanning the pH-induced conformational transitions, protein stability, and stopped-flow folding-unfolding kinetics, we detected a molten globule (MG) transition of the CARD at pH <4. In a bid to reduce the surface-accessible hydrophobic patches in the MG state, the CARD monomer undergoes self-association to produce soluble oligomers that serve as precursor aggregates for protofibril formation. The monomer-to-oligomer self-association process is akin to the well-known homophilic CARD-CARD interaction by which CARDs of the same or different apoptotic proteins associate to transduce and regulate the apoptotic signal. The fibrillation reaction of the Apaf-1 CARD was conducted at pH 2.1 and 60 degrees C, because reduction of exposed hydrophobic surfaces in the MG state is more favored under the moderated solution condition. The Gaussian distributions of diameters of the fibril population suggest values of 2.1 and 2.7 nm for the mean diameter of precursor aggregates and protofibrils or elongated fibrils, respectively.

Differential PARP cleavage: an indication of heterogeneous forms of cell death and involvement of multiple proteases in the infarct of focal cerebral ischemia in rat

AIM

Poly (ADP-ribose) polymerase (PARP) is a nuclear repair enzyme whose role is widely depicted in various physiological and pathological processes. In the present study, we wanted to check the status of PARP and the role of various cell death proteases involved in apoptotic and non-apoptotic forms of cell death during transient focal cerebral ischemia in rat model. The activation of these proteases can result in the production of PARP fragments which can be treated as specific signature fragments to the particular protease involved in the pathology and hence the type of cell death.

RESULTS

In the ischemic samples, we observed activation of calpain, cathepsin-b, caspase-3, and granzyme-b which were known to act on and cleave PARP to produce specific signature fragments by Western blot and immunohistochemical analysis. Cresyl violet staining showed the presence of apoptotic and necrotic cell deaths. Further we observed interaction of AIF and gra-b with PARP in double immunofluorescence and co-immunoprecipitation experiments.

CONCLUSION

Activation of calpains, cathepsin-b, caspase-3, and granzyme-b correlated with either apoptotic or necrotic cell deaths in cresyl violet staining. The appearance of PARP signature fragments gives a clear idea on the involvement of particular protease in the pathology. Appearance of signature fragments like 89- and 50-kDa indicates the involvement of apoptotic and necrotic cell death in the pathology. Further interaction of AIF and gra-b with PARP also indicates the involvement of non-apoptotic modes of cell death during the pathology of focal cerebral ischemia.