pH-Dependent peroxidase activity of yeast cytochrome c and its triple mutant adsorbed on kaolinite

Enhancing Enzyme Activity by the Modulation of Covalent Interactions in the Confined Channels of Covalent Organic Frameworks

Controllable regulations on the enzyme conformation to optimize catalytic performance are highly desired for the immobilized biocatalysts yet remain challenging. Covalent organic frameworks (COFs) possess confined channels with finely tunable pore environment, offering a promising platform for enzyme encapsulation. Herein, we covalently immobilized the cytochrome c (Cyt c) in the size-matched channels of COFs with different contents of anchoring site, and significant enhancement of the stability and activity (≈600 % relative activity compared with free enzyme) can be realized by optimizing the covalent interactions. Structural analyses on the immobilized Cyt c suggest that covalent bonding could induce conformational perturbation resulting in more accessible active sites. The effectiveness of the covalent interaction modulation together with the tailorable confined channels of COFs offers promise to develop high-performance biocatalysts.

Catalytic Reactions and Energy Conservation in the Cytochrome bc1 and b6f Complexes of Energy-Transducing Membranes

This review focuses on key components of respiratory and photosynthetic energy-transduction systems: the cytochrome bc1 and b6f (Cytbc1/b6f) membranous multisubunit homodimeric complexes. These remarkable molecular machines catalyze electron transfer from membranous quinones to water-soluble electron carriers (such as cytochromes c or plastocyanin), coupling electron flow to proton translocation across the energy-transducing membrane and contributing to the generation of a transmembrane electrochemical potential gradient, which powers cellular metabolism in the majority of living organisms. Cytsbc1/b6f share many similarities but also have significant differences. While decades of research have provided extensive knowledge on these enzymes, several important aspects of their molecular mechanisms remain to be elucidated. We summarize a broad range of structural, mechanistic, and physiological aspects required for function of Cytbc1/b6f, combining textbook fundamentals with new intriguing concepts that have emerged from more recent studies. The discussion covers but is not limited to (i) mechanisms of energy-conserving bifurcation of electron pathway and energy-wasting superoxide generation at the quinol oxidation site, (ii) the mechanism by which semiquinone is stabilized at the quinone reduction site, (iii) interactions with substrates and specific inhibitors, (iv) intermonomer electron transfer and the role of a dimeric complex, and (v) higher levels of organization and regulation that involve Cytsbc1/b6f. In addressing these topics, we point out existing uncertainties and controversies, which, as suggested, will drive further research in this field.

Enhancing Peroxidase Activity of Cytochrome c by Modulating Interfacial Interaction Forces with Graphene Oxide

Graphene oxide (GO) has drawn worldwide attention in various biomedical fields because of its unique properties, and great progress has been made in the past years. Probing the interaction between GO and proteins, understanding and evaluating potential impact of GO on the protein structure and function, is of significant importance for design and optimization of functional interfaces and revealing the bioeffect of GO materials. Cytochrome c (cyt c), one of the key components of respiratory chain, has played important roles in energy generation/consumption and many cellular processes including growth, proliferation, differentiation, and apoptosis. In this study, by combination of solution chemistry and spectroscopy, we systematically studied the interfacial interaction between GO and cyt c. Results suggest that GO could slightly perturb the active site of cyt c, enhancing its peroxidase activity. Structure of the active site is obviously changed with elapsed time, which in turn reduces peroxidase activity. Further study suggests that adsorption of cyt c on GO and the resulted structure change is a complex process resulting from the cooperation of various interaction forces. Hydrophobic interaction and π-π stacking, as well as electrostatic attraction, only slightly perturb the microenvironment of the active site of cyt c while hydrogen-bonding interaction is the main driving force for the structural change of the active site. Furthermore, long range electrostatic attraction between GO and cyt c may facilitate the short range hydrogen-bonding interaction, which intensifies the hydrogen-bonding-induced structural change. In addition, cyt c is partially reduced by GO in an alkaline environment. Based on the understanding of interfacial interaction mechanism between GO and cyt c, stable nanocomposites with enhanced peroxidase activity are successfully constructed by modulating the interfacial interaction forces. This work not only deepens the understanding of interaction between GO and functional protein, but also is of great importance for designing and applying of GO-based biomaterials.

Determination of proton concentration at cardiolipin-containing membrane interfaces and its relation with the peroxidase activity of cytochrome c

The interface –log[H⁺] defined as pH′ of a mimic inner mitochondrial membrane is ∼3.9 at bulk pH ∼ 6.8, which affects cytochrome c activity.

The activities of biomolecules are affected by the proton concentrations at biological membranes. Here, we succeeded in evaluating the interface proton concentration (–log[H⁺] defined as pH′) of cardiolipin (CL)-enriched membrane models of the inner mitochondrial membrane (IMM) using a spiro-rhodamine-glucose molecule (RHG). According to fluorescence microscopy and ¹H-NMR studies, RHG interacted with the Stern layer of the membrane. The acid/base equilibrium of RHG between its protonated open form (o-RHG) and deprotonated closed spiro-form (c-RHG) at the membrane interface was monitored with UV-vis absorption and fluorescence spectra. The interface pH′ of 25% cardiolipin (CL)-containing large unilamellar vesicles (LUVs), which possess similar lipid properties to those of the IMM, was estimated to be ∼3.9, when the bulk pH was similar to the mitochondrial intermembrane space pH (6.8). However, for the membranes containing mono-anionic lipids, the interface pH′ was estimated to be ∼5.3 at bulk pH 6.8, indicating that the local negative charges of the lipid headgroups in the lipid membranes are responsible for the deviation of the interface pH′ from the bulk pH. The peroxidase activity of cyt c increased 5–7 fold upon lowering the pH to 3.9–4.3 or adding CL-containing (10–25% of total lipids) LUVs compared to that at bulk pH 6.8, indicating that the pH′ decrease at the IMM interface from the bulk pH enhances the peroxidase activity of cyt c. The peroxidase activity of cyt c at the membrane interface of tetraoleoyl CL (TOCL)-enriched (50% of total lipids) LUVs was higher than that estimated from the interface pH′, while the peroxidase activity was similar to that estimated from the interface pH′ for tetramyristoyl CL (TMCL)-enriched LUVs, supporting the hypothesis that when interacting with TOCL (not TMCL), cyt c opens the heme crevice to substrates. The present simple methodology allows us to estimate the interface proton concentrations of complex biological membranes.

A switchable peroxidase mimic derived from the reversible co-assembly of cytochrome c and carbon dots

We describe a straightforward tactic to boost the inherently low peroxidase-like activity of the heme-protein equine cytochrome c (cyt c) following its electrostatic assembly onto the carbon nanodot surface. This represents the first time that carbon nanodot interaction has been demonstrated to switch a protein into a high-performance enzyme for speeding up a reaction it was not evolved to catalyze. The dramatic enhancement in peroxidase-like activity stems in part from favorable local perturbations within the heme microenvironment of cyt c which are influenced by the chemistry presented at the carbon dot surface. That is, the observed peroxidase activity is clearly moderated by the choice of molecular precursors used to prepare the carbon dots, a choice which ultimately determines the surface charges present. An exceptional catalytic efficiency (k_cat/K_M) of 8.04 (±1.74) × 10⁷ M^-1 s^-1 was determined for carbon dot/cyt c co-assemblies, close to the theoretical diffusion-controlled limit. Notably, the activity of the carbon dot/cyt c assembly can be switched off simply by increasing the ionic strength which results in dissociation into non-catalytic components.

Immobilized cytochrome c bound to cardiolipin exhibits peculiar oxidation state-dependent axial heme ligation and catalytically reduces dioxygen

Mitochondrial cytochrome c (cytc) plays an important role in programmed cell death upon binding to cardiolipin (CL), a negatively charged phospholipid of the inner mitochondrial membrane (IMM). Although this binding has been thoroughly investigated in solution, little is known on the nature and reactivity of the adduct (cytc-CL) immobilized at IMM. In this work, we have studied electrochemically cytc-CL immobilized on a hydrophobic self-assembled monolayer (SAM) of decane-1-thiol. This construct would reproduce the motional restriction and the nonpolar environment experienced by cytc-CL at IMM. Surface-enhanced resonance Raman (SERR) studies allowed the axial heme iron ligands to be identified, which were found to be oxidation state dependent and differ from those of cytc-CL in solution. In particular, immobilized cytc-CL experiences an equilibrium between a low-spin (LS) 6c His/His and a high-spin (HS) 5c His/- coordination states. The former prevails in the oxidized and the latter in the reduced form. Axial coordination of the ferric heme thus differs from the (LS) 6c His/Lys and (LS) 6c His/OH(-) states observed in solution. Moreover, a relevant finding is that the immobilized ferrous cytc-CL is able to catalytically reduce dioxygen, likely to superoxide ion. These findings indicate that restriction of motional freedom due to interaction with the membrane is an additional factor playing in the mechanism of cytc unfolding and cytc-mediated peroxidation functional to the apoptosis cascade.

Conformational changes of enzymes upon immobilisation

Protein conformation plays a crucial role in determining both the catalytic efficiency and the chemo-, regio- and enantioselectivity of enzymes, thus eventually influencing their exploitability in biotechnological applications. Inevitably, immobilisation processes alter the natural molecular environment of enzymes, and quite often affect their catalytic activity through different mechanisms such as reduced accessibility of the substrate to the catalytic active centre, loss of the enzyme dynamic properties and alteration of the conformational integrity of the enzyme. This tutorial review outlines first the most common spectroscopic techniques used for investigating the conformation of immobilized proteins, and then examines how protein loading and polar and hydrophobic/hydrophilic interactions with the carrier affect the structural and dynamic features of enzymes. The nanoscale-level studies in which protein conformational changes, determined either by experimental approaches or by homology modelling, are correlated with the size and shape of the support are also discussed. Altogether, these results should provide useful information on how supports and/or enzymes have to be tailored to improve biocatalyst performance.