Enhancement of cytochrome c catalytic behaviour by affecting the heme environment using functionalized carbon-based nanomaterials

Bidirectional extracellular electron transfer pathways of Geobacter sulfurreducens biofilms: Molecular insights into extracellular polymeric substances

The basis for bioelectrochemical technology is the capability of electroactive bacteria (EAB) to perform bidirectional extracellular electron transfer (EET) with electrodes, i.e. outward- and inward-EET. Extracellular polymeric substances (EPS) surrounding EAB are the necessary media for EET, but the biochemical and molecular analysis of EPS of Geobacter biofilms on electrode surface is largely lacked. This study constructed Geobacter sulfurreducens-biofilms performing bidirectional EET to explore the bidirectional EET mechanisms through EPS characterization using electrochemical, spectroscopic fingerprinting and proteomic techniques. Results showed that the inward-EET required extracellular redox proteins with lower formal potentials relative to outward-EET. Comparing to the EPS extracted from anodic biofilm (A-EPS), the EPS extracted from cathodic biofilm (C-EPS) exhibited a lower redox activity, mainly due to a decrease of protein/polysaccharide ratio and α-helix content of proteins. Furthermore, less cytochromes and more tyrosine- and tryptophan-protein like substances were detected in C-EPS than in A-EPS, indicating a diminished role of cytochromes and a possible role of other redox proteins in inward-EET. Proteomic analysis identified a variety of redox proteins including cytochrome, iron-sulfur clusters-containing protein, flavoprotein and hydrogenase in EPS, which might serve as an extracellular redox network for bidirectional EET. Those redox proteins that were significantly stimulated in A-EPS and C-EPS might be essential for outward- and inward-EET and warranted further research. This work sheds light on the mechanism of bidirectional EET of G. sulfurreducens biofilms and has implications in improving the performance of bioelectrochemical technology.

Enhanced stability and catalytic performance of laccase immobilized on magnetic graphene oxide modified with ionic liquids

Graphite oxide (GO) is an excellent laccase immobilization material. However, the electrostatic interaction between graphene leads to the accumulation of GO, as well as the interaction with the surface of enzyme molecules causing protein denaturation and deactivation, which limits its further industrial application. In this study, the ionic liquids (ILs) modification strategy was proposed to improve the stability and catalytic performance of immobilized laccase. The laccase-ILs-MGO exhibited remarkable enzymatic properties, with significant enhancements in organic solvent tolerance, thermal and operational stability. The laccase-ILs-MGO system exhibited a remarkable removal efficiency of 95.5% towards 2,4-dichlorophenol (2,4-DCP) within 12 h and maintained over 70.0% removal efficiency after seven reaction cycles. In addition, the efficient elimination of other phenolic compounds and recalcitrant polycyclic aromatic hydrocarbons could also be accomplished. Molecular dynamics simulation and molecular docking studies demonstrated that immobilized laccase exhibited superior structural rigidity and stronger hydrogen bond interactions with substrates compared to free laccase, which was beneficial for the stability of both the laccase and substrate degradation efficiency. Therefore, this study proposed a simple and practical strategy for modifying GO with ILs, providing novel insights into developing efficient enzyme immobilization techniques.

Sub-inhibitory concentrations of ampicillin affect microbial Fe(III) oxide reduction

Antibiotics are ubiquitous in the iron-rich environments but their roles in microbial reduction of Fe(III) oxides are still unclear. Using ampicillin and Geobacter soli, this study investigated the underlying mechanism by which antibiotic regulated microbial reduction of Fe(III) oxides. Results showed that sub-minimal inhibitory concentrations (sub-MIC) of ampicillin significantly affected ferrihydrite reduction by G. soli, with a stimulatory effect at 1/64 and 1/32 MIC and an inhibitory effect at 1/8 MIC. Increasing ampicillin concentration resulted in increasing cell length and decreasing bacterial zeta potential that were beneficial for ferrihydrite reduction, and decreasing outer membrane permeability that was unfavorable for ferrihydrite reduction. The respiratory metabolism ability was enhanced by 1/64 and 1/32 MIC ampicillin and reduced by 1/8 MIC ampicillin, which was also responsible for regulation of ferrihydrite reduction by ampicillin. The ferrihydrite reduction showed a positive correlation with the redox activity of extracellular polymeric substances (EPS) which was tied to the cytochrome/polysaccharide ratio and the content of α-helices and β-sheet in EPS. These results suggested that ampicillin regulated microbial Fe(III) oxide reduction through modulating the bacterial morphology, metabolism activity and extracellular electron transfer ability. Our findings provide new insights into the environmental factors regulating biogeochemical cycling of iron.

Graphene Oxide-Cytochrome c Multilayered Structures for Biocatalytic Applications: Decrypting the Role of Surfactant in Langmuir-Schaefer Layer Deposition

Graphene, a two-dimensional single-layer carbon allotrope, has attracted tremendous scientific interest due to its outstanding physicochemical properties. Its monatomic thickness, high specific surface area, and chemical stability render it an ideal building block for the development of well-ordered layered nanostructures with tailored properties. Herein, biohybrid graphene-based layer-by-layer structures are prepared by means of conventional and surfactant-assisted Langmuir-Schaefer layer deposition techniques, whereby cytochrome c molecules are accommodated within ordered layers of graphene oxide. The biocatalytic activity of the as-developed nanobio-architectures toward the enzymatic oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt and decolorization of pinacyanol chloride is tested. The results show that the multilayer structures exhibit high biocatalytic activity and stability in the absence of surfactant molecules during the deposition of the monolayers.

Trends in the development of innovative nanobiocatalysts and their application in biocatalytic transformations

The ever-growing demand for cost-effective and innocuous biocatalytic transformations has prompted the rational design and development of robust biocatalytic tools. Enzyme immobilization technology lies in the formation of cooperative interactions between the tailored surface of the support and the enzyme of choice, which result in the fabrication of tremendous biocatalytic tools with desirable properties, complying with the current demands even on an industrial level. Different nanoscale materials (organic, inorganic, and green) have attracted great attention as immobilization matrices for single or multi-enzymatic systems. Aiming to unveil the potentialities of nanobiocatalytic systems, we present distinct immobilization strategies and give a thorough insight into the effect of nanosupports specific properties on the biocatalysts' structure and catalytic performance. We also highlight the development of nanobiocatalysts for their incorporation in cascade enzymatic processes and various types of batch and continuous-flow reactor systems. Remarkable emphasis is given on the application of such nanobiocatalytic tools in several biocatalytic transformations including bioremediation processes, biofuel production, and synthesis of bioactive compounds and fine chemicals for the food and pharmaceutical industry.

Artificial Photosynthesis: Is Computation Ready for the Challenge Ahead?

A tremendous effort is currently devoted to the generation of novel hybrid materials with enhanced electronic properties for the creation of artificial photosynthetic systems. This compelling and challenging problem is well-defined from an experimental point of view, as the design of such materials relies on combining organic materials or metals with biological systems like light harvesting and redox-active proteins. Such hybrid systems can be used, e.g., as bio-sensors, bio-fuel cells, biohybrid photoelectrochemical cells, and nanostructured photoelectronic devices. Despite these efforts, the main bottleneck is the formation of efficient interfaces between the biological and the organic/metal counterparts for efficient electron transfer (ET). It is within this aspect that computation can make the difference and improve the current understanding of the mechanisms underneath the interface formation and the charge transfer efficiency. Yet, the systems considered (i.e., light harvesting protein, self-assembly monolayer and surface assembly) are more and more complex, reaching (and often passing) the limit of current computation power. In this review, recent developments in computational methods for studying complex interfaces for artificial photosynthesis will be provided and selected cases discussed, to assess the inherent ability of computation to leave a mark in this field of research.

Modified silicates and carbon nanotubes for immobilization of lipase from Rhizomucor miehei: Effect of support and immobilization technique on the catalytic performance of the immobilized biocatalysts

Lipase from Rhizomucor miehei (RML) was covalently immobilized on different supports, two silica gels and two carbon nanotube samples, using two different strategies. RML was immobilized on 3-carboxypropyl silica gel (RML@Si-COOH) and multi-wall carbon nanotubes containing carboxylic acid functionalities (RML@MCNT-COOH) using a two-step carbodiimide activation/immobilization reaction. Moreover, the enzyme was also immobilized on 3-aminopropyl silica (RML@Si-Glu) and single-wall carbon nanotubes functionalized with 3-APTES and activated with glutaraldehyde (RML@SCNT-Glu). Before and after RML immobilization, the structurel properties of supports were characterized and compared in detail. After immobilization, the expressed activities were 36.9, 90.2, 16.9, and 26.1 % for RML@Si-COOH, RML@Si-Glu, RML@MCNT-COOH, and RML@SCNT-Glu, respectively. The kinetic parameters of free and immobilized RML samples were determined for three substrates, p-nitrophenyl acetate, p-nitrophenyl butyrate and p-nitrophenyl palmitate, and RML@Si-Glu showed higher catalytic efficiency than the other immobilized RML samples. RML@Si-COOH, RML@Si-Glu, RML@MCNT-COOH, and RML@SCNT-Glu exhibited 5.8, 7.6, 4.2 and 4.6 folds longer half-life values than those of the free enzyme at pH 7.5 and 40 °C. Recyclability studies showed that all the immobilized RML biocatalysts retained over 90 % of their initial activities after ten cycles in the hydrolysis of p-nitrophenyl butyrate.

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.

Influence of Structured Water Layers on Protein Adsorption Process: A Case Study of Cytochrome c and Carbon Nanotube Interactions and Its Implications

Cytochrome c, an essential protein of the electron transport chain, is known to be capable of amplifying the toxicity of carbon nanomaterials via free-radical generation. To understand their interaction, as well as the more general protein-nanoparticle interaction at molecular levels, we investigate the adsorptions between cytochrome c and carbon nanotubes (CNTs) in dynamic and thermodynamic ways using molecular dynamics simulations. The results reveal a well-defined three-phase process separated by two transition points: the diffusion phase where the protein diffuses in the water box, the lockdown phase I where the protein inserts into the surface-bound water layers and rearranges its conformation to fit to the surface of the CNT, and the lockdown phase II where cytochrome c repels the water molecules standing in its way to the surface of CNT and reaches stable adsorption states. The structured water layers affect the movement of atoms by electrostatic forces. In lockdown phase I, the conformation adjustment of the protein dominates the adsorption process. The most thermally favorable adsorption conformation is determined. It shows that except for the deformation of short β sheets and some portions of α helixes, most of the secondary structures of cytochrome c remain unchanged, implying that most of the functions of cytochrome c are preserved. During these processes, the energy contributions of the hydrophilic residues of cytochrome c are much larger than those of hydrophobic residues. Interestingly, the structured water layers at the CNT surface allow more hydrophilic residues such as Lys to get into close contact with the CNT, which plays a significant role during the anchoring process of adsorption. Our results demonstrate that the heme group is in close contact with the CNT in some of the adsorbed states, which hence provides a way for electron transfer from cytochrome c to the CNT surface.

MH, Bisht M, Nataraj SK, Venkatesu P, Mondal D. Multifunctional solvothermal carbon derived from alginate using ‘water-in-deep eutectic solvents’ for enhancing enzyme activity

The use of a water-in-DES system for conversion of a seaweed biopolymer to a highly oxygenated functional carbon is reported for protein packaging with improved activity and stability.

Biosynthetic Electronic Interfaces for Bridging Microbial and Inorganic Electron Transport

Electron transport in biological and inorganic systems is mediated through distinct mechanisms and pathways. Their fundamental mismatch in structural and thermodynamic properties has imposed a significant challenge on the effective coupling at the biotic/abiotic interface, which is central to the design and development of bioelectronic devices and their translation toward various engineering applications. Using electrochemically active bacteria, such as G. sulfurreducens, as a model system, here we report a bottom-up, biosynthetic approach to synergize the electron transport and significantly enhance the coupling at the heterogeneous junction. In particular, graphene oxide was exploited as the respiratory electron acceptors, which can be directly reduced by G. sulfurreducens through extracellular electron transfer, closely coupled with outer membrane cytochromes in electroactive conformation, and actively "wire" the redox centers to external electrical contacts. Through this strategy, the contact resistance at the biofilm/electrode interface can be effectively reduced by 90%. Furthermore, the cyclic voltammetry reveals that the electron transfer of the DL-1 biofilm transformed from a low-current (∼0.36 μA), rate-limited profile to a high-current (∼5 μA), diffusion-limited profile. These results suggested that the integration of rGO can minimize the charge transfer barriers at the biofilm/electrode interface. The more transparent contact at the DL-1/electrode interface also enables unambiguous characterization of the inherent electron transport kinetics across the electroactive biofilm independent of cell/electrode interactions. The current work represents a strategically new approach toward the seamless integration of biological and artificial electronics, which is expected to provide critical insights into the fundamentals of biological electron transport and open up new opportunities for applications in biosensing, biocomputing, and bioenergy conversion.

Enzymatic Conversion of Oleuropein to Hydroxytyrosol Using Immobilized β-Glucosidase on Porous Carbon Cuboids

In the present study, we developed novel β-glucosidase-based nano-biocatalysts for the bioconversion of oleuropein to hydroxytyrosol. Using non-covalent or covalent immobilization approaches, β-glucosidases from almonds and Thermotoga maritima were attached for the first time on oxidized and non-oxidized porous carbon cuboids (PCC). Various methods were used for the characterization of the bio-nanoconjugates, such as Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), and fluorescence spectroscopy. The oxidation state of the nanο-support and the immobilization procedure play a key role for the immobilization efficiency or the catalytic activity of the immobilized β-glucosidases. The nano-biocatalysts were successfully used for the hydrolysis of oleuropein, which leads to the formation of its bioactive derivative, hydroxytyrosol (up to 2.4 g L-1), which is a phenolic compound with numerous health benefits. The bio-nanoconjugates exhibited high thermal and operational stability (up to 240 hours of repeated use), which indicated that they are efficient tools for various bio-transformations.

Cytochrome c–poly(acrylic acid) conjugates with improved peroxidase turnover number

Cytochrome c–poly(acrylic acid) conjugates with 34-fold enhanced peroxidase activity due to acidification of enzyme microenvironment and suppression of wasteful intermediates.

Influence of cytochrome charge and potential on the cathodic current of electroactive artificial biofilms

An electroactive artificial biofilm has been optimized for the cathodic reduction of fumarate by Shewanella oneidensis. The system is based on the self-assembly of multi-walled carbon nanotubes with bacterial cells in the presence of a c-type cytochrome. The aggregates are then deposited on an electrode to form the electroactive artificial biofilm. Six c-type cytochromes have been studied, from bovine heart or Desulfuromonas and Desulfuvibrio strains. The isoelectric point of the cytochrome controls the self-assembly process that occurs only with positively-charged cytochromes. The redox potential of the cytochrome is critical for electron transfer reactions with membrane cytochromes of the Mtr pathway. Optimal results have been obtained with c₃ from Desulfovibrio vulgaris Hildenborough having an isoelectric point of 10.2 and redox potentials of the four hemes ranging between -290 and -375 mV vs SHE. A current density of 170 μA cm^-2 could be achieved in the presence of 50 mM fumarate. The stability of the electrochemical response was evaluated, showing a regular decrease of the current within 13 h, possibly due to the inactivation or leaching of loosely-bound cytochromes from the biofilm.

Synthesis, characterization and assessment of hydrophilic oxidized carbon nanodiscs in bio-related applications

Hydrophilic oxidized carbon nanodiscs able to be used as drug delivery system and as support in nanobiocatalytic applications.

Enriching the biological space of natural products and charting drug metabolites, through real time biotransformation monitoring: The NMR tube bioreactor

BACKGROUND

Natural products offer a wide range of biological activities, but they are not easily integrated in the drug discovery pipeline, because of their inherent scaffold intricacy and the associated complexity in their synthetic chemistry. Enzymes may be used to perform regioselective and stereoselective incorporation of functional groups in the natural product core, avoiding harsh reaction conditions, several protection/deprotection and purification steps.

METHODS

Herein, we developed a three step protocol carried out inside an NMR-tube. 1st-step: STD-NMR was used to predict the: i) capacity of natural products as enzyme substrates and ii) possible regioselectivity of the biotransformations. 2nd-step: The real-time formation of multiple-biotransformation products in the NMR-tube bioreactor was monitored in-situ. 3rd-step: STD-NMR was applied in the mixture of the biotransformed products to screen ligands for protein targets.

RESULTS

Herein, we developed a simple and time-effective process, the "NMR-tube bioreactor", that is able to: (i) predict which component of a mixture of natural products can be enzymatically transformed, (ii) monitor in situ the transformation efficacy and regioselectivity in crude extracts and multiple substrate biotransformations without fractionation and (iii) simultaneously screen for interactions of the biotransformation products with pharmaceutical protein targets.

CONCLUSIONS

We have developed a green, time-, and cost-effective process that provide a simple route from natural products to lead compounds for drug discovery.

GENERAL SIGNIFICANSE

This process can speed up the most crucial steps in the early drug discovery process, and reduce the chemical manipulations usually involved in the pipeline, improving the environmental compatibility.

Improved activity and thermo-stability of the horse radish peroxidase with graphene quantum dots and its application in fluorometric detection of hydrogen peroxide

Graphene quantum dots (GQDs) have received extensive concern in many fields such as optical probe, bioimaging and biosensor. However, few reports refer on the influence of GQDs on enzyme performance. The paper reports two kinds of graphene quantum dots (termed as GO-GQDs and N,S-GQDs) that were prepared by cutting of graphene oxide and pyrolysis of citric acid and l-cysteine, and their use for the horse radish peroxidase (HRP) modification. The study reveals that GO-GQDs and N,S-GQDs exhibit an opposite effect on the HRP performance. Only HRP modified with GO-GQDs offers an enhanced activity (more than 1.9 times of pristine enzyme) and thermo-stability. This is because GO-GQDs offer a larger conjugate rigid plane and fewer hydrophilic groups compared to N,S-GQDs. The characteristics can make GO-GQDs induce a proper conformational change in the HRP for the catalytic performance, improving the enzyme activity and thermo-stability. The HRP modified with green luminescent GO-GQDs was also employed as a biocatalyst for sensing of H2O2 by a fluorometric sensor. The colorless tetramethylbenzidine (TMB) is oxidized into blue oxidized TMB in the presence of H2O2 by the assistance of HRP/GO-GQDs, leading to an obvious fluorescence quenching. The fluorescence intensity linearly decreases with the increase of H2O2 concentration in the range from 2×10-9 to 2×10-4M with the detection limit of 6.8×10-10M. The analytical method provides the advantage of sensitivity, stability and accuracy compared with present H2O2 sensors based on the pristine HRP. It has been successfully applied in the determination of H2O2 in real water samples. The study also opens a new avenue for modification of enzyme activity and stability that offers great promise in applications such as biological catalysis, biosensing and enzyme engineering.

Laccase-Functionalized Graphene Oxide Assemblies as Efficient Nanobiocatalysts for Oxidation Reactions

Multi-layer graphene oxide-enzyme nanoassemblies were prepared through the multi-point covalent immobilization of laccase from Trametes versicolor (TvL) on functionalized graphene oxide (fGO). The catalytic properties of the fGO-TvL nanoassemblies were found to depend on the number of the graphene oxide-enzyme layers present in the nanostructure. The fGO-TvL nanoassemblies exhibit an enhanced thermal stability at 60 °C, as demonstrated by a 4.7-fold higher activity as compared to the free enzyme. The multi-layer graphene oxide-enzyme nanoassemblies can efficiently catalyze the oxidation of anthracene, as well as the decolorization of an industrial dye, pinacyanol chloride. These materials retained almost completely their decolorization activity after five reaction cycles, proving their potential as efficient nano- biocatalysts for various applications.

Synthesis of lipase nano-bio-conjugates as an efficient biocatalyst: characterization and activity–stability studies with potential biocatalytic applications

Synthesis of lipase nano-bio-conjugate and their detail biocatalytic application studies.

Preparation and catalytic applications of nanomaterials: a review

The present review systematically summarizes the synthesis and specific catalytic applications of nanomaterials such as MSN, nanoparticles, LD hydroxides, nanobubbles, quantum dots,etc.

Graphene-based nanobiocatalytic systems: recent advances and future prospects

Graphene-based nanomaterials are particularly useful nanostructured materials that show great promise in biotechnology and biomedicine. Owing to their unique structural features, exceptional chemical, electrical, and mechanical properties, and their ability to affect the microenvironment of biomolecules, graphene-based nanomaterials are suitable for use in various applications, such as immobilization of enzymes. We present the current advances in research on graphene-based nanomaterials used as novel scaffolds to build robust nanobiocatalytic systems. Their catalytic behavior is affected by the nature of enzyme-nanomaterial interactions and, thus, the availability of methods to couple enzymes with nanomaterials is an important issue. We discuss the implications of such interactions along with future prospects and possible challenges in this rapidly developing area.