Stabilization of d-lactate dehydrogenase diagnostic enzyme via immobilization on pristine and carboxyl-functionalized carbon nanotubes, a combined experimental and molecular dynamics simulation study

Immobilization of recombinant serine protease from Virgobacillus natechei FarDT on amino graphene-chitosan biocompatible nanohybrid for enhancing pH and thermal stability

The serine protease gene was heterologously expressed in Escherichia coli BL21 (DE3) using the PET 28a vector. The purified enzyme was immobilized on a nanohybrid of amino graphene and chitosan. The characterization of synthesized nanohybrids and immobilized enzymes was confirmed by Fourier transform infrared (FTIR), X-ray diffraction (XRD), dynamic light scattering (DLS), and field emission scanning electron microscopy (FE-SEM). Immobilization increased the temperature optimum from 60 to 70 °C for both free and immobilized enzymes, while the optimal pH of the enzymes did not change post-immobilization (pH 8). The immobilized biocatalyst significantly enhanced thermal stability, as well as enzyme stability at significant pH ranges. After 30 days of storage, the immobilized enzymes exhibited approximately 83 % of their relative activity, while the free protease retained only 56 % of its initial activity. Stabilization also altered the kinetic parameters (increasing Km, decreasing Kcat/Km, and Vmax) and thermodynamic parameters (increasing enzyme half-life and activation energy). The study's outcomes represent a significant advancement in the realm of enzyme synthesis and its stabilization using several combined technologies, including enzyme production with recombinant DNA technology based on gene synthesis, and its stabilization using a hybrid substrate synthesized from nanomaterials. Based on these findings, the immobilized recombinant enzyme has high potential for industrial use as an efficient and stable biocatalyst.

Exploring the impact of taurine on the biochemical properties of urate oxidase: response surface methodology and molecular dynamics simulation

This paper investigates the impact of taurine as an additive on the structural and functional stability of urate oxidase. First, the effect of the processing parameters for the stabilization of Urate Oxidase (UOX) using taurine was examined using the response surface methodology (RSM) and the central composite design (CCD) model. Also, the study examines thermodynamic and kinetic parameters as well as structural changes of urate oxidase with and without taurine. Fluorescence intensity changes indicated static quenching during taurine binding. The obtained result indicates that taurine has the ability to preserve the native structural conformation of UOX. Furthermore, molecular dynamics simulation is conducted in order to get insights into the alterations in the structure of urate oxidase in the absence and presence of taurine under optimal conditions. The molecular dynamics simulation section investigated the formation of hydrogen bonds (H-bonds) between different components as well as analysis of root mean square deviation (RMSD), root mean square fluctuations (RMSF) and secondary structure. Lower Cα-RMSD and RMSF values indicate greater stabilization of the taurine-treated UOX structure compared to the free enzyme. The results of molecular docking indicate that the binding of taurine to the UOX enzyme through hydrophobic interactions is associated with a negative value for the Gibbs free energy.

Enzyme immobilization studied through molecular dynamic simulations

In recent years, simulations have been used to great advantage to understand the structural and dynamic aspects of distinct enzyme immobilization strategies, as experimental techniques have limitations in establishing their impact at the molecular level. In this review, we discuss how molecular dynamic simulations have been employed to characterize the surface phenomenon in the enzyme immobilization procedure, in an attempt to decipher its impact on the enzyme features, such as activity and stability. In particular, computational studies on the immobilization of enzymes using i) nanoparticles, ii) self-assembled monolayers, iii) graphene and carbon nanotubes, and iv) other surfaces are covered. Importantly, this thorough literature survey reveals that, while simulations have been primarily performed to rationalize the molecular aspects of the immobilization event, their use to predict adequate protocols that can control its impact on the enzyme properties is, up to date, mostly missing.

Protease immobilization on a novel activated carrier alginate/dextrose beads: Improved stability and catalytic activity via covalent binding

Protease from Bacillus thuringiensis strain-MA8 was successfully immobilized onto activated Alginate/dextrose (Alg/dex) beads as a new carrier with immobilization yield 77.6 %. The carrier was characterized using Scanning electron microscopy and Fourier transforms infrared spectrophotometer at every step of the immobilization process. Immobilized protease showed an increase of 10 °C in the optimum temperature compared to the free enzyme. However, the optimum pH for both the free and the Alg/dex/protease was found to be 8. The lower activation energy and deactivation rate constant and the higher half-life time and D-value confirm that the new Alg/dex carrier is suitable for promoting enzyme stability. The raise in thermal stability is also shown by the increased deactivation energy of the Alg/dex/protease compared to its free form by 1.47-fold. Likewise, the enzyme immobilization enhancement of Alg/dex/protease was accompanied by a marked increase in enthalpy and Gibbs free energy. The negative entropy for both free and Alg/dex/protease indicates that the enzyme is more stable in thermal deactivation. The Km and Vmax for the Alg/dex/protease were 2.05 and 1.22-times greater than the free form. Furthermore, Alg/dex/protease displayed good reusability as it retained 92.7 and 52.4 % of its activity after 8 and 12 hydrolysis cycles.

A comprehensive review on bio-mimicked multimolecular frameworks and supramolecules as scaffolds for enzyme immobilization

Immobilization depicts a propitious route to optimize the catalytic performances, efficient recovery, minimizing autocatalysis, and also augment the stabilities of enzymes, particularly in unnatural environments. In this opinion, supramolecules and multimolecular frameworks have captivated immense attention to achieve profound controllable interactions between enzyme molecules and well-defined natural or synthetic architectures to yield protein bioconjugates with high accessibility for substrate binding and enhanced enantioselectivities. This scholastic review emphasizes the possibilities of associating multimolecular complexes with biological entities via several types of interactions, namely covalent interactions, host-guest complexation, π - π ${\rm{\pi }}-{\rm{\pi }}$ interactions, intra/inter hydrogen bondings, electrostatic interactions, and so forth offers remarkable applications for the modulations of enzymes. The potential synergies between artificial supramolecular structures and biological systems are the primary concern of this pedagogical review. The majority of the research primarily focused on the dynamic biomolecule-responsive supramolecular assemblages and multimolecular architectures as ideal platforms for the recognition and modulation of proteins and cells. Embracing sustainable green demeanors of enzyme immobilizations in a quest to reinforce site-selectivity, catalytic efficiency, and structural integrality of enzymes are the contemporary requirements of the biotechnological sectors that instigate the development of novel biocatalytic systems.

Preparation and characterization of sugilite glass from basalt for α-amylase immobilization, statistical optimization of the immobilization process and description of free and immobilized enzyme

Bacterial α-amylase was immobilized on sugilite from modified basalt rock as a new carrier. A set of glass compositions based on sugilite formula KNa₂M₂Li₃Si₁₂O₃₀ (M = Al or Mn or Fe) were prepared. The glasses were prepared through melting–quenching technique and samples of glass were converted to glass ceramic. Among the tested glasses and glass ceramic only sugilite glass based on M = Fe (BSF) give promising results. The sugilite BSF glass was characterized using DSC analysis, FTIR absorption, and SEM. The sugilite glass revealed high thermal resistant till ∼770 °C. Under optimized conditions of the Central composite design, the immobilization yield improved by 4.7-fold. The affinity to starch increased after enzyme immobilization by 4.3-fold. The lower rate of deactivation constant and the increase of t_½ and D-value confirm the suitability of BSF and immobilization method in enhancing enzyme stability. The improvement in thermostability of immobilized α-amylase was judged by the change in thermodynamic parameters. In conclusion, the prepared sugilite BSF glass can be utilized as a new carrier suitable for stabilization of α-amylase enzyme by immobilization.

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Lemon peels induced α-amylase production by isolated Rhizobium sp. strain A1.

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Using basalt as raw material for sugilite glass synthesis as new immobilization carriers.

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Sugilite BSF glass the suitable carrier was characterized by DSC, FTIR and SEM.

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Central composite design increased immobilization yield by 4.7–fold.

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Thermal and thermodynamic properties emphasize increased stability upon immobilization.

Atomistic insight into 2D COFs as antiviral agents against SARS-CoV-2

The recent pandemic of COVID-19 has raised global health concerns. Preventing severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) activity in the body is a very promising method to overcome the COVID-19 pandemic. One of the prevention methods is constraining the binding process among the human cell receptor-ACE2 and coronavirus spike protein. In the research done, the effect of deformation of the spike protein structure, due to the covalent organic frameworks (COFs), in reducing the interactions of ACE2 and the spike protein by the computational method was investigated. In this regard, atomic analysis of the interactions of ACE2 and the spike protein is provided using a molecular dynamics simulation. First, we investigated the interactions of the three different COFs, including COF-78, DAAQ-TFP, and COF-OEt, with the spike protein by analyzing the bond energies, as well as structural changes of the spike protein. Then, intermolecular interactions of the deformed spike protein along with ACE2 were assessed to clarify the protein's fusion after the deformation. As indicated by the results, although all introduced COFs deformed the spike protein in an effective way, COF-78 showed the best performance in the prevention of spike protein-ACE2 interactions by changing the molecular structure of the protein. Indeed, the interaction analysis of the deformed spike protein by COF-78 with the ACE2 showed that their interactions had the lowest absolute value of energy, along with the least amount of hydrogen bonds, in which the compaction of the protein was lower compared to the other deformed proteins. Moreover, having a high contact area with an aqueous media as well as severe fluctuations during the simulation time confirmed the positive performance of COF-78. In the current study, we aimed to introduce novel materials and COVID-19 prevention methodology that can be used in face masks and for surface disinfection.

Recent advances in carbon nanotubes-based biocatalysts and their applications

Enzymes have been incorporated into a wide variety of fields and industries as they catalyze many biochemical and chemical reactions. The immobilization of enzymes on carbon nanotubes (CNTs) for generating nano biocatalysts with high stability and reusability is gaining great attention among researchers. Functionalized CNTs act as excellent support for effective enzyme immobilization. Depending on the application, the enzymes can be tailored using the various surface functionalization techniques on the CNTs to extricate the desirable characteristics. Aiming at the preparation of efficient, stable, and recyclable nanobiocatalysts, this review provides an overview of the methods developed to immobilize the various enzymes. Various applications of carbon nanotube-based biocatalysts in water purification, bioremediation, biosensors, and biofuel cells have been comprehensively reviewed.

Boosted activity by engineering the enzyme microenvironment in cascade reaction: A molecular understanding

Engineering of enzyme microenvironment can surprisingly boost the apparent activity. However, the underlying regulation mechanism is not well-studied at a molecular level so far. Here, we present a modulation of two model enzymes of cytochrome c (Cty C) and _d-amino acid oxidase (DAAO) with opposite pH-activity profiles using ionic polymers. The operational pH of poly (acrylic acid) modified Cyt C and polyallylamine modified DAAO was extended to 3–7 and 2–10 where the enzyme activity was larger than that at their optimum pH of 4.5 and 8.5 by 106% and 28%, respectively. The cascade reaction catalyzed by two modified enzymes reveals a 1.37-fold enhancement in catalytic efficiency compared with their native counterparts. The enzyme activity boosting is understood by performing the UV–vis/CD spectroscopy and molecular dynamics simulations in the atomistic level. The increased activity is ascribed to the favorable microenvironment in support of preserving enzyme native structures nearby cofactor under external perturbations.

Investigation of nanotubes as the smart carriers for targeted delivery of mercaptopurine anticancer drug

Mercaptopurine (MCP) is an anticancer drug that is used to treat acute lymphoblastic leukemia. The therapeutic effect of the mercaptopurine limits its severe side effects like other cytotoxic (anti-cancer) drugs. Nanostructures or nanoparticles can be widely used as potential drug carriers for diagnosis and treatment of cancer. In the current study, the boron nitride nanotube (BNNT) and carbon nanotube (CNT) were studied as the delivery carriers of MCP using the density functional theory (DFT) calculations and molecular dynamics (MDs) simulation studies. To further understand the electronic properties of mercaptopurine, the partial density of states (PDOS) was calculated. The PDOS results depicted that the electronic features of the MCP do not change after the adsorption on the surface of the nanotubes. More stability of the MCP/BNNT complexes may be attributed to the existence of the intermolecular hydrogen bonds (H-bonds) between the hydrogen atoms of the MCP molecule and the N atoms of the BNNT. The results of the quantum theory of atoms in molecules (QTAIM) confirmed the presence of H-bonds in these complexes. Moreover, MD simulation studies were done in the presence of five drug molecules. The results revealed that the strongest van der Waals (vdW) interaction energy was found between the BNNT and MCP among the studied nanotubes, indicating the BNNT is a better nanocarrier than carbon nanotube for delivery of the MCP drug within the biological systems. In general, the obtained results may present helpful information on the nature of the interactions between mercaptopurine anticancer drug with BNNT and/or CNT.Communicated by Ramaswamy H. Sarma.

Immobilization of enzymes on nanoinorganic support materials: An update

Despite the widespread use in various industries, enzyme's instability and non-reusability limit their applications which can be overcome by immobilization. The nature of the enzyme's support material and method of immobilization affect activity, stability, and kinetics properties of enzymes. Here, we report a comparative study of the effects of inorganic support materials on immobilized enzymes. Accordingly, immobilization of enzymes on nanoinorganic support materials significantly improved thermal and pH stability. Furthermore, immobilizations of enzymes on the materials mainly increased K_m values while decreased the V_max values of enzymes. Immobilized enzymes on nanoinorganic support materials showed the increase in ΔG value, and decrease in both ΔH and ΔS values. In contrast to weak physical adsorption immobilization, covalently-bound and multipoint-attached immobilized enzymes do not release from the support surface to contaminate the product and thus the cost is decreased while the product quality is increased. Nevertheless, nanomaterials can enter the environment and increase health and environmental risks and should be used cautiously. Altogether, it can be predicated that hybrid support materials, directed immobilization methods, site-directed mutagenesis, recombinant fusion protein technology, green nanomaterials and trailor-made supports will be used increasingly to produce more efficient immobilized industrial enzymes in near future.

New insight into the molecular mechanism of the trehalose effect on urate oxidase stability

Urate oxidase (EC 1.7.3.3) is a key enzyme in the purine metabolism which is applied in the treatment of gout and also, as a diagnostic reagent for uric acid detection. In the current study, the trehalose (TRE) effects as an additive on the structural stability and function of uricase were investigated. For recombinant expression of UOX in E. coli BL21 cells, firstly the coding sequence was subcloned into the pET-28a vector and after induction with IPTG, the recombinant UOX was purified by affinity chromatography using a Ni-NTA agarose column. To specify the trehalose effects on the urate oxidase (UOX) structure, optimum pH, optimum temperature, kinetic and thermodynamic parameters and also, the intrinsic fluorescence of UOX in the absence and presence of trehalose were examined. The UOX half-life is 24.32 min at 40 °C, whereas the UOX-TRE has a higher half-life (32.09 min) at this temperature. Generally, our findings confirm that trehalose has a protective effect on the enzyme structure. Optimum pH and temperature were 9 and 25 °C, respectively for both the naked and treated enzymes and their activity retained 42.18 and 64.80%, respectively after 48 h of incubation at room temperature. Also, theoretical results indicate that the random coil of the enzyme was converted to α-helix and β-sheet in the presence of trehalose which may preserve the integrity of the active site of the enzyme and increased the enzymatic activity. The MD simulation results indicated greater stability of the uricase structure in the presence of trehalose.Communicated by Ramaswamy H. Sarma.

Graphene-Based Nanoparticles as Potential Treatment Options for Parkinson's Disease: A Molecular Dynamics Study

INTRODUCTION

The study of abnormal aggregation of proteins in different tissues of the body has recently earned great attention from researchers in various fields of science. Concerning neurological diseases, for instance, the accumulation of amyloid fibrils can contribute to Parkinson's disease, a progressively severe neurodegenerative disorder. The most prominent features of this disease are the degeneration of neurons in the substantia nigra and accumulation of α-synuclein aggregates, especially in the brainstem, spinal cord, and cortical areas. Dopamine replacement therapies and other medications have reduced motor impairment and had positive consequences on patients' quality of life. However, if these medications are stopped, symptoms of the disease will recur even more severely. Therefore, the improvement of therapies targeting more basic mechanisms like prevention of amyloid formation seems to be critical. It has been shown that the interactions between monolayers like graphene and amyloids could prevent their fibrillation.

METHODS

For the first time, the impact of four types of last-generation graphene-based nanostructures on the prevention of α-synuclein amyloid fibrillation was investigated in this study by using molecular dynamics simulation tools.

RESULTS

Although all monolayers were shown to prevent amyloid fibrillation, nitrogen-doped graphene (N-Graphene) caused the most instability in the secondary structure of α-synuclein amyloids. Moreover, among the four monolayers, N-Graphene was shown to present the highest absolute value of interaction energy, the lowest contact level of amyloid particles, the highest number of hydrogen bonds between water and amyloid molecules, the highest instability caused in α-synuclein particles, and the most significant decrease in the compactness of α-synuclein protein.

DISCUSSION

Ultimately, it was concluded that N-Graphene could be the most effective monolayer to disrupt amyloid fibrillation, and consequently, prevent the progression of Parkinson's disease.

Catalytic, kinetic and thermal properties of free andimmobilized Bacillus subtilis -MK1 α-amylase on Chitosan-magnetic nanoparticles

Bacillus subtilis strain-MK1 α-amylase was successfully immobilized on Chitosan-magnetic nanoparticles (Ch-MNP) that had been modified with polyethyleneimine (PEI) and glutaraldehyde (GA). Optimization of Ch-MNP/PEI/GA beads modification by Central Composite design enhanced the immobilization yield (IY %) by 1.5-fold. Ch-MNP/PEI/GA was characterized before and after modification and immobilization by FTIR and SEM. Ch-MNP/PEI/GA/Enzyme showed the same pH optima of free enzyme, while an elevation 10 °C in temperature optima was observed after its immobilization. Ch-MNP/PEI/GA/Enzyme displayed higher Km and Vmax values (2.1 and 1.2-fold) and lower Vmax/Km ratio (1.7-fold), respectively than the free enzyme. Compared to the free enzyme, Ch-MNP/PEI/GA/Enzyme exhibited lower activation energy, lower deactivation constant rate, higher D-values, higher half-life, and higher energy for denaturation. Immobilization of α-amylase increased enthalpy (4.2-fold), free energy (1.1-fold) and decreased entropy (4.6-fold) of thermal inactivation. A significant increase in pH stability of Ch-MNP/PEI/GA/Enzyme was observed especially at alkaline pH values. In addition, Ch-MNP/PEI/GA/Enzyme preserved 83.2 % of its initial activity after 15 consecutive cycles. When storing Ch-MNP/PEI/GA/Enzyme at 4 °C the residual activity was 100 and 86 %, respectively after 21 and 40 days. Finally, immobilization process improved the catalytic properties and stabilities, thus raising the suitability for industrial processes with lower cost and time.

From in vitro to in silico: Modeling and recombinant production of DT-Diaphorase enzyme

DT-Diaphorase (DTD) belonging to the oxidoreductase family, is among the most important enzymes and is of great significance in present-day biotechnology. Also, it has potential applications in glucose and pyruvate biosensors. Another important role of the DTD enzyme is in the detection of Phenylketonuria disease. According to the above demands, at first, we tried to study molecular cloning and production of recombinant DTD in E. coli BL21 strain. We have successfully cloned, expressed, and purified functionally active diaphorase. The amount of enzyme was increased in 10-h using IPTG induction, and the recombinant protein was purified by Ni-NTA agarose affinity chromatography. After that, the kinetic and thermodynamic parameters of the enzyme, optimum temperature and pH were also investigated to find more in-depth information. In the end, to represent the connections between the structures and function of this enzyme, the molecular dynamics simulations have been considered at two temperatures in which DTD had maximum and minimum activity (310 and 293 K, respectively). The results of MD simulations indicated that the interaction between NADH with phenylalanine 232 residue at 310 K is more severe than other residues. So, to investigate the interaction details of NADH/PHE 232 the DFT calculations were done.