Hydrophobin-1 promotes thermostability of firefly luciferase

Biophysical insights into osmolytes-driven enhancements in urate oxidase activity and stability

The thermal instability of pharmaceutical enzymes such as uricase or urate oxidase (UOX) in liquid solutions is a major problem. Notably, compatible osmolytes are a specific class of osmolytes that can preferentially stabilize the folded state of proteins. However, the detailed molecular interactions that enable them to affect protein stability are still not completely elucidated. This study aimed to investigate how the enzyme environment could be altered using osmolytes to improve its catalytic activity and stability. Initially, experimental conditions were optimized using response surface methodology (RSM). Then, kinetic and thermodynamic properties, as well as structural changes of urate oxidase, were assessed using spectroscopic and computational techniques in the presence and absence of mixed osmolytes. Kinetic parameters indicated an improvement in the catalytic function of urate oxidase and the results of thermodynamic analysis indicated that the van der Waals forces and hydrogen bonding network played a crucial role in the UOX-osmolytes interactions. Fluorescence measurements suggested that osmolyte-UOX interactions alter the enzyme's structure. The data revealed a complex quenching mechanism between the enzyme and osmolyte. Molecular dynamics (MD) simulations showed an increase in stability and structural compactness of the enzyme in the presence of mixed osmolytes. Furthermore, it depicted an increase in the abundance of secondary structure contents of the enzyme, which in turn maintained the integrity of its active site. Also, the molecular docking analysis further supported the experimental results. These findings revealed mechanisms by which binary-compatible osmolytes could have relevant effects on the catalytic function and stability of urate oxidase.

Chirality governs the structure and activity changes of Photinus pyralis firefly luciferase induced by carbon quantum dots

Nanobiocatalysis is a novel area integrating various advantages of nanotechnology and enzymatic catalysis. However, great efforts are still needed to fully understand the interactions between nanostructures and enzymes. The biological properties of nano-hybrid enzymes greatly depend on the size and chemical properties of their nano element. However, the impact of nanostructure chirality on the structure/function of the enzymes has not yet been fully investigated. In this study, using experimental and computational approaches, the interaction of Photinus pyralis firefly luciferase with chiral carbon quantum dots containing l and d-tryptophan constituent (l/d-Trp-CQDs) was investigated. Both the CQDs increased K m of the enzyme for luciferin and resulted in the loss of luciferase activity dose-dependently with more profound effects for d-Trp-CQDs. d-Trp-CQD treatment had significantly increased K m of the enzyme for ATP (3.5 fold) compared to the untreated enzyme. The changes in the secondary structure of luciferase upon interaction with d-Trp-CQDs were more drastic compared to l-Trp-CQDs, as determined by circular dichroism spectroscopy. Molecular dynamic simulation further confirmed higher conformational changes of luciferase induced by d-Trp-CQDs compared to l-Trp-CQDs. d-Trp-CQD has led to conformational changes of several amino acids involved in the active site, substrate binding site and the flexible loop of luciferase (352-359 residues) that governs the activity of luciferase.

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.

Label-Free and Bioluminescence-Based Nano-Biosensor for ATP Detection

A bioluminescence-based assay for ATP can measure cell viability. Higher ATP concentration indicates a higher number of living cells. Thus, it is necessary to design an ATP sensor that is low-cost and easy to use. Gold nanoparticles provide excellent biocompatibility for enzyme immobilization. We investigated the effect of luciferase proximity with citrate-coated gold, silver, and gold-silver core-shell nanoparticles, gold nanorods, and BSA-Au nanoclusters. The effect of metal nanoparticles on the activity of luciferases was recorded by the luminescence assay, which was 3-5 times higher than free enzyme. The results showed that the signal stability in presence of nanoparticles improved and was reliable up to 6 h for analytes measurements. It has been suggested that energy is mutually transferred from luciferase bioluminescence spectra to metal nanoparticle surface plasmons. In addition, we herein report the 27-base DNA aptamer for adenosine-5'-triphosphate (ATP) as a suitable probe for the ATP biosensor based on firefly luciferase activity and AuNPs. Due to ATP application in the firefly luciferase reaction, the increase in luciferase activity and improved detection limits may indicate more stability or accessibility of ATP in the presence of nanoparticles. The bioluminescence intensity increased with the ATP concentration up to 600 µM with a detection limit of 5 µM for ATP.

Aspergillus Hydrophobins: Physicochemical Properties, Biochemical Properties, and Functions in Solid Polymer Degradation

Hydrophobins are small amphipathic proteins conserved in filamentous fungi. In this review, the properties and functions of Aspergillus hydrophobins are comprehensively discussed on the basis of recent findings. Multiple Aspergillus hydrophobins have been identified and categorized in conventional class I and two non-conventional classes. Some Aspergillus hydrophobins can be purified in a water phase without organic solvents. Class I hydrophobins of Aspergilli self-assemble to form amphipathic membranes. At the air–liquid interface, RolA of Aspergillus oryzae self-assembles via four stages, and its self-assembled films consist of two layers, a rodlet membrane facing air and rod-like structures facing liquid. The self-assembly depends mainly on hydrophobin conformation and solution pH. Cys4–Cys5 and Cys7–Cys8 loops, disulfide bonds, and conserved Cys residues of RodA-like hydrophobins are necessary for self-assembly at the interface and for adsorption to solid surfaces. AfRodA helps Aspergillus fumigatus to evade recognition by the host immune system. RodA-like hydrophobins recruit cutinases to promote the hydrolysis of aliphatic polyesters. This mechanism appears to be conserved in Aspergillus and other filamentous fungi, and may be beneficial for their growth. Aspergilli produce various small secreted proteins (SSPs) including hydrophobins, hydrophobic surface–binding proteins, and effector proteins. Aspergilli may use a wide variety of SSPs to decompose solid polymers.

Improving the Stability of Protein-Protein Interaction Assay FlimPIA Using a Thermostabilized Firefly Luciferase

The protein–protein interaction assay is a key technology in various fields, being applicable in drug screening as well as in diagnosis and inspection, wherein the stability of assays is important. In a previous study, we developed a unique protein–protein interaction assay “FlimPIA” based on the functional complementation of mutant firefly luciferases (Fluc). The catalytic step of Fluc was divided into two half steps: D-luciferin was adenylated in the first step, while adenylated luciferin was oxidized in the second step. We constructed two mutants of Fluc from Photinus pyralis (Ppy); one mutant named Donor is defective in the second half reaction, while the other mutant named Acceptor exhibited low activity in the first half reaction. To date, Ppy has been used in the system; however, its thermostability is low. In this study, to improve the stability of the system, we applied Fluc from thermostabilized Luciola lateralis to FlimPIA. We screened suitable mutants as probes for FlimPIA and obtained Acceptor and Donor candidates. We detected the interaction of FKBP12-FRB with FlimPIA using these candidates. Furthermore, after the incubation of the probes at 37°C for 1 h, the luminescence signal of the new system was 2.4-fold higher than that of the previous system, showing significant improvement in the stability of the assay.

Enhancement of Thermostability of Aspergillus flavus Urate Oxidase by Immobilization on the Ni-Based Magnetic Metal-Organic Framework

The improvement in the enzyme activity of Aspergillus flavus urate oxidase (Uox) was attained by immobilizing it on the surface of a Ni-based magnetic metal–organic framework (NimMOF) nanomaterial; physicochemical properties of NimMOF and its application as an enzyme stabilizing support were evaluated, which revealed a significant improvement in its stability upon immobilization on NimMOF (Uox@NimMOF). It was affirmed that while the free Uox enzyme lost almost all of its activity at ~40–45 °C, the immobilized Uox@NimMOF retained around 60% of its original activity, even retaining significant activity at 70 °C. The activation energy (Ea) of the enzyme was calculated to be ~58.81 kJ mol⁻¹ after stabilization, which is approximately half of the naked Uox enzyme. Furthermore, the external spectroscopy showed that the MOF nanomaterials can be coated by hydrophobic areas of the Uox enzyme, and the immobilized enzyme was active over a broad range of pH and temperatures, which bodes well for the thermal and long-term stability of the immobilized Uox on NimMOF.

Improvement Thermal Stability of D-Lactate Dehydrogenase by Hydrophobin-1 and in Silico Prediction of Protein-Protein Interactions

Hydrophobins are small surface-active proteins. They can connect to hydrophobic or hydrophilic regions and oligomerize in solution to form massive construction. In nature, these proteins are produced by filamentous fungi at different stages of growth. So far, researchers have used them in various fields of biotechnology. In this study, recombinant hydrophobin-1 (rHFB1, 7.5 kDa) was used to stabilize recombinant D-lactate dehydrogenase (rD-LDH, 35 kDa). rD-LDH is a sensitive enzyme deactivated and oxidized by external agents such as O₂ and lights. So, its stabilization with rHFB1 can be the best index to demonstrate the positive effect of rHFB1 on preserving and improving enzyme's activity. The unique ability of rHFB1 for interacting with hydrophobic regions of rD-LDH was predicted by protein-protein docking study with ClusPro and PIC servers and confirmed by fluorescence experiments, and Colorless Native-PAGE. Measurement of thermodynamic parameters allows for authenticating the role of rHFB1 as a thermal stabilizer in the protein-protein complex (rD-LDH@rHFB1). Interaction between rHFB1 and rD-LDH improved half-life of enzyme 2.25-fold at 40 °C. Investigation of the kinetic parameters proved that the presence of rHFB1 along with the rD-LDH enhancement strongly the affinity of the enzyme for pyruvate. Furthermore, an increase of Kcat/Km for complex displayed the effect of rHFB1 for improving the enzyme's catalytic efficiency.

Role of Hsp90 and ATP in modulating apyrase activity and firefly luciferase kinetics

The present manuscript describes a novel bioassay consisting of apyrase and heat shock protein 90 (Hsp90) without additional co-chaperone supplementation; intended for high-throughput screening of anti-cancer drugs and prognosis of stress. In this regard, Hsp90 and adenosine 5'-triphosphate (ATP) mediated firefly luciferase (FLuc) kinetics was investigated using apyrase and FLuc as client proteins. Bioluminescent assay containing Hsp90, ATP, and apyrase led to complete loss of luminescence at 50 °C which indicates the protective role of Hsp90 against thermal denaturation. Similarly, the assay sample comprising Hsp90, ATP, and FLuc showed 2 fold increments in luminescence than their counterparts. Introduction of bovine serum albumin (BSA) to the pre-incubated assay mixture led to an initial rise in the luminescence (28%) in comparison to the sample containing Hsp90, ATP and FLuc. Therefore, FLuc based HTS assays are not suitable for clinical samples which may contain stabilizing agents. However, thermally denatured FLuc and apyrase could not regain their active conformation even when Hsp90 and ATP were introduced in the assay system. This observation justifies the role of Hsp90 to be protective rather than a reparation agent when acts without co-chaperones.

Luciferin-Regenerating Enzyme Crystal Structure Is Solved but its Function Is Still Unclear

Contribution of luciferin-regenerating enzyme (LRE) for in vitro recycling of D-luciferin has been reported. According to crystal structure of LRE, it is a beta-propeller protein which is a type of all β-protein architecture. In this overview, reinvestigation of the luciferase-based LRE assays and its function is reported. Until now, sequence of LRE genes from four different species of firefly has been reported. In spite of previous reports, T-LRE (from Lampyris turkestanicus) was cloned and expressed in Escherichia coli as well as Pichia pastoris in a nonsoluble form as inclusion body. According to recent investigations, bioluminescent signal of soluble T-LRE-luciferase-coupled assay increased and then reached an equilibrium state in the presence of D-cysteine. In addition, the results revealed that both D- and L-cysteine in the absence of T-LRE caused a significant increase in bioluminescence intensity of luciferase over a long time. Based on activity measurements and spectroscopic results, D-cysteine increased the activity of luciferase due to its redox potential and induction of conformational changes in structure and kinetics properties. In conclusion, in spite of previous reports on the effect of LRE (at least T-LRE) on luciferase activity, most of the increase in luciferase activity is caused by direct effect of D-cysteine on structure and activity of firefly luciferase. Moreover, bioinformatics analysis cannot support the presence of LRE in peroxisome of photocytes in firefly lanterns.