Thermal, chemical and pH induced denaturation of a multimeric β-galactosidase reveals multiple unfolding pathways

Identification and characterisation of moderately thermostable diisobutyl phthalate degrading esterase from a Great Artesian Basin Bacillus velezensis NP05

Phthalate esters are known to be endocrine disrupting chemicals and are documented to pollute environments. Enzymatic degradation of PAEs is a potential bioremedial strategy to manage contamination. Thermostable bioremedial enzymes have advantages in enzyme manufacturing and storage. In this study, we identified, overexpressed, and characterised a moderately thermostable para-nitrobenzyl esterase from whole genome sequencing of a Bacillus velezensis NP05 from the Great Artesian Basin, capable of sequential 2-step hydrolysis of diisobutyl phthalate. The pnbA enzyme has a molecular weight of 55.14 kDa and pI of 5.31. It preferentially degrades para-nitrophenyl butanoate and has an optimal pH of 7-8. The pnbA esterase has an optimal temperature of 55 °C with a half-life of 4 h. Using HPLC we found that pnbA (0.122 U) can hydrolyse 0.83 mM of DIBP within 25 min. Lastly, pnbA is potentially a more economically viable candidate for enzymatic bioremediation of diisobutyl phthalate as a free enzyme.

The potential of lactose to inhibit cereulide biosynthesis of emetic Bacillus cereus in milk

This study aims to investigate the potential role of lactose on cereulide biosynthesis by emetic Bacillus cereus in dairy matrices. The cereulide yields in whole milk and lactose-free milk were investigated using the emetic reference strain F4810/72. To eliminate the influence of complex food substrates, the LB medium model was further used to characterize the effect of lactose on cereulide produced by F4810/72 and five other emetic B. cereus strains. Results showed that the lactose-free milk displayed a 13-fold higher amount of cereulide than whole milk, but the cereulide level could be reduced by 91 % when the lactose content was restored. The significant inhibition of lactose on cereulide yields of all tested B. cereus strains was observed in LB medium, showing a dose-dependent manner with inhibition rates ranging of 89-98 %. The growth curves and lactose utilization patterns of all strains demonstrated that B. cereus cannot utilize lactose as a carbon source and lactose might act as a signal molecule to regulate cereulide production. Moreover, lactose strongly repressed the expression of cereulide synthetase genes (ces), possibly by inhibiting the key regulator Spo0A at the transcriptional level. Our findings highlight the potential of lactose as an effective strategy to control cereulide production in food.

Elucidating the structure-function attributes of a trypanosomal arginyl-tRNA synthetase

Aminoacyl-tRNA synthetases (aaRSs) are fundamental components of the protein translation machinery. In light of their pivotal role in protein synthesis and structural divergence among species, they have always been considered potential targets for the development of antimicrobial compounds. Arginyl-tRNA synthetase from Trypanosoma cruzi (TcArgRS), the parasite responsible for causing Chagas Disease, contains a 100-amino acid insertion that was found to be completely absent in the human counterpart of similar length, as ascertained from multiple sequence alignment results. Thus, we were prompted to perform a preliminary characterization of TcArgRS using biophysical, biochemical, and bioinformatics tools. We expressed the protein in E. coli and validated its in-vitro enzymatic activity. Additionally, analysis of DTNB kinetics, Circular dichroism (CD) spectra, and ligand-binding studies using intrinsic tryptophan fluorescence measurements aided us to understand some structural features in the absence of available crystal structures. Our study indicates that TcArgRS can discriminate between L-arginine and its analogues. Among the many tested substrates, only L-canavanine and L-thioarginine, a synthetic arginine analogue exhibited notable activation. The binding of various substrates was also determined using in silico methods. This study may provide a viable foundation for studying small compounds that can be targeted against TcArgRS.

Systematic review and meta-analysis of human health-related protein markers for realizing real-time wastewater-based epidemiology

For effective implementation of the wastewater-based epidemiology (WBE) approach, real-time quantification of markers in wastewater is critical for data acquisition before data interpretation, dissemination, and decision-making. This can be achieved by using biosensor technology, but whether the quantification/detection limits of different types of biosensors comply with the concentration of WBE markers in wastewater is unclear. In the present study, we identified promising protein markers with relatively high concentrations in wastewater samples and analyzed biosensor technologies that are potentially available for real-time WBE. The concentrations of potential protein markers in stool and urine samples were obtained through systematic review and meta-analysis. We examined 231 peer-review papers to collect information regarding potential protein markers that can enable us to achieve real-time monitoring using biosensor technology. Fourteen markers in stool samples were identified at the ng/g level, presumably equivalent to ng/L of wastewater after dilution. Moreover, relatively high average concentrations of fecal inflammatory proteins were observed, e.g., fecal calprotectin, clusterin, and lactoferrin. Fecal calprotectin exhibited the highest average log concentration among the markers identified in stool samples with its mean value being 5.24 [95 % CI: 5.05, 5.42] ng/g. We identified 50 protein markers in urine samples at the ng/mL level. Uromodulin (4.48 [95 % CI: 4.20, 4.76] ng/mL) and plasmin (4.18 [95 % CI: 3.15, 5.21] ng/mL) had the top two highest log concentrations in urine samples. Furthermore, the quantification limit of some electrochemical- and optical-based biosensors was found to be around the femtogram/mL level, which is sufficiently low to detect protein markers in wastewater even after dilution in sewer pipes.

Development of a multiplex-based immunoassay for the characterization of diphtheria, tetanus and acellular pertussis antigens in human combined DTaP vaccines

Routine batch quality testing before vaccine release, notably for potency evaluation, still relies on animal use for several animal and human vaccines. In this context, the VAC2VAC project is a public-private consortium of 22 partners funded by EU whose the main objective is to reduce the number of animal used for batch testing by developing immunoassays that could be implemented for routine potency assessment of vaccines. This paper focused on the development of a Luminex-based multiplex assay to monitor the consistency of antigen quantity and quality throughout the production process of DTaP vaccines from two human vaccine manufacturers. Indepth characterized monoclonal antibody pairs were used for development and optimization of the Luminex assay with non-adsorbed and adsorbed antigens and with complete vaccine formulations from both manufacturers. The multiplex assay demonstrated good specificity, reproducibility and absence of cross-reactivity. Analysis of over and underdosed formulations, heat and H2O2-degraded products as well as batch to batch consistency of vaccines from both manufacturers brought the proof of concept for a future application of the multiplex immunoassay as a useful tool in the frame of DTaP vaccine quality control.

Production, optimization, and purification of alkaline thermotolerant protease from newly isolated Phalaris minor seeds

The present work aims to purify and perform a preliminary analysis on a thermostable serine alkaline protease from a recently identified P. minor. The enzyme was purified 2.7-fold with a 12.4 % recovery using Sephadex G-100 chromatography, DEAE-cellulose, and ammonium sulphate precipitation. The isolated enzyme has a specific activity of 473 U/mg. The purified protease had a molecular mass of 29 kDa, and just one band was seen, which matched the band obtained using SDS-PAGE. High thermostability was demonstrated by the enzymes, which had half-lives of 31.79 and 6.0 min (a 5.3-fold improvement), enthalpies of denaturation (ΔH°) of 119.53 and 119.35 KJ mol^-1, entropies of denaturation (ΔS°) of 32.96 and 41.11 J/mol·K, and free energies of denaturation (ΔG°) of 108.87 and 105.58 KJ mol^-1 for the protease enzyme. Studies on the folding and stability of alkaline proteases are important since their use in biotechnology requires that they operate in settings of extreme pH and temperature. According to the kinetic and thermodynamic properties, the protease produced by P. minor is superior to that produced by other sources and previously described plants, and it might find utility in a variety of industrial fields.

Folding of heterologous proteins in bacterial cell factories: Cellular mechanisms and engineering strategies

The expression of correctly folded and functional heterologous proteins is important in many biotechnological production processes, whether it is enzymes, biopharmaceuticals or biosynthetic pathways for production of sustainable chemicals. For industrial applications, bacterial platform organisms, such as E. coli, are still broadly used due to the availability of tools and proven suitability at industrial scale. However, expression of heterologous proteins in these organisms can result in protein aggregation and low amounts of functional protein. This review provides an overview of the cellular mechanisms that can influence protein folding and expression, such as co-translational folding and assembly, chaperone binding, as well as protein quality control, across different model organisms. The knowledge of these mechanisms is then linked to different experimental methods that have been applied in order to improve functional heterologous protein folding, such as codon optimization, fusion tagging, chaperone co-production, as well as strain and protein engineering strategies.

Heat treatment in the presence of arginine increases the emulsifying properties of soy proteins

This study aimed to improve the emulsifying properties of commercial soy protein isolates (CSPIs). CSPIs were thermally denatured without additives (CSPI_H) and with arginine (CSPI_A), urea (CSPI_U), and guanidine hydrochloride (CSPI_G), which improve protein solubility to prevent aggregation. These additives were removed by dialysis, and the samples were lyophilized. CSPI_A resulted in high emulsifying properties. FT-IR analysis showed that the β-sheet content in CSPI_A was reduced compared to that of untreated CSPI (CSPI_F). Fluorescence analysis showed that the tryptophan-derived emission peak of CSPI_A shifted between CSPI_F and CSPI_H which was exposed to hydrophobic amino acid chains with aggregation. As a result, the structure of CSPI_A became moderately unfolded and exposed the hydrophobic amino acid chains without aggregation. The CSPI_A solution had a more reduced oil-water interface tension than other CSPIs. These results support that CSPI_A attaches efficiently to the oil-water interface and produces small, less flocculated emulsions.

Fabrication and Bioactivity of Peptide-Conjugated Biomaterial Tissue Engineering Constructs

Tissue engineering combines materials engineering, cells and biochemical factors to improve, restore or replace various types of biological tissues. A nearly limitless combination of these strategies can be combined, providing a means to augment the function of a number of biological tissues such as skin tissue, neural tissue, bones, and cartilage. Compounds such as small molecule therapeutics, proteins, and even living cells have been incorporated into tissue engineering constructs to influence biological processes at the site of implantation. Peptides have been conjugated to tissue engineering constructs to circumvent limitations associated with conjugation of proteins or incorporation of cells. This review highlights various contemporary examples in which peptide conjugation is used to overcome the disadvantages associated with the inclusion of other bioactive compounds. This review covers several peptides that are commonly used in the literature as well as those that do not appear as frequently to provide a broad scope of the utility of the peptide conjugation technique for designing constructs capable of influencing the repair and regeneration of various bodily tissues. Additionally, a brief description of the construct fabrication techniques encountered in the covered examples and their advantages in various tissue engineering applications is provided.

Optimization of amylase production using response surface methodology from newly isolated thermophilic bacteria

Present study was aimed at screening and characterizing thermostable amylase-producing bacteria from water and sediment samples of unexplored hot spring of Tatta Pani Kotli Azad Kashmir. Four thermophilic isolates were characterized on morphological, biochemical, physiological basis and were authenticated by molecular analysis. By 16S rDNA sequencing, isolates were identified as Anoxybacillus mongoliensis (MBT001), Anoxybacillus flavithermus (MBT002), Bacillus (MBT004). Among all identified strains, MBT003 showed maximum homology with both Anoxybacillus mongoliensis and Anoxybacillus flavithermus. Amylase activity was analyzed qualitatively in starch agar and quantitatively by DNS method. The optimal enzyme production was observed and authenticated by Response Surface Methodology at 7 pH, 70 °C, 1.25% substrate concentration, 300 μL of inocula volume after 48 h of incubation. Optimum amylase activity (4.4 U/mL) and stability (3.3 U/mL) was observed with 1.5% soluble starch at 70 °C. Maximum activity (3.7 U/mL) and stability (1.5 U/mL) was found at pH 8. Enzyme activity was increased in the presence of MgSO4 and CaCl2. Amylase was stable with surfactants and commercial detergents for 30 min. Supplementation of the enzyme with commercial detergent improved the washing ability of the detergent. This investigation has revealed that these thermostable bacteria are excellent source of amylase which can be used commercially for generating economic activity on sustainable basis.

Using Intrinsic Fluorescence to Measure Protein Stability Upon Thermal and Chemical Denaturation

Understanding how point mutations affect the performance of protein stability has been the focus of several studies all over the years. Intrinsic fluorescence is commonly used to follow protein unfolding since during denaturation, progressive redshifts on tryptophan fluorescence emission are observed. Since the unfolding process (achieved by chemical or physical denaturants) can be considered as two-state N➔D, it is possible to utilize the midpoint unfolding curves (fU = 50%) as a parameter to evaluate if the mutation destabilizes wild-type protein. The idea is to determine the [D]_1/2 or T_m values from both wild type and mutant and calculate the difference between them. Positive values indicate the mutant is less stable than wild type.

Atomic Force Microscopy Study of the Temperature and Storage Duration Dependencies of Horseradish Peroxidase Oligomeric State

This paper presents an investigation of the temperature dependence of the oligomeric state of the horseradish peroxidase (HRP) enzyme on the temperature of its solution, and on the solution storage time, at the single-molecule level. Atomic force microscopy has been employed to determine how the temperature and the storage time of the HRP solution influence its aggregation upon direct adsorption of the enzyme from the solution onto bare mica substrates. In parallel, spectrophotometric measurements have been performed in order to estimate whether the HRP enzymatic activity changes over time upon the storage of the enzyme solution. The temperature dependence of the HRP oligomeric state has been studied within a broad (15–40 °C) temperature range. It has been demonstrated that the storage of the HRP solution for 14 days does not have any considerable effect on the oligomeric state of the enzyme, neither does it affect its activity. At longer storage times, AFM has allowed us to reveal a tendency of HRP to oligomerization during the storage of its buffered solution, while the enzymatic activity remains virtually unchanged even after a 1-month-long storage. By AFM, it has been revealed that after the incubation of a mica substrate in the HRP solution at various temperatures, the content of the mica-adsorbed oligomers increases insignificantly owing to a high-temperature stability of the enzyme.

An SPR-based method for Hill coefficient measurements: the case of insulin-degrading enzyme

Insulin-degrading enzyme (IDE) is a highly conserved zinc metallopeptidase and is capable to catalytically cleave several substrates besides insulin, playing a pivotal role in several different biochemical pathways. Although its mechanism of action has been widely investigated, many conundrums still remain, hindering the possibility to rationally design specific modulators which could have important therapeutical applications in several diseases such as diabetes and Alzheimer's disease. In this scenario, we have developed a novel surface plasmon resonance (SPR) method which allows for directly measuring the enzyme cooperativity for the binding of insulin in the presence of different IDE activity modulators: carnosine, ATP, and EDTA. Results indicate that both positive and negative modulations of the IDE activity can be correlated to an increase and a decrease of the measured Hill coefficient, respectively, giving a new insight into the IDE activity mechanism. The use of the IDE R767A mutant for which oligomerization is hindered confirmed that the positive allosteric modulation of IDE by carnosine is due to a change in the enzyme oligomeric state occurring also for the enzyme immobilized on the gold SPR chip.

Microwave-induced biocatalytic reactions toward medicinally important compounds

Microwaves in the presence of enzymes are used to execute a number of reactions for the preparation of biologically active compounds. The success of microwave-induced enzymatic reactions depends on frequencies, field strength, waveform, duration, and modulation of the exposure. Enzymes under microwave irradiation become activated and this activation is sufficient to investigate simple to complex reactions that were not reported under these reaction conditions before. Enzymatic catalysis together with microwave technology and solvent-free chemical reaction is a nature-friendly procedure. The most interesting reactions that are performed by enzymes in the microwave are documented here with reference to examples that are related to medicinally active molecules.

CRISPR/Cas12a-based fluorescence immunoassay: combination of efficient signal generation with specific molecule recognition

The sensing strategy ingeniously combines the efficient signal generation of the CRISPR/Cas12a system with antigen–antibody-specific recognition.

Structural Alterations of Antigens at the Material Interface: An Early Decision Toolbox Facilitating Safe-by-Design Nanovaccine Development

Nanomaterials have found extensive interest in the development of novel vaccines, as adjuvants and/or carriers in vaccination platforms. Conjugation of protein antigens at the particle surface by non-covalent adsorption is the most widely used approach in licensed particulate vaccines. Hence, it is essential to understand proteins' structural integrity at the material interface in order to develop safe-by-design nanovaccines. In this study, we utilized two model proteins, the wild-type allergen Bet v 1 and its hypoallergenic fold variant (BM4), to compare SiO2 nanoparticles with Alhydrogel® as particulate systems. A set of biophysical and functional assays including circular dichroism spectroscopy and proteolytic degradation was used to examine the antigens' structural integrity at the material interface. Conjugation of both biomolecules to the particulate systems decreased their proteolytic stability. However, we observed qualitative and quantitative differences in antigen processing concomitant with differences in their fold stability. These changes further led to an alteration in IgE epitope recognition. Here, we propose a toolbox of biophysical and functional in vitro assays for the suitability assessment of nanomaterials in the early stages of vaccine development. These tools will aid in safe-by-design innovations and allow fine-tuning the properties of nanoparticle candidates to shape a specific immune response.

Unfolding Mechanisms and Conformational Stability of the Dimeric Endophilin N-BAR Domain

Endophilin, which is a member of the Bin-amphiphysin-Rvs (BAR) domain protein superfamily, contains a homodimeric N-BAR domain of a characteristic crescent shape. The N-BAR domain comprises a six-helix bundle and is known to sense and generate membrane curvature. Here, we characterize aspects of the unfolding mechanism of the endophilin A1 N-BAR domain during thermal denaturation and examine factors that influence the thermal stability of this domain. Far-UV circular dichroism (CD) spectroscopy was applied to monitor changes in the secondary structure above room temperature. The protein's conformational changes were further characterized through Foerster resonance energy transfer and cross-linking experiments at varying temperatures. Our results indicate that thermal unfolding of the endophilin N-BAR is (minimally) a two-step process, with a dimeric intermediate that displays partial helicity loss. Furthermore, a thermal shift assay and temperature-dependent CD were applied to compare the unfolding processes of several truncated versions of endophilin. The melting temperature of the N-BAR domain decreased when we deleted either the N-terminal H0 helix or the unstructured linker of endophilin. This result suggests that these intrinsically disordered domains may play a role in structurally stabilizing the functional N-BAR domain in vivo. Finally, we show that single-site mutations can also compromise endophilin's thermal stability.

Aspartic protease-pepstatin A interactions: Structural insights on the thermal inactivation mechanism

Aspartic proteases are the targets for structure-based drug design for their role in physiological processes and pharmaceutical applications. Structural insights into the thermal inactivation mechanism of an aspartic protease in presence and absence of bound pepstatin A have been obtained by kinetics of thermal inactivation, CD, fluorescence spectroscopy and molecular dynamic simulations. The irreversible thermal inactivation of the aspartic protease comprised of loss of tertiary and secondary structures succeeded by the loss of activity, autolysis and aggregation The enthalpy and entropy of thermal inactivation of the enzyme in presence of pepstatin A increased from 81.2 to 148.5 kcal mol^-1, and from 179 to 359 kcal mol^-1 K^-1 respectively. Pepstatin A shifted the mid-point of thermal inactivation of the protease from 58 °C to 77 °C. The association constant (K) for pepstatin A with aspartic protease was 2.5 ± 0.3 × 10 ⁵ M^-1 and ΔG^o value was -8.3 kcal mol^-1. Molecular dynamic simulation studies were able to delineate the role of pepstatin A in stabilizing backbone conformation and side chain interactions. In the Cα-backbone, the short helical segments and the conserved glycines were part of the most unstable segments of the protein. Understanding the mechanism of thermal inactivation has the potential to develop re-engineered thermostable proteases.

Investigating thermal stability based on the structural changes of lactase enzyme by several orthogonal methods

Thermal stability of lactase (β-galactosidase) enzyme has been studied by a variety of physico-chemical methods. β-galactosidase is the main active ingredient of medications for lactose intolerance. It is typically produced industrially by the Aspergillus oryzae filamentous fungus. Lactase was used as a model to help understand thermal stability of enzyme-type biopharmaceuticals. Enzyme activity (hydrolyzation of lactose) of β-galactosidase was determined after storing the solid enzyme substance at various temperatures. For a better understanding of the relationship between structure and activity changes we determined the mass and size of the molecules with gel electrophoresis and dynamic light scattering and detected aggregation processes. A bottom-up proteomic procedure was used to determine the primary amino acid sequence and to investigate changes in the N-glycosylation pattern of the protein. NMR and CD spectroscopic methods were used to observe changes in higher order structures and to reveal relationships between structural and functional changes.

Self-reconfigurable high-weight-per-volume-gelatin films for all-solution-processed on-skin electronics with ultra-conformal contact

Although conventional skin-attachable electronics exhibit good functionalities, their direct attachment (without any adhesive) to human skin with sufficient conformal contact is challenging. Herein, all-solution-processed on-skin electronics based on self-reconfigurable high-weight-per- volume-gelatin (HWVG) film constructed using an effective, biocompatible water absorption-evaporation technique are demonstrated. Completely conformal contact of self-reconfigurable HWVG films is realized by rapidly inducing anisotropic swelling in the perpendicular direction and covering any curvature on the skin without spatial gap or void after shrinking. A sufficiently thin HWVG film (~2 um) exhibited higher adhesion owing to van der Waals force and the carboxylic acid and amine groups in HWVG film form cross-linkages through intermolecular bonds with human skin. Self-reconfigurable HWVG films with high biocompatibility are optimized to afford a superior efficiency of 87.83 % at a concentration of 20 % (w/v) and a storage modulus of 1822 MPa at 36.5 °C. Furthermore, functional nanoelectrodes consisting of self-reconfigurable silver nanowires/HWVG films for high-performance on-skin sensors allowing the detection of sensitive motion and electrophysiological signals, as well as an armband-type sensor system incorporated with a smartphone for health-care monitoring are demonstrated. Outstanding performances, including stability, reliability, flexibility, re-usability, biocompatibility, and permeability of on-skin electronics based on HWVG films can open-up a prospective route to realizing breathable human-machine interfaces based on biocompatible materials and processes.

Microwave Drying for Production of Rehydrated Foods: A Case Study of Stink Bean (Parkia speciosa) Seed

The potential of microwave drying in the production of rehydrated foods is demonstrated with stink beans (Parkia speciosa), smelly legumes of Africa and Asia. Compared to stink beans dehydrated by convective drying and freeze drying, the microwave products exhibit higher moisture contents, but the distribution of microscopic pores leads to good rehydration characteristics. Dehydration by microwave drying is also achieved within a much shorter period than that commonly used in freeze drying. The dehydration time can be further reduced to 6 h comparable to convective drying, and the moisture content is dropped to 11% by decreasing the pressure during microwave drying. However, the rehydration time remains around 65 min for products from both ambient and low-pressure (400 Pa) microwave drying. In rehydration, the period is successfully reduced to 30 min by increasing the water temperature to 70 °C. The results indicate that microwave drying does not affect the value of crude protein and rehydrated products are comparable to fresh stink beans. From these findings, the microwave drying technique is an applicable technology for both manufacturers and consumers, with acceptable drying time and rehydration characteristics.

Investigating the thermodynamic and kinetics properties of acid phosphatase extracted and purified from seedlings of Chenopodium murale

Herein acid phosphatase isoenzyme was extracted from the C. murale seedlings. The purification was accomplished by chromatographic techniques and passing through DEAE-cellulose and Sephadex G-100 column. The specific activity of acid phosphatase 5.75 U/mg of protein was obtained with 66 purification fold 15.8% yield and molecular mass was 29 kDa with very faint bands corresponding to 18 kDa and 14 kDa. The maximal activity at pH 5.0 and 50 °C best illustrated by first order kinetics. When temperature was raised (55 °C to 75 °C), the deactivation rate constant was increased from 0.001 to 0.014 min^-1, while half-life was decreased from 693 to 49 min^-1. The results of activity collected at different temperature were then used to estimate, activation energy of hydrolysis reaction (Ea = 47.59 kJmol^-1). A high Z-value (18.86 °C min^-1) was obtained indicating a less sensitivity towards temperatures. The residual activity examinations were carried out from 55 °C to 75 °C and assessing the Deactivation Energy (Ed 116.39 kJmol^-1), Enthalpy change (ΔH° 113.55kJmol^-1), Entropy change (ΔS° 110.33kJmol^-1) and change in Gibbs free energy (ΔG° 10.02 kJmol^-1). Taken together, thermodynamic parameters confirm the high stability of enzyme and show potential commercial applicability.

Following Structural Changes by Thermal Denaturation Using Trapped Ion Mobility Spectrometry-Mass Spectrometry

The behavior of biomolecules as a function of the solution temperature is often crucial to assessing their biological activity and function. While heat-induced changes of biomolecules are traditionally monitored using optical spectroscopy methods, their conformational changes and unfolding transitions remain challenging to interpret. In the present work, the structural transitions of bovine serum albumin (BSA) in native conditions (100 mM aqueous ammonium acetate) were investigated as a function of the starting solution temperature (T ∼ 23-70 °C) using a temperature-controlled nanoelectrospray ionization source (nESI) coupled to a trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) instrument. The charge state distribution of the monomeric BSA changed from a native-like, narrow charge state ([M + 12H]12+ to [M + 16H]16+ at ∼23 °C) and narrow mobility distribution toward an unfolded-like, broad charge state (up to [M + 46H]46+ at ∼70 °C) and broad mobility distribution. Inspection of the average charge state and collision cross section (CCS) distribution suggested a two-state unfolding transition with a melting temperature Tm ∼ 56 ± 1 °C; however, the inspection of the CCS profiles at the charge state level as a function of the solution temperature showcases at least six structural transitions (T1-T7). If the starting solution concentration is slightly increased (from 2 to 25 μM), this method can detect nonspecific BSA dimers and trimers which dissociate early (Td ∼ 34 ± 1 °C) and may disturb the melting curve of the BSA monomer. In a single experiment, this technology provides a detailed view of the solution, protein structural landscape (mobility vs solution temperature vs relative intensity for each charge state).

Denaturant Induced Equilibrium Unfolding and Conformational Transitional Studies of Germinated Fenugreek β-Amylase Revealed Molten Globule like State at Low pH

BACKGROUND

β-Amylase (EC 3.2.1.2) is a maltogenic enzyme, which releases β-maltose from the non-reducing end of the substrates. The enzyme plays important roles for the production of vaccine, maltiol and maltose rich syrups. Apart from these applications the enzyme protects cells from abiotic as well as oxidative damage. The enzyme is βwell characterized in βplants and microbes and crystal structures of β-amylases βhave been βobtained from sweet potato, soybean and Bacillus cereus.

OBJECTIVE

Find out correlation between structural and functional stability induced by change in pH, temperature and chaotropes.

METHODS

Activity, intrinsic fluorescence, extrinsic fluorescence, near- and far- ultraviolet circular dichroism spectroscopic measurements were performed.

RESULTS

Peaks about 208 nm and 222 nm obtained by near-ultraviolet circular dichroism correspond to α-helix whereas peak at 215 nm shows presence of β-sheet. At pH 2.0, absence of tertiary structures, exposed of hydrophobic regions and presence of substantial secondary structures, revealed the existence of molten globule like state. Temperature induced denaturation studies showed that the enzyme was stable up to 75 ºC and the process was found to be irreversible in nature. Chaotropes dependent equilibrium unfolding studies revealed that at low concentration of chaotropes, ellipticity and intrinsic fluorescence βintensity were βdecreased βwhereas βenzymatic activity remained unchanged, which revealed fenugreek β-amylase is multi-domains enzyme and catalytic βdomain βis more βstable compare to non-catalytic domain. Moreover, the transition was sigmoidal and non-coincidental.

CONCLUSION

Results indicate the probable existence of intermediate states that might perform significant role in physiological process and biotechnological applications.

Towards Controlling the Reactivity of Enzymes in Mechanochemistry: Inert Surfaces Protect β-Glucosidase Activity During Ball Milling

The activity of β-glucosidases-the enzymes responsible for the final step in the enzymatic conversion of cellulose to glucose-can be maintained and manipulated under mechanochemical conditions in the absence of bulk solvent, either through an unexpected stabilization effect of inert surfaces, or by altering the enzymatic equilibrium. The reported results illustrate unique aspects of mechanoenzymatic reactions that are not observable in conventional aqueous solutions. They also represent the first reported strategies to enhance activity and favor either direction of the reaction under mechanochemical conditions.

Bacterial sugar-binding protein as a one-step affinity purification tag on dextran-containing resins

Marinobacter hydrocarbonoclasticus is an oil-eating bacterium that possesses a large adhesion protein (MhLap) with the potential to bind extracellular ligands. One of these ligand-binding modules is the ~20-kDa PA14 domain (MhPA14) that has affinity for glucose-based carbohydrates. Previous studies showed this sugar-binding domain is retained on dextran-based size-exclusion resins during chromatography, requiring the introduction of glucose or EDTA to remove the protein from the column. Given the ready availability of such size-exclusion resins in biochemistry laboratories, this study explores the use of MhPA14 as an affinity tag for recombinant protein purification. Two different fusion proteins were tested: 1) Green fluorescent protein (GFP) linked to the N-terminus of the MhPA14 tag; and 2) the ice-binding domain from the Marinomonas primoryensis ice-binding protein (MpIBD) linked to the MhPA14 C-terminus by a TEV cut site. The GFP_MhPA14 fusion visibly bound to Superdex, Sephadex, and Sephacryl resins, but did not bind to Sepharose. Using Superdex resin, dextran-affinity purification proved to be an effective one-step purification strategy for both proteins, superior to even nickel-affinity chromatography. Dextran-affinity chromatography was also the most effective method of separating the MhPA14 tag from MpIBD following TEV proteolysis, as compared to both nickel-affinity and ice-affinity methods. These results indicate that MhPA14 has potential for widespread use in recombinant protein purification.

pH-Dependent Thermal Stability of Vibrio cholerae L-asparaginase

BACKGROUND

pH is one of the decisive macromolecular properties of proteins that significantly affects enzyme structure, stability and reaction rate. Change in pH may protonate or deprotonate the side group of aminoacid residues in the protein, thereby resulting in changes in chemical and structural features. Hence studies on the kinetics of enzyme deactivation by pH are important for assessing the bio-functionality of industrial enzymes. L-asparaginase is one such important enzyme that has potent applications in cancer therapy and food industry.

OBJECTIVE

The objective of the study is to understand and analyze the influence of pH on deactivation and stability of Vibrio cholerae L-asparaginase.

METHODS

Kinetic studies were conducted to analyze the effect of pH on stability and deactivation of Vibrio cholerae L-asparaginase. Circular Dichroism (CD) and Differential Scanning Calorimetry (DSC) studies have been carried out to understand the pH-dependent conformational changes in the secondary structure of V. cholerae L-asparaginase.

RESULTS

The enzyme was found to be least stable at extreme acidic conditions (pH< 4.5) and exhibited a gradual increase in melting temperature from 40 to 81 °C within pH range of 4.0 to 7.0. Thermodynamic properties of protein were estimated and at pH 7.0 the protein exhibited ΔG37of 26.31 kcal mole-1, ΔH of 204.27 kcal mole-1 and ΔS of 574.06 cal mole-1 K-1.

CONCLUSION

The stability and thermodynamic analysis revealed that V. cholerae L-asparaginase was highly stable over a wide range of pH, with the highest stability in the pH range of 5.0-7.0.

Insight into the structural stability of wild-type and histidine mutants in Pin1 by experimental and computational methods

Pin1, a polypeptide proline isomerase parvulin, plays a key role in Alzheimer's disease (AD), common tumors and cancers. Two conservative histidine residues, His59 and His157, are important for maintaining the stability of the PPIase domain. Hence multiple spectral and computational techniques were performed to investigate the potential mechanism of two histidine residues. Thermal denaturation indicated that both residues His59 and His157 are not sensitive to the lower temperatures, while residue His59 is more sensitive to the higher temperatures than residue His157. Acidic denaturation suggested that influences of both residues His59 and His157 to acidic stability were the difference from Pin1-WT. ANS and RLS spectra hinted that there was no significant effect on hydrophobic change and aggregation by histidine mutations. The GndHCl-induced denaturation implied that residues His59 and His157 contributed the most to the chemical stability. MD simulations revealed that residues His59 and His157 mutations resulted in that the hydrogen bond network of the dual histidine motif was destroyed wholly. In summary, these histidine residues play an important role in maintaining the structural stability of the PPIase domain.

Spectroscopic probing of the refolding of an unfolded protein through the formation of mixed-micelles

We report the unfolding of the globular protein, Bovine Serum Albumin (BSA) induced by anionic surfactant sodium dodecyl sulfate (SDS) and subsequently monitored the refolding of this denatured BSA using triblock copolymers F127 and P123 through the formation of mixed micelles. Our study exclusively represents the reversibility of this unfolding-refolding process using pluronic triblock copolymers F127/P123 as refolding agents. We confirm the recovery of its native state from its denatured state estimating the α-helical structure of the denatured protein from the CD data which support our steady state fluorescence spectra monitoring the fluorescence of the intrinsic Trp molecules present in BSA. Time resolved study also corroborates the stepwise recovery of the denatured BSA as well as the reversibility of the processes. Isothermal Titration Calorimetry (ITC) data explain the negligible interactions between the triblock copolymers and the native state of BSA. The high binding constant of SDS and triblock copolymers probably play the crucial role in the stepwise recovery of the unfolded BSA followed by reversibility of the refolding processes through the formation of the mixed micelles. The mechanism of mixed-micelle formation has been substantiated by the fact that the Guanidine Hydrochloride denatured BSA does not react with F127/P123 whereby no recovery of the protein was observed.

The Molecular Basis for Apolipoprotein E4 as the Major Risk Factor for Late-Onset Alzheimer's Disease

Apolipoprotein E4 (ApoE4) is one of three (E2, E3 and E4) human isoforms of an α-helical, 299-amino-acid protein. Homozygosity for the ε4 allele is the major genetic risk factor for developing late-onset Alzheimer's disease (AD). ApoE2, ApoE3 and ApoE4 differ at amino acid positions 112 and 158, and these sequence variations may confer conformational differences that underlie their participation in the risk of developing AD. Here, we compared the shape, oligomerization state, conformation and stability of ApoE isoforms using a range of complementary biophysical methods including small-angle x-ray scattering, analytical ultracentrifugation, circular dichroism, x-ray fiber diffraction and transmission electron microscopy We provide an in-depth and definitive study demonstrating that all three proteins are similar in stability and conformation. However, we show that ApoE4 has a propensity to polymerize to form wavy filaments, which do not share the characteristics of cross-β amyloid fibrils. Moreover, we provide evidence for the inhibition of ApoE4 fibril formation by ApoE3. This study shows that recombinant ApoE isoforms show no significant differences at the structural or conformational level. However, self-assembly of the ApoE4 isoform may play a role in pathogenesis, and these results open opportunities for uncovering new triggers for AD onset.

Graphene-Based Smart Platforms for Combined Cancer Therapy

The extensive research of graphene and its derivatives in biomedical applications during the past few years has witnessed its significance in the field of nanomedicine. Starting from simple drug delivery systems, the application of graphene and its derivatives has been extended to a versatile platform of multiple therapeutic modalities, including photothermal therapy, photodynamic therapy, magnetic hyperthermia therapy, and sonodynamic therapy. In addition to monotherapy, graphene-based materials are widely applied in combined therapies for enhanced anticancer activity and reduced side effects. In particular, graphene-based materials are often designed and fabricated as "smart" platforms for stimuli-responsive nanocarriers, whose therapeutic effects can be activated by the tumor microenvironment, such as acidic pH and elevated glutathione (termed as "endogenous stimuli"), or light, magnetic, or ultrasonic stimuli (termed as "exogenous stimuli"). Herein, the recent advances of smart graphene platforms for combined therapy applications are presented, starting with the principle for the design of graphene-based smart platforms in combined therapy applications. Next, recent advances of combined therapies contributed by graphene-based materials, including chemotherapy-based, photothermal-therapy-based, and ultrasound-therapy-based synergistic therapy, are outlined. In addition, current challenges and future prospects regarding this promising field are discussed.

Computational insights into pH-dependence of structure and dynamics of pyrazinamidase: A comparison of wild type and mutants

The mycobacterial enzyme pyrazinamidase (PZase) is the target of key tuberculosis drug, pyrazinamide. Mutations in PZase cause drug resistance. Herein, three point mutations, W68G, L85P, and V155G, were investigated through over 8 µs of molecular dynamics simulations coupled with essential dynamics and binding pocket analysis at neutral (pH = 7) and acidic (pH = 4) ambient conditions. The 51-71 flap region exhibited drastic displacement leading to enlargement of binding cavity, especially at the lower pH. Accessibility of solvent to the active site of the mutant enzymes was also reduced. The protonation of key surface residues at low pH results in more contribution of these residues to structural stability and integrity of the enzyme and reduced interactions with solvent molecules, which acts as a cage, keeping the enzyme together. The observed results suggest a pattern of structural alterations due to point mutations in PZase, which is consistent with other experimental and theoretical investigations and, can be harnessed for drug design purposes.

Screening of Neem extracts for microbial anti-chaperone activity by employing in vitro enzyme refolding assay

Microbial heat shock proteins (Hsps) play an important role in pathogenesis and development of resistance to existing drugs. New compounds that target microbial molecular chaperones have the potential of combating the challenge of anti-microbial resistance. The present study was aimed at assessing the employment of in vitro enzyme refolding assay to detect anti-chaperone activity of Neem (Azadirachta indica) extracts. Protein extracts of thermotolerant Escherichia coli cells were used as a source of Hsps or chaperones. Thermotolerance was found to be induced by pre-treating E. coli cells at 47 °C before subjecting them to a lethal temperature of 55 °C. This thermotolerance correlated with over-expression of specific proteins and reduced aggregation as evident from the SDS-PAGE profiles. Refolding assays of denatured enzymes exhibited 45% activity regain in presence of cell protein extracts containing chaperones compared to less than 5% regain in BSA negative controls. The chaperone activity was found to be ATP dependent. Addition of Neem extracts to refolding reaction mixtures distinctly reduced the activity regain (20%) in a dose dependent manner (500 and 1000 ppm). The negative influence of plant extract on refolding of the enzyme in the presence of chaperones gives evidence to its anti-chaperone activity. We propose that the employment of in vitro enzyme refolding assays will help not only to analyze the activity of known and putative chaperones but also to screen natural compounds for anti-microbial-Hsp activity.

Sensitive Detection of Immunoglobulin G Stability Using in Real-Time Isothermal Differential Scanning Fluorimetry: Determinants of Protein Stability for Antibody-Based Therapeutics

Protein instability is a major obstacle in the production and delivery of monoclonal antibody-based therapies for cancer. This study presents real-time isothermal differential scanning fluorimetry as an emerging method to evaluate the stability of human immunoglobulin G protein with high sensitivity. The stability of polyclonal human immunoglobulin G against urea-induced denaturation was assessed following: (1) oxidation by the free-radical generator 2,2-Azobis[2-amidinopropane]dihydrochloride and (2) in selected storage buffers. Significant differences in immunoglobulin G stability were detected by real-time isothermal differential scanning fluorimetry when the immunoglobulin G was stored in 1,4-Piperazinediethanesulfonic acid buffer compared to phosphate-buffered saline, with half-maximal rate of denaturation occurring at a higher urea concentration in 1,4-Piperazinediethanesulfonic acid than phosphate-buffered saline (K_nd;PIPES = 3.56 ± 0.09 M, K_nd;PBS = 2.94 ± 0.08 M; P < .01), but differential scanning fluorimetry did not detect differences in unfolding temperature (T_m;PIPES = 70.5 ± 0.3°C, T_m;PBS = 69.7 ± 0.2°C). The effects of 2,2-Azobis[2-amidinopropane]dihydrochloride-induced oxidation on immunoglobulin G stability were analyzed by real-time isothermal differential scanning fluorimetry; the oxidized protein showed greater sensitivity to urea (K_nd;CNTRL = 3.96 ± 0.19 M, K_nd;AAPH = 3.49 ± 0.07 M; P < .05). Similarly, differential scanning fluorimetry indicated greater thermal sensitivity of oxidized immunoglobulin G (T_m;CNTRL = 70.5 ± 0.3°C, T_m;AAPH = 62.9 ± 0.1°C; P < .001). However, a third method for assessing protein stability, pulse proteolysis, proved to be substantially less sensitive and did not detect significant effects of 2,2-Azobis[2-amidinopropane]dihydrochloride on the half-maximal concentration of urea needed to denature immunoglobulin G (C_m;CNTRL= 6.8 ± 0.1 M; C_m;AAPH = 6.4 ± 0.7 M). Overall these results demonstrate the merit of using real-time isothermal differential scanning fluorimetry as a rapid and sensitive technique for the evaluation of protein stability in solution using a quantitative real-time thermocycler.

Biophysical insight into structure-function relation of Allium sativum Protease Inhibitor by thermal, chemical and pH-induced modulation using comprehensive spectroscopic analysis

In this study, we have analyzed the structural and functional changes in the nature of Allium sativum Protease Inhibitor (ASPI) on undergoing various denaturation with variable range of pH, temperature and urea (at pH 8.2). ASPI being anti-tryptic in nature has native molecular mass of ∼15kDa. The conformational stability, functional parameters and their correlation were estimated under different conditions using circular dichroism, fluorescence and activity measurements. ASPI was found to fall in belongs to α+β protein. It demonstrated structural and functional stability in the pH range 5.0-12.0 and up to70°C temperature. Further decrease in pH and increase in temperature induces unfolding followed by aggregation. Chemical induced denaturation was found to be cooperative and transitions were reversible and sigmoid. T_m (midpoint of denaturation), ΔC_p (constant pressure heat capacity change) and ΔH_m (van't Hoff enthalpy change at T_m were calculated to be 41.25±0.2°C, 1.3±0.07kcalmol^-1K^-1 and 61±2kcalmol^-1 respectively for thermally denatured ASPI earlier. The reversibility of the protein was confirmed for both thermally and chemically denatured ASPI. The results obtained from trypsin inhibitory activity assay and structural studies are found to be in a significant correlation and hence established structure-function relationship of ASPI.