Thermal inactivation and chaperonin-mediated renaturation of mitochondrial aspartate aminotransferase

Regulation by Different Types of Chaperones of Amyloid Transformation of Proteins Involved in the Development of Neurodegenerative Diseases

The review highlights various aspects of the influence of chaperones on amyloid proteins associated with the development of neurodegenerative diseases and includes studies conducted in our laboratory. Different sections of the article are devoted to the role of chaperones in the pathological transformation of alpha-synuclein and the prion protein. Information about the interaction of the chaperonins GroE and TRiC as well as polymer-based artificial chaperones with amyloidogenic proteins is summarized. Particular attention is paid to the effect of blocking chaperones by misfolded and amyloidogenic proteins. It was noted that the accumulation of functionally inactive chaperones blocked by misfolded proteins might cause the formation of amyloid aggregates and prevent the disassembly of fibrillar structures. Moreover, the blocking of chaperones by various forms of amyloid proteins might lead to pathological changes in the vital activity of cells due to the impaired folding of newly synthesized proteins and their subsequent processing. The final section of the article discusses both the little data on the role of gut microbiota in the propagation of synucleinopathies and prion diseases and the possible involvement of the bacterial chaperone GroE in these processes.

Protein purification from Arachis hypogaea in one step: stability studies and anticarcinogenic analysis

The study involved purification of trypsin inhibitor from the seeds of Indian peanuts (Arachis hypogaea), a member of leguminosae family. The inhibitor was purified to homogeneity via three sequential step procedure i.e., salt precipitation to anion-exchange chromatography. The purity and molecular mass was detected using SDS PAGE analysis i.e. ~ 16 kDa. The purified inhibitor termed as Peanut Trypsin Inhibitor (PTI) which inhibits trypsin belonging to serpins family. Anti- neoplastic potential on breast cancer cells (MCF-7) and normal Human Embryonic Kidney cells (HEK) was determined using MTT assay. PTI exhibited IC50 value of ~ 18.412 µg/mL in HEK cells compared to ~ 9.635 µg/mL in MCF-7 cells. The values were quite comparable to curcumin, the standard anticancer drug demonstrating IC50 values of ~ 21.581 µg/mL and ~ 7.135 µg/mL in HEK and MCF-7 respectively. Therefore, we conclude that PTI may be used as supplement along with the conventional drugs for increased efficacy in the treatment of cancer.

Modeling protein folding in vivo

A half century of studying protein folding in vitro and modeling it in silico has not provided us with a reliable computational method to predict the native conformations of proteins de novo, let alone identify the intermediates on their folding pathways. In this Opinion article, we suggest that the reason for this impasse is the over-reliance on current physical models of protein folding that are based on the assumption that proteins are able to fold spontaneously without assistance. These models arose from studies conducted in vitro on a biased sample of smaller, easier-to-isolate proteins, whose native structures appear to be thermodynamically stable. Meanwhile, the vast empirical data on the majority of larger proteins suggests that once these proteins are completely denatured in vitro, they cannot fold into native conformations without assistance. Moreover, they tend to lose their native conformations spontaneously and irreversibly in vitro, and therefore such conformations must be metastable. We propose a model of protein folding that is based on the notion that the folding of all proteins in the cell is mediated by the actions of the "protein folding machine" that includes the ribosome, various chaperones, and other components involved in co-translational or post-translational formation, maintenance and repair of protein native conformations in vivo. The most important and universal component of the protein folding machine consists of the ribosome in complex with the welcoming committee chaperones. The concerted actions of molecular machinery in the ribosome peptidyl transferase center, in the exit tunnel, and at the surface of the ribosome result in the application of mechanical and other forces to the nascent peptide, reducing its conformational entropy and possibly creating strain in the peptide backbone. The resulting high-energy conformation of the nascent peptide allows it to fold very fast and to overcome high kinetic barriers along the folding pathway. The early folding intermediates in vivo are stabilized by interactions with the ribosome and welcoming committee chaperones and would not be able to exist in vitro in the absence of such cellular components. In vitro experiments that unfold proteins by heat or chemical treatment produce denaturation ensembles that are very different from folding intermediates in vivo and therefore have very limited use in reconstructing the in vivo folding pathways. We conclude that computational modeling of protein folding should deemphasize the notion of unassisted thermodynamically controlled folding, and should focus instead on the step-by-step reverse engineering of the folding process as it actually occurs in vivo.

REVIEWERS

This article was reviewed by Eugene Koonin and Frank Eisenhaber.

Preparation of Stable Cross-Linked Enzyme Aggregates (CLEAs) of a Ureibacillus thermosphaericus Esterase for Application in Malathion Removal from Wastewater

In this study, the active and stable cross-linked enzyme aggregates (CLEAs) of the thermostable esterase estUT1 of the bacterium Ureibacillus thermosphaericus were prepared for application in malathion removal from municipal wastewater. Co-expression of esterase with an E. coli chaperone team (KJE, ClpB, and ELS) increased the activity of the soluble enzyme fraction up to 200.7 ± 15.5 U mg−1. Response surface methodology (RSM) was used to optimize the preparation of the CLEA-estUT1 biocatalyst to maximize its activity and minimize enzyme loss. CLEA-estUT1 with the highest activity of 29.4 ± 0.5 U mg−1 (90.6 ± 2.7% of the recovered activity) was prepared with 65.1% (w/v) ammonium sulfate, 120.6 mM glutaraldehyde, and 0.2 mM bovine serum albumin at 5.1 h of cross-linking. The biocatalyst has maximal activity at 80 °С and pH 8.0. Analysis of the properties of CLEA-estUT1 and free enzyme at 50–80 °C and pH 5.0–10.0 showed higher stability of the biocatalyst. CLEA-estUT1 showed marked tolerance against a number of chemicals and high operational stability and activity in the reaction of malathion hydrolysis in wastewater (up to 99.5 ± 1.4%). After 25 cycles of malathion hydrolysis at 37 °С, it retained 55.2 ± 1.1% of the initial activity. The high stability and reusability of CLEA-estUT1 make it applicable for the degradation of insecticides.

Allium sativum Protease Inhibitor: A Novel Kunitz Trypsin Inhibitor from Garlic Is a New Comrade of the Serpin Family

PURPOSE

This study was aimed to purify and characterize the Protease inhibitor (PI) from a plant Allium sativum (garlic) with strong medicinal properties and to explore its phytodrug potentials.

METHODS

Allium sativum Protease Inhibitor (ASPI) was purified using ammonium sulphate fractionation and Fast Protein Liquid Chromatography on anion exchanger Hi-Trap DEAE column. The purified protein was analyzed for its purity and molecular weight by SDS PAGE. The confirmation of presence of trypsin inhibiting PI was performed by MALDI TOF-TOF and analyzed by MASCOT database. The ASPI was further investigated for its kinetic properties and stability under extreme conditions of pH, temperature and chemical denaturants. Secondary structure was determined by Circular Dichorism (CD) spectroscopy.

RESULTS

ASPI of ~15 kDa inhibited trypsin and matched "truncated kunitz Trypsin Inhibitor (Glycine max)" in MASCOT database. The purified ASPI showed 30376.1371 U/mg specific activity with a fold purity of 159.92 and yield ~93%. ASPI was quite stable in the range of pH 2-12 showing a decline in the activity around pH 4-5 suggesting that the pI value of the protein as ASPI aggregates in this range. ASPI showed stability to a broad range of temperature (10-80°C) but declined beyond 80°C. Further, detergents, oxidizing agents and reducing agents demonstrated change in ASPI activity under varying concentrations. The kinetic analysis revealed sigmoidal relationship of velocity with substrate concentration with Vmax 240.8 (μM/min) and Km value of 0.12 μM. ASPI showed uncompetitive inhibition with a Ki of 0.08±0.01 nM). The Far UV CD depicted 2.0% α -helices and 51% β -sheets at native pH.

CONCLUSIONS

To conclude, purified ~15 kDa ASPI exhibited fair stability in wide range of pH and temperature Overall, there was an increase in purification fold with remarkable yield. Chemical modification studies suggested the presence of lysine and tryptophan residues as lead amino acids present in the reactive sites. Therefore, ASPI with trypsin inhibitory property has the potential to be used as a non-cytotoxic clinical agents.

Production of fungal glucoamylase for glucose production from food waste

The feasibility of using pastry waste as resource for glucoamylase (GA) production via solid state fermentation (SSF) was studied. The crude GA extract obtained was used for glucose production from mixed food waste. Our results showed that pastry waste could be used as a sole substrate for GA production. A maximal GA activity of 76.1 ± 6.1 U/mL was obtained at Day 10. The optimal pH and reaction temperature for the crude GA extract for hydrolysis were pH 5.5 and 55 °C, respectively. Under this condition, the half-life of the GA extract was 315.0 minutes with a deactivation constant (kd) 2.20 × 10-3minutes-1. The application of the crude GA extract for mixed food waste hydrolysis and glucose production was successfully demonstrated. Approximately 53 g glucose was recovered from 100 g of mixed food waste in 1 h under the optimal digestion conditions, highlighting the potential of this approach as an alternative strategy for waste management and sustainable production of glucose applicable as carbon source in many biotechnological processes.

Engineering a thermo-stable superoxide dismutase functional at sub-zero to >50°C, which also tolerates autoclaving

Superoxide dismutase (SOD) is a critical enzyme associated with controlling oxygen toxicity arising out of oxidative stress in any living system. A hyper-thermostable SOD isolated from a polyextremophile higher plant Potentilla atrosanguinea Lodd. var. argyrophylla (Wall. ex Lehm.) was engineered by mutation of a single amino acid that enhanced the thermostability of the enzyme to twofold. The engineered enzyme was functional from sub-zero temperature to >50°C, tolerated autoclaving (heating at 121°C, at a pressure of 1.1 kg per square cm for 20 min) and was resistant to proteolysis. The present work is the first example to enhance the thermostability of a hyper-thermostable protein and has potential to application to other proteins for enhancing thermostability.

Study of kinetics of thermal aggregation of mitochondrial aspartate aminotransferase by dynamic light scattering: protective effect of alpha-crystallin

Thermal aggregation of aspartate aminotransferase from pig heart mitochondria (mAAT) has been studied at various temperatures and various protein concentrations by dynamic light scattering. The character of the dependence of protein aggregate size on time indicates that aggregation of mAAT proceeds in the regime of diffusion-limited cluster-cluster aggregation. Suppression of mAAT aggregation by alpha-crystallin is due to transition of the aggregation process into the regime of reaction-limited cluster-cluster aggregation. Realization of this regime of aggregation means that the sticking probability for the colliding particles is less than unity.

Unfolded, oxidized, and thermoinactivated forms of glyceraldehyde-3-phosphate dehydrogenase interact with the chaperonin GroEL in different ways

The interaction of GroEL with different denatured forms of glyceraldehyde-3-phosphate dehydrogenase* (GAPDH) has been investigated. GroEL does not prevent thermal denaturation of GAPDH, but effectively interacts with the thermodenatured enzyme, thus preventing the aggregation of denatured molecules. Binding of the thermodenatured GAPDH shifts the Tm value of the GroEL thermodenaturation curve by 3 degrees towards higher temperatures and increases the DeltaHcal value 1.44-fold, indicating a significant increase in the thermal stability of the resulting complex. GAPDH thermodenatured in the presence of GroEL cannot be reactivated by the addition of GroES, Mg2+, and ATP. In contrast, GAPDH denatured in guanidine hydrochloride (GAPDHden) is reactivated in the presence of GroEL, GroES, Mg2+, and ATP, yielding 11-15% of its original activity, while the spontaneous reactivation yields only 2-3%. The oxidation of GAPDH with hydrogen peroxide in the presence of 4 M guanidine hydrochloride results in the formation of the enzyme (GAPDHox) that cannot acquire its native conformation and binds to GroEL irreversibly. Binding of GAPDHox to one of the GroEL rings completely inhibits the GroEL-assisted reactivation of GAPDHden, but does not affect the GroEL-assisted reactivation of lactate dehydrogenase (LDH). The data suggest that LDH can be successfully reactivated due to the binding of the denatured molecules to the apical domain of the opposite GroEL ring with their subsequent release into the solution without encapsulation (trans-mechanism). In contrast, GAPDH requires the hydrophilic cavity for the reactivation (cis-mechanism).

On the chaperonin activity of GroEL at heat-shock temperature

The studies of GroEL, almost exclusively, have been concerned with the function of the chaperonin under non-stress conditions, and little is known about the role of GroEL during heat shock. Being a heat shock protein, GroEL deserves to be studied under heat shock temperature. As a model for heat shock in vitro, we have investigated the interaction of GroEL with the enzyme rhodanese undergoing thermal unfolding at 43 degrees C. GroEL interacted strongly with the unfolding enzyme forming a binary complex. Active rhodanese (82%) could be recovered by releasing the enzyme from GroEL after the addition of several components, e.g. ATP and the co-chaperonin GroES. After evaluating the stability of the GroEL-rhodanese complex, as a function of the percentage of active rhodanese that could be released from GroEL with time, we found that the complex had a half-life of only one and half-hours at 43 degrees C; while, it remained stable at 25 degrees C for more than 2 weeks. Interestingly, the GroEL-rhodanese complex remained intact and only 13% of its ATPase activity was lost during its incubation at 43 degrees C. Further, rhodanese underwent a conformational change over time while it was bound to GroEL at 43 degrees C. Overall, our results indicated that the inability to recover active enzyme at 43 degrees C from the GroEL-rhodanese complex was not due to the disruption of the complex or aggregation of rhodanese, but rather to the partial loss of its ATPase activity and/or to the inability of rhodanese to be released from GroEL due to a conformational change.

Active rhodanese lacking nonessential sulfhydryl groups contains an unstable C-terminal domain and can be bound, inactivated, and reactivated by GroEL

Mutation of all nonessential cysteine residues in rhodanese turns the enzyme into a form (C3S) that is fully active but less stable than wild type (WT). This less stable mutant allowed testing of two hypotheses; (a) the two domains of rhodanese are differentially stable, and (b) the chaperonin GroEL can bind better to less stable proteins. Reduced temperatures during expression and purification were required to limit inclusion bodies and obtain usable quantities of soluble C3S. C3S and WT have the same secondary structures by circular dichroism. C3S, in the absence of the substrate thiosulfate, is cleaved by trypsin to give a stable 21-kDa species. With thiosulfate, C3S is resistant to proteolysis. In contrast, wild type rhodanese is not proteolyzed significantly under any of the experimental conditions used here. Mass spectrometric analysis of bands from SDS gels of digested C3S indicated that the C-terminal domain of C3S was preferentially digested. Active C3S can exist in a state(s) recognized by GroEL, and it displays additional accessibility of tryptophans to acrylamide quenching. Unlike WT, the sulfur-loaded mutant form (C3S-ES) shows slow inactivation in the presence of GroEL. Both WT and C3S lacking transferred sulfur (WT-E and C3S-E) become inactivated. Inactivation is not due to irreversible covalent modification, since GroEL can reactivate both C3S-E and WT-E in the presence of GroES and ATP. C3S-E can be reactivated to 100%, the highest reactivation observed for any form of rhodanese. These results suggest that inactivation of C3S-E or WT-E is due to formation of an altered, labile conformation accessible from the native state. This conformation cannot as easily be achieved in the presence of the substrate, thiosulfate.

Isolation and characterization of rhodanese intermediates during thermal inactivation and their implications for the mechanism of protein aggregation

The initial steps of heat-induced inactivation and aggregation of the enzyme rhodanese have been studied and found to involve the early formation of modified but catalytically active conformations. These intermediates readily form active dimers or small oligomers, as evident from there being only a small increase in light scattering and an increase in fluorescence energy homotransfer from rhodanese labeled with fluorescein. These species are probably not the domain-unfolded form, as they show activity and increased protection of hydrophobic surfaces. Cross-linking with glutaraldehyde and fractionation by gel filtration show the predominant formation of dimer during heat incubation. Comparison between the rates of aggregate formation at 50 degrees C after preincubation at 25 or 40 degrees C gives evidence of product-precursor relationships, and it shows that these dimeric or small oligomeric species are the basis of the irreversible aggregation. The thermally induced species is recognized by and binds to the chaperonin GroEL. The unfoldase activity of GroEL subsequently unfolds rhodanese to produce an inactive conformation and forms a stable, reactivable complex. The release of 80% active rhodanese upon addition of GroES and ATP indicates that the thermal incubation induces an alteration in conformation, rather than any covalent modification, which would lead to formation of irreversibly inactive species. Once oligomeric species are formed from the intermediates, GroEL cannot recognize them. Based on these observations, a model is proposed for rhodanese aggregation that can explain the paradoxical effect in which rhodanese aggregation is reduced at higher protein concentration.