What is the role of thermodynamics on protein stability?

Fluorescence-Based Protein Stability Monitoring-A Review

Proteins are large biomolecules with a specific structure that is composed of one or more long amino acid chains. Correct protein structures are directly linked to their correct function, and many environmental factors can have either positive or negative effects on this structure. Thus, there is a clear need for methods enabling the study of proteins, their correct folding, and components affecting protein stability. There is a significant number of label-free methods to study protein stability. In this review, we provide a general overview of these methods, but the main focus is on fluorescence-based low-instrument and -expertise-demand techniques. Different aspects related to thermal shift assays (TSAs), also called differential scanning fluorimetry (DSF) or ThermoFluor, are introduced and compared to isothermal chemical denaturation (ICD). Finally, we discuss the challenges and comparative aspects related to these methods, as well as future opportunities and assay development directions.

Recombinant pseudorabies virus (PRV) expressing stabilized E2 of classical swine fever virus (CSFV) protects against both PRV and CSFV

Pseudorabies (PR) and classical swine fever (CSF) are economically important infectious diseases of pigs. Most pig farms in China are immunized against these two diseases. Here, we describe a stabilized E2 protein as an immunogen inserted into the PRV genome as a bivalent live virus-vectored vaccine. The E2 protein has 48 variant sites, there are 2-5 candidate amino acids per variant site, and the relative energy contribution of each amino acid to E2 energy was calculated. Combined substitutions of amino acids at the neighbor variant site (neighbor substitution) were performed to obtain the E2 protein sequence with the lowest energy (stabilized E2). Multiple amino acid substitutions at 48 variant sites were performed, and the results were consistent with neighbor substitutions. The stabilized E2 sequence was obtained, and its energy decreased by 22 Rosetta Energy Units (REUs) compared with the original sequence. After the recombinant PRV expressing stabilized E2 of CSFV was constructed, the secretion efficiency of stabilized E2 was increased by 2.97 times, and the thermal stability was increased by 10.5 times. Immunization of mice resulted in a 2-fold increase in antibody production, and a balanced antibody level against subtype 1.1 and subtype 2.1d E2 was achieved. In rabbits immunized, the lethal challenge of PRV-ZJ and the fever response induced by CSFV could be prevented simultaneously. These findings suggest that rPRV-muta/287aaE2 is a promising bivalent vaccine against CSFV and PRV infections.

Ionic Liquid-Based Strategy for Predicting Protein Aggregation Propensity and Thermodynamic Stability

Novel drug candidates are continuously being developed to combat the most life-threatening diseases; however, many promising protein therapeutics are dropped from the pipeline. During biological and industrial processes, protein therapeutics are exposed to various stresses such as fluctuations in temperature, solvent pH, and ionic strength. These can lead to enhanced protein aggregation propensity, one of the greatest challenges in drug development. Recently, ionic liquids (ILs), in particular, biocompatible choline chloride ([Cho]Cl)-based ILs, have been used to hinder stress-induced protein conformational changes. Herein, we develop an IL-based strategy to predict protein aggregation propensity and thermodynamic stability. We examine three key variables influencing protein misfolding: pH, ionic strength, and temperature. Using dynamic light scattering, zeta potential, and variable temperature circular dichroism measurements, we systematically evaluate the structural, thermal, and thermodynamic stability of fresh immunoglobin G4 (IgG4) antibody in water and 10, 30, and 50 wt % [Cho]Cl. Additionally, we conduct molecular dynamics simulations to examine IgG4 aggregation propensity in each system and the relative favorability of different [Cho]Cl-IgG4 packing interactions. We re-evaluate each system following 365 days of storage at 4 °C and demonstrate how to predict the thermodynamic properties and protein aggregation propensity over extended storage, even under stress conditions. We find that increasing [Cho]Cl concentration reduced IgG4 aggregation propensity both fresh and following 365 days of storage and demonstrate the potential of using our predictive IL-based strategy and formulations to radically increase protein stability and storage.

Biochemical and Thermodynamic Studies on a Novel Thermotolerant GH10 Xylanase from Bacillus safensis

Xylanases have a broad range of applications in agro-industrial processes. In this study, we report on the discovery and characterization of a new thermotolerant GH10 xylanase from Bacillus safensis, designated as BsXyn10. The xylanase gene (bsxyn10) was cloned from Bacillus safensis and expressed in Escherichia coli. The reduced molecular mass of BsXyn10 was 48 kDa upon SDS-PAGE. Bsxyn10 was optimally active at pH 7.0 and 60 °C, stable over a broad range of pH (5.0–8.0), and also revealed tolerance toward different modulators (metal cations, EDTA). The enzyme was active toward various xylans with no activity on the glucose-based polysaccharides. K_M, v_max, and k_cat for oat spelt xylan hydrolysis were found to be 1.96 g·L⁻¹, 58.6 μmole·min⁻¹·(mg protein)⁻¹, and 49 s⁻¹, respectively. Thermodynamic parameters for oat spelt xylan hydrolysis at 60 °C were ΔS* = −61.9 J·mol⁻¹·K⁻¹, ΔH* = 37.0 kJ·mol⁻¹ and ΔG* = 57.6 kJ·mol⁻¹. BsXyn10 retained high levels of activity at temperatures up to 60 °C. The thermodynamic parameters (ΔH*_D, ΔG*_D, ΔS*_D) for the thermal deactivation of BsXyn10 at a temperature range of 40–80 °C were: 192.5 ≤ ΔH*_D ≤ 192.8 kJ·mol⁻¹, 262.1 ≤ ΔS*_D ≤ 265.8 J·mol⁻¹·K⁻¹, and 99.9 ≤ ΔG*_D ≤ 109.6 kJ·mol⁻¹. The BsXyn10-treated oat spelt xylan manifested the catalytic release of xylooligosaccharides of 2–6 DP, suggesting that BsXyn10 represents a promising candidate biocatalyst appropriate for several biotechnological applications.

Interaction between phloretin and insulin: a spectroscopic study

Diabetes is among the top ten deadly diseases in the world. It occurs either when the pancreas does not produce enough insulin (INS) or when the body cannot effectively use the insulin it produces. Phloretin (PHL) has a biological effect that can treat diabetes. A spectroscopic study was carried out to explore the interaction between phloretin and insulin. UV/Vis spectroscopy, fluorescence spectroscopy, and circular dichroism spectropolarimeter were used in the study. UV/Vis spectra showed that the interaction between PHL and INS produced strong absorption at a wavelength of 282 nm. The fluorescence analysis results showed that the excitation and emission occurred at 280-nm and 305-nm wavelengths, respectively. Temperature changes did not affect INS emissions. However, the interaction of PHL–INS caused a redshift at 305 to 317 nm. Temperature affected the binding constant (Ka) and the binding site (n). Ka decreased with increasing temperature and increased the binding site. The thermodynamic parameters such as enthalpy (ΔH0) and entropy (ΔS0) each had a value of − 16,514 kJ/mol and 22.65 J/mol·K. PHL and INS interaction formed hydrogen bonds and hydrophobic interaction. The free energy (ΔG0) recorded was negative. PHL and INS interactions took place spontaneously. The quenching effect was dynamic and static. KD values were greater than KS. The higher the temperature, the less was KD and KS. The appearance of two negative signals on circular dichroism (CD) spectropolarimeter implies that phloretin could induce regional configuration changes in insulin. The addition of PHL has revealed that the proportion of α-helix in the insulin stabilizes its structure. Phloretin’s stabilization and enhancement of the α-helix structural configuration in insulin indicate that phloretin can improve insulin resistance.

Identification and computational analysis of mutations in SARS-CoV-2

SARS-CoV-2 infection has become a worldwide pandemic and is spreading rapidly to people across the globe. To combat the situation, vaccine design is the essential solution. Mutation in the virus genome plays an important role in limiting the working life of a vaccine. In this study, we have identified several mutated clusters in the structural proteins of the virus through our novel 2D Polar plot and qR characterization descriptor. We have also studied several biochemical properties of the proteins to explore the dynamics of evolution of these mutations. This study would be helpful to understand further new mutations in the virus and would facilitate the process of designing a sustainable vaccine against the deadly virus.

Recent Progress in the Understanding and Engineering of Coenzyme B12-Dependent Glycerol Dehydratase

Coenzyme B₁₂-dependent glycerol dehydratase (GDHt) catalyzes the dehydration reaction of glycerol in the presence of adenosylcobalamin to yield 3-hydroxypropanal (3-HPA), which can be converted biologically to versatile platform chemicals such as 1,3-propanediol and 3-hydroxypropionic acid. Owing to the increased demand for biofuels, developing biological processes based on glycerol, which is a byproduct of biodiesel production, has attracted considerable attention recently. In this review, we will provide updates on the current understanding of the catalytic mechanism and structure of coenzyme B₁₂-dependent GDHt, and then summarize the results of engineering attempts, with perspectives on future directions in its engineering.

Purification, characterization and anticancer evaluation of l-methioninase from Trichoderma harzianum

The Trichoderma harzianum l-methioninase was purified 7.15-fold with a recovery of 47.9% and the specific activity of 74.4 U/mg of protein. The purified enzyme has an apparent molecular mass of 48 kDa on SDS-PAGE and exhibited maximum activity at pH 8 and 35 °C. The enzyme was catalytically stable below 50 °C and at a pH range of 6.0-8.5. The thermal inactivation of l-methioninase exhibited first-order kinetics with the k value between 5.71 × 10-4 min-1 and 1.83 × 10-2 min-1. The studies on thermodynamic parameters of l-methioninase indicated the compaction and aggregation of the enzyme molecule during denaturation. This is the first report of thermodynamic analysis of thermal inactivation in l-methioninase. The enzyme activity was enhanced by Li+ and inhibited by Cu2+, Co2+, Fe2+, Hydroxylamine and PMSF. The purified enzyme showed K m , V max and k cat value of 1.19 mM, 21.27 U/mg/min and 16.11 s-1, respectively. The l-methioninase inhibited the growth of human cell lines hepatocellular carcinoma (Hep-G2) and breast carcinoma (MCF-7) with IC50 values of 14.12 μg/ml and 20.07 μg/ml, respectively. The in vivo antitumor activity of l-methioninase was evaluated against DAL cell lines bearing in Swiss albino mice. The enzyme effectively reduced tumor volume, packed cell volume, viable cell count and restored hematological parameters, serum enzyme and lipid profile to normal levels compared to DAL control mice. The present study has demonstrated the high efficacy of Trichoderma harzianum l-methioninase against cancer cell lines in vitro and in vivo conditions. The purified l-methioninase has significant thermal stability and better catalytic properties than the enzyme purified from other sources.

Catalytic and thermodynamic properties of an acidic α-amylase produced by the fungus Paecilomyces variotii ATHUM 8891

An extracellular acid stable α-amylase from Paecilomyces variotii ATHUM 8891 (PV8891 α-amylase) was purified to homogeneity applying ammonium sulfate fractionation, ion exchange and gel filtration chromatography and exhibited a reduced molecular weight of 75 kDa. The purified enzyme was optimally active at pH 5.0 and 60 °C and stable in acidic pH (3.0-6.0). K _m, v _max and k _cat for starch hydrolysis were found 1.1 g L^-1, 58.5 μmole min^-1 (mg protein)^-1, and 73.1 s^-1, respectively. Amylase activity was marginally enhanced by Ca²⁺ and Fe²⁺ ions while Cu²⁺ ions strongly inhibited it. Thermodynamic parameters determined for starch hydrolysis (Ε _α, ΔH*, ΔG*, ΔS*, Δ G E - S ∗ and Δ G E - T ∗ ) suggests an effective capacity of PV8891 α-amylase towards starch hydrolysis. Thermal stability of PV8891 α-amylase was assessed at different temperatures (30-80 ^οC). Thermodynamic parameters ( E a d , ΔH*, ΔG*, ΔS*) as well as the integral activity of a continuous system for starch hydrolysis by the PV8891 α-amylase revealed satisfactory thermostability up to 60 °C. The acidic nature and its satisfactory performance at temperatures lower than the industrially used amylases may represent potential applications of PV8891 α-amylase in starch processing industry.

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.

Evaluating new bio-hydrogen producers: Clostridium perfringens strain JJC, Clostridium bifermentans strain WYM and Clostridium sp. strain Ade.TY

Three newly discovered H₂ producing bacteria namely Clostridium perfringens strain JJC, Clostridium bifermentans strain WYM and Clostridium sp. strain Ade.TY originated from landfill leachate sludge have demonstrated highly efficient H₂ production. The maximum H₂ production attained from these isolates are in the descending order of strain C. perfringens strain JJC > C. bifermentans strain WYM > Clostridium sp. strain Ade.TY with yield of 4.68 ± 0.12, 3.29 ± 0.11, and 2.87 ± 0.10 mol H₂/mol glucose, respectively. The result has broken the conventional theoretical yield of 4 mol H₂/mol glucose. These isolates were thermodynamically favourable with Gibbs free energy between -33 and -35 kJ/mol (under process conditions: pH 6, 37 °C and 5 g/L glucose). All three isolates favour butyrate pathway for H₂ production with the ratio of acetate and butyrate of 0.77, 0.65 and 0.80 for strain JJC, WYM and Ade.TY, respectively. This study reported provides a new insight on the potential of unique bacteria in H₂ production.

Extraction of Thermodynamic Parameters of Protein Unfolding Using Parallelized Differential Scanning Fluorimetry

Thermodynamic properties of protein unfolding have been extensively studied; however, the methods used have typically required significant preparation time and high protein concentrations. Here we present a facile, simple, and parallelized differential scanning fluorimetry (DSF) method that enables thermodynamic parameters of protein unfolding to be extracted. This method assumes a two-state, reversible protein unfolding mechanism and provides the capacity to quickly analyze the biophysical mechanisms of changes in protein stability and to more thoroughly characterize the effect of mutations, additives, inhibitors, or pH. We show the utility of the DSF method by analyzing the thermal denaturation of lysozyme, carbonic anhydrase, chymotrypsin, horseradish peroxidase, and cellulase enzymes. Compared with similar biophysical analyses by circular dichroism, DSF allows for determination of thermodynamic parameters of unfolding while providing greater than 24-fold reduction in experimental time. This study opens the door to rapid characterization of protein stability on low concentration protein samples.

Characterization of a Hyperthermostable Alkaline Lipase from Bacillus sonorensis 4R

Hyperthermostable alkaline lipase from Bacillus sonorensis 4R was purified and characterized. The enzyme production was carried out at 80°C and 9.0 pH in glucose-tween inorganic salt broth under static conditions for 96 h. Lipase was purified by anion exchange chromatography by 12.15 fold with a yield of 1.98%. The molecular weight of lipase was found to be 21.87 KDa by SDS-PAGE. The enzyme activity was optimal at 80°C with t_1/2 of 150 min and at 90°C, 100°C, 110°C, and 120°C; the respective values were 121.59 min, 90.01 min, 70.01 min, and 50 min. The enzyme was highly activated by Mg and t_1/2 values at 80°C were increased from 150 min to 180 min when magnesium and mannitol were added in combination. The activation energy calculated from Arrhenius plot was 31.102 KJ/mol. At 80–120°C, values of ΔH and ΔG were in the range of 28.16–27.83 KJ/mol and 102.79 KJ/mol to 111.66 KJ/mol, respectively. Lipase activity was highest at 9.0 pH and stable for 2 hours at this pH at 80°C. Pretreatment of lipase with MgSO₄ and CaSO₄ stimulated enzyme activity by 249.94% and 30.2%, respectively. The enzyme activity was greatly reduced by CoCl₂, CdCl₂, HgCl₂, CuCl₂, Pb(NO₃)₂, PMSF, orlistat, oleic acid, iodine, EDTA, and urea.

Temperature responses of the Rubisco maximum carboxylase activity across domains of life: phylogenetic signals, trade-offs, and importance for carbon gain

Temperature response of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalytic properties directly determines the CO2 assimilation capacity of photosynthetic organisms as well as their survival in environments with different thermal conditions. Despite unquestionable importance of Rubisco, the comprehensive analysis summarizing temperature responses of Rubisco traits across lineages of carbon-fixing organisms is lacking. Here, we present a review of the temperature responses of Rubisco carboxylase specific activity (c(cat)(c)) within and across domains of life. In particular, we consider the variability of temperature responses, and their ecological, physiological, and evolutionary controls. We observed over two-fold differences in the energy of activation (ΔH(a)) among different groups of photosynthetic organisms, and found significant differences between C3 plants from cool habitats, C3 plants from warm habitats and C4 plants. According to phylogenetically independent contrast analysis, ΔH(a) was not related to the species optimum growth temperature (T growth), but was positively correlated with Rubisco specificity factor (S(c/o)) across all organisms. However, when only land plants were analyzed, ΔH(a) was positively correlated with both T(growth) and S(c/o), indicating different trends for these traits in plants versus unicellular aquatic organisms, such as algae and bacteria. The optimum temperature (T(opt)) for k(cat)(c) correlated with S(c/o) for land plants and for all organisms pooled, but the effect of T growth on T(opt) was driven by species phylogeny. The overall phylogenetic signal was significant for all analyzed parameters, stressing the importance of considering the evolutionary framework and accounting for shared ancestry when deciphering relationships between Rubisco kinetic parameters. We argue that these findings have important implications for improving global photosynthesis models.

Effect of polyols on thermostability of xylanase from a tropical isolate of Aureobasidium pullulans and its application in prebleaching of rice straw pulp

In an attempt to find a thermostable xylanase enzyme for potential application in the pretreatment prior to H2O2 bleaching of paper pulp for industry, an extracellular xylanase from Aureobasidium pullulans CBS 135684 was purified 17.3-fold to apparent homogeneity with a recovery yield of 13.7%. Its molecular mass was approximately 72 kDa as determined by SDS-PAGE. The optimal pH and temperature for activity of the purified enzyme were pH 6.0 and 70°C, respectively. The enzyme was relatively stable at 50°C, retaining more than half of its original activity after 3-h incubation. The thermostability of the enzyme was improved by the addition of 0.75 mM sorbitol prolonging the enzyme's activity up to 10-fold at 70°C. When the potential of using the enzyme in pretreatment of rice straw pulp prior to bleaching was evaluated, the greatest efficiency was obtained in a mixture containing xylanase and sorbitol. Treatment of the rice straw pulp with xylanase prior to treatment with 10% (v/v) H2O2 and production of hand sheets increased the ISO sheet brightness by 13.5% and increased the tensile and tear strengths of the pulp by up to 1.16 and 1.71-fold, respectively, compared with pulps treated with H2O2 alone. The results suggested the potential application of the enzyme before the bleaching process of paper pulp when the maintenance of high temperature and enzyme stability are desirable.

Conformation change of bovine serum albumin induced by bioactive titanium metals and its effects on cell behaviors

The conformation change of bovine serum albumin (BSA) induced by bioactive titanium surfaces, including acid-alkali-treated titanium (AA-Ti) and alkali-heat-treated titanium (AH-Ti), was studied, and its effects on the activity of MC3T3-E1 cell were evaluated. Pure titanium metal (P-Ti) was used as control. The AA-Ti could adsorb more BSA on its surface than AH-Ti and P-Ti. The α-helix part of the protein adsorbed on P-Ti has weakly decreased compared with native BSA, and it dramatically decreased on AA-Ti and AH-Ti. The β-sheet segment of proteins adsorbed on P-Ti and AH-Ti had obviously increased. Much more tryptophan residues were exposed after the protein conformation changed when it interacted with AH-Ti, and some tryptophan residues were enveloped after it interacted with AA-Ti and P-Ti. AA-Ti has more tryptophan residues enveloped than P-Ti. All titanium surfaces induced tyrosine residues exposed, especially for the P-Ti. The higher ratio of COO(-)/NH3(+) for the proteins on P-Ti and AA-Ti indicated an orientation of proteins on P-Ti and AA-Ti, which makes more COO(-) exposed. The lower ratio of COO(-)/NH3(+) on AH-Ti indicates that more NH3(+) is exposed on its surface. The cell proliferation ability on different treated titanium surfaces coated with BSA followed by the order: P-Ti > AA-Ti > AH-Ti, which indicated that the protein conformation change on different bioactive titanium surfaces has great effect on the cell activity. Our results showed that the different biological response of bioactive titanium metals might depend on the protein conformation change induced by the surface structure.

pH-Dependent aggregation and disaggregation of native β-lactoglobulin in low salt

The aggregation of β-lactoglobulin (BLG) near its isoelectric point was studied as a function of ionic strength and pH. We compared the behavior of native BLG with those of its two isoforms, BLG-A and BLG-B, and with that of a protein with a very similar pI, bovine serum albumin (BSA). Rates of aggregation were obtained through a highly precise and convenient pH/turbidimetric titration that measures transmittance to ±0.05 %T. A comparison of BLG and BSA suggests that the difference between pHmax (the pH of the maximum aggregation rate) and pI is systematically related to the nature of protein charge asymmetry, as further supported by the effect of localized charge density on the dramatically different aggregation rates of the two BLG isoforms. Kinetic measurements including very short time periods show well-differentiated first and second steps. BLG was analyzed by light scattering under conditions corresponding to maxima in the first and second steps. Dynamic light scattering (DLS) was used to monitor the kinetics, and static light scattering (SLS) was used to evaluate the aggregate structure fractal dimensions at different quench points. The rate of the first step is relatively symmetrical around pHmax and is attributed to the local charges within the negative domain of the free protein. In contrast, the remarkably linear pH dependence of the second step is related to the uniform reduction in global protein charge with increasing pH below pI, accompanied by an attractive force due to surface charge fluctuations.