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In this study, we report a detailed experimental, binding free energy calculation and molecular dynamics (MD) simulation investigation of the interactions of carboxylic-functionalized multi-walled carbon nanotubes (COOH-f-MWCNTs) with porcine trypsin (pTry). The enzyme exhibits decreased thermostability at 330K in the presence of COOH-f-MWCNTs. Furthermore, the activity of pTry also decreases in the presence of COOH-f-MWCNTs. The restricted diffusion of the substrate to the active site of the enzyme was observed in the experiment. The MD simulation analysis suggested that this could be because of the blocking of the S1 pocket of pTry, which plays a vital role in the substrate selectivity. The intrinsic fluorescence of pTry is quenched with increase in the COOH-f-MWCNTs concentration. Circular dichroism (CD) and UV–visible absorption spectroscopies indicate the ability of COOH-f-MWCNTs to experience conformational change in the native structure of the enzyme. The binding free energy calculations also show that electrostatics, π-cation, and π-π stacking interactions play important roles in the binding of the carboxylated CNTs with pTry. The MD simulation results demonstrated that the carboxylated CNTs adsorb to the enzyme stronger than the CNT without the–COOH groups. Our observations can provide an example of the nanoscale toxicity of COOH-f-MWCNTs for proteins, which is a critical issue for in vivo application of COOH-f-MWCNTs. [ABSTRACT FROM AUTHOR]

G-quadruplexes are supramolecular structures of G-rich nucleic acid, formed by non-canonical base pairing in the presence of specific environmental inducers. These structures have been vastly considered in diagnostic and therapeutic applications. However, detailed information on structure, optical properties and thermal stability of G-quadruplex potent oligonucleotides is scarce. Herein, optical properties and thermodynamic stability of AS1411 quadruplex is reported for various concentrations of potassium and lead ions. Circular dichroism showed that AS1411 ss-DNA folds into parallel conformation in the presence of metal ions and molecular crowding condition. UV–vis spectroscopy indicated formation of quadruplex and fluorescent spectroscopy revealed intercalation of PicoGreen in its structure, with enhancement of emission intensity upon increment of metal ion concentration. This investigation also proposes high-throughput and reliable analysis of AS1411 quadruplex's thermal stability by real-time PCR technique, which can be further applied for other quadruplex structures. [ABSTRACT FROM AUTHOR]

In our previous study, we reported an increase in the thermal stability of bacterial laccase from Bacillus sp. HR03 using site-directed mutagenesis. Three-dimensional model of this enzyme showed a negative patch in the connecting loop between domains 1 and 2. In the present study, the stability of laccase in organic solvents was improved by introducing nonpolar (E188 → A, I, L, and V) and positively charged (E188 → K and R) residues in this region by site-directed mutagenesis. Irreversible thermoinactivation, C50 value (organic solvent concentration at which 50% of enzyme activity remains), change in transition-state stabilization energy, and kinetic parameters of the wild type and its variants were calculated in the presence and absence of various organic solvents (ethanol, methanol, and 1-propanol). All variants showed higher C50 values when compared to the wild type. Nonpolar amino acid substitutions were found to be the most efficient mutants for their remarkable increase in C50 value and a decrease in thermoinactivation rate in the presence of mentioned solvents. Data showed that replacing a negative residue with hydrophobic residues on the surface of a protein could enhance thermoresistance as well as solvent stability. The stability of the resulting enzymes was dependent on the length of the alkyl chain. Results demonstrated that solvent tolerance was positively correlated with thermal stability. [ABSTRACT FROM AUTHOR]

The crystal structure of Bacillus amyloliquefaciensα-amylase (BAA) at 1.4 Å resolution revealed ambiguities in the thermal adaptation of homologous proteins in this family. The final model of BAA is composed of two molecules in a back-to-back orientation, which is likely to be a consequence of crystal packing. Despite a high degree of identity, comparison of the structure of BAA with those of other liquefying-type α-amylases indicated moderate discrepancies at the secondary-structural level. Moreover, a domain-displacement survey using anisotropic B-factor and domain-motion analyses implied a significant contribution of domain B to the total flexibility of BAA, while visual inspection of the structure superimposed with that of B. licheniformisα-amylase (BLA) indicated higher flexibility of the latter in the central domain A. Therefore, it is suggested that domain B may play an important role in liquefying α-amylases, as its rigidity offers a substantial improvement in thermostability in BLA compared with BAA. [ABSTRACT FROM AUTHOR]

Abstract: Horseradish peroxidase is an important heme-containing plant enzyme with enormous medical diagnostic, biosensing, bioremediation and biotechnological applications. Any improvement in the stability of the enzyme will greatly enhance its application in mentioned areas. In the present study, the stabilizing effects of certain additives and chemical modification by citraconic anhydride on the thermal behavior of HRP were investigated. Both strategies brought about dramatic enhancement of the thermostability of the enzyme. Results obtained on T m, changes in the circular dichroism (CD) spectra and kinetic parameters of HRP and its modified form are discussed in terms of contributions to the mechanism of the thermal stability and the activity enhancement. Polyols were very effective in providing protection against the irreversible thermoinactivation of the native and the modified forms of the enzyme. Our results reveal that a combination of medium change and surface modification may provide an effective strategy for the enhancement of the thermodynamic and the kinetic stability of the enzyme. [Copyright &y& Elsevier]

We had previously investigated the role of a loop on the activity and conformational stability of chondroitinase ABC Ι (cABC Ι) by constructing some representative mutants in which a network interaction around Asp 689 was manipulated. Here we extended our study by measuring the proteolytic resistance, long term and thermal stability as well as unfolding kinetics of these variants. Long term stability data at 4 and 25 °C for 3 weeks indicates that all mutants remain considerably active at 4 °C. Thermoinactivation rates for all variants shows that the wild type (WT) enzyme retained 50% of its activity after 2 min keeping at 40 °C, while L701T, H700N and H700N/L701T as conformationally stabilized variants, have slower inactivation rate. It was also found that compact and thermodynamically stabilized variants are more resistant to tryptolytic digestion. Also, kinetic curves of chemical unfolding of the enzyme variants from stopped-flow fluorescence measurements were best fitted into a three-exponential function with three rate constants and corresponding amplitudes. We found that the energy barrier of the fast unfolding phase is lower in stabilized variants; while the amplitude of this phase to the whole amplitude of the unfolding reaction is lower than that of destabilized variants, indicating more population of stabilized mutants unfold via slower unfolding phase. We concluded that the rate of local conformational change alone is not the same that is expected from global thermodynamic stability; however the corresponding amplitude can compensate the rate constant toward thermodynamic stability. [ABSTRACT FROM AUTHOR]

Abstract: The industrial utilization of savinase is mainly constrained by its stability limitations. In the present study, the irreversible thermoinactivation of savinase has been evaluated at 70°C, and various possible mechanisms for irreversible thermoinactivation of savinase were examined. The main process seemed to be autodigestion of savinase at higher temperatures. To improve the thermal stability of the enzyme, the effect of two co-solvents (sorbitol and trehalose) on the enzyme''s activity and stability was investigated. Both osmolytes prevented the autolysis of savinase at 70°C without inactivating the enzyme; furthermore, the structural and kinetic stabilities of the enzyme increased in the presence of additives. [Copyright &y& Elsevier]

Laccases are multicopper oxidases that catalyze the oxidation of variety of substrates. The specificity and efficiency of laccases are clearly the important components leading to their remarkable uses. To develop an improved biocatalysts, site directed mutagenesis of laccase from Bacillus HR03 was carried out in the current study. Based on the ABTS-bound crystal structure of CotA from B. subtilis and alignment with closely related enzymes, T415 and T418 at the vicinity of the type 1 copper site were chosen and several mutants (T415I, T418I, T415G, T415G/T418I) were made. Kinetic parameters of the constructs were then determined using ABTS and SGZ as substrates. In comparison with the wild-type, catalytic efficiency toward ABTS was improved by 4 fold in T415I and 1.5 fold in T418I and T415G. T415I and T418I variants were identified to be almost 11 and 27 times more specific for ABTS than for SGZ compared with the wild type. T415I was also found to acquire enhanced thermal stability with the half-life of 60 min at 80 °C. Secondary and tertiary structure of mutants were analyzed by CD and fluorescence spectroscopy. Our result illustrated that replacement of residues in the substrate-binding pocket would change the specificity and efficiency of variants. [ABSTRACT FROM AUTHOR]

We used a combination of experimental and bioinformatic studies to elucidate the importance of Serine 128 and Valine 183 on the activity and thermal stability of mnemiopsin 1 by substitution of S 128 and V 183 with glycine and threonine, respectively (S128G and V183T mutants). Luminescence emissions of S128G and V183T were reduced to 71.6% and 46.6% with respect to the original activity of the wild type protein. According to circular dichroism (CD) measurements, compactness of mutants decreased in comparison with wild type (WT) protein. Differential scanning calorimetry (DSC) indicated that T m values of thermal unfolding are not changed significantly upon mutation. Herein, we suggest that the protein variants unfold through molecular association and intermediate states. Bioinformatic studies revealed that local fluctuation of residues in S128G increased with respect to WT protein. However, S128G mutation leads to increment of the accessible surface area of lysine188. Therefore, this change is thermodynamically favorable. Finally, both experimental and theoretical studies showed a delicate balance between all structural alterations, determining total conformational stability of the protein. [ABSTRACT FROM AUTHOR]

Laccases are particularly promising enzymes for biotechnology and bioremediation purposes. They are among the most effective enzymes capable of catalyzing the degradation of phenolic compounds with poor water solubility. The technological utility of lacasses can be enhanced greatly by their use in ionic liquids rather than in conventional organic solvents or in their natural aqueous reaction media. In the current study, a laccase from Bacillus HR03 has been engineered through a semi rational method. By screening a library of 450 clones, Glu188Tyr and Glu188Phe showed a distinct improvement in thermal stability and ionic liquid tolerance. In comparison with the wild type, selected mutants exhibited higher k cat / K m against ABTS in the imidazolium based ionic liquids, (1-ethyl-3-methyl imidazolium chloride [EMIm][Cl], butyl-3-methyl imidazolium chloride [BMIm][Cl] and hexyl-3-methyl imidazolium chloride [HMIm][Cl]). Glu188Tyr had a catalytic efficiency, two times greater when compared to the wild type in [HMIm][Cl]. Far-UV circular dichroism (CD) exhibited no significant changes in the secondary structure of the mutants and wild type. Glu188Tyr revealed a more compact structure using Near-UV CD and fluorescence spectroscopy that could account for its high thermal stability. According to bioinformatic analysis, π–π and anion–π interactions played the dominant role in stabilizing both variants. [ABSTRACT FROM AUTHOR]

Abstract: It has been lately proposed that the interaction between like-charged residues stabilizes the native state of proteins. To explore this, we created a histidine–histidine pair in the Ca-III binding site of the Bacillus amyloliquefaciens α-amylase (BAA) and then examined the impact of this pairing on the BAA. For this purpose, we used site-directed mutagenesis (SDM) to substitute Pro407 with His, Ala, Gln, Arg, and Glu in the BAA. Subsequently, thermostability, kinetic parameters and structural properties of these variants were measured. Moreover, His–His pairing effect on the BAA thermostability was examined by simultaneous mutation of two residues (P407H/H406A and P407H/H406N). The data exhibited a significant improve in thermostability and structural features of enzyme by His replacement instead of Pro407. Other substitutions in this site did not have a significant effect on the enzyme properties, except for P407R, which yielded a partial improvement. The results also showed that the thermostabilities of double mutants significantly decreased compared with that of the P407H mutant. Moreover, the thermostability of P407H remarkably increased compared with that of other variants even in the absence of Ca2+. Our data clearly demonstrated that His406–His407 pairing was the major cause for improved thermal stability. [Copyright &y& Elsevier]