A chemically modified alpha-amylase with a molten-globule state has entropically driven enhanced thermal stability

Investigation into the chemical modification of α-amylase using octenyl succinic anhydride: enzyme characterisation and stability studies

The present study describes the chemical modification of α-amylase using succinic anhydride (SA), phthalic anhydride (PA) and a novel modifier viz. 2-octenyl succinic anhydride (2-OSA). SA-, PA- and 2-OSA-α-amylases displayed a 50%, 91% and 46% increase in stability at pH 9, respectively; as compared to unmodified α-amylase. PA-α-amylase showed a significant increase in Ea and ΔH_a^#, and a concomitant decrease in ΔS_a^#. The modified α-amylases exhibited improved thermostability as reflected by significant reductions in K_d and ΔS_d^#, and increments in t_1/2, D-, E_d, ΔH_d^# and ΔG_d^# values. The modified α-amylases displayed variable stabilities in the presence of different surfactants, inhibitors, metal ions and organic solvents. Interestingly, the chemical modification was found to confer resistance against inactivation by Hg²⁺ on α-amylase. The conformational changes in modified α-amylases were investigated using intrinsic tryptophan fluorescence, ANS (extrinsic) tryptophan fluorescence, and dynamic fluorescence quenching. Both intrinsic and extrinsic tryptophan fluorescence spectra showed increased fluorescence intensity for the modified α-amylases. Chemical modification was found to induce a certain degree of structural rigidity to α-amylase, as shown by dynamic fluorescence quenching. Analysis of the CD spectra by the K2d method using the DichroWeb online tool indicated evident changes in the α-helix, β-sheet and random coil fractions of the α-amylase secondary structure, following chemical modification using anhydrides. PA-α-amylase exhibited the highest productivity in terms of hydrolysis of starch at 60 °C over a period of 5 h indicating potential in varied biotechnological applications.

Structural Transitions of Alpha-Amylase Treated with Pulsed Electric Fields: Effect of Coexisting Carrageenan

Pulsed electric field (PEF) is an effective way to modulate the structure and activity of enzymes; however, the dynamic changes in enzyme structure during this process, especially the intermediate state, remain unclear. In this study, the molten globule (MG) state of α-amylase under PEF processing was investigated using intrinsic fluorescence, surface hydrophobicity, circular dichroism, etc. Meanwhile, the influence of coexisting carrageenan on the structural transition of α-amylase during PEF processing was evaluated. When the electric field strength was 20 kV/cm, α-amylase showed the unique characteristics of an MG state, which retained the secondary structure, changed the tertiary structure, and increased surface hydrophobicity (from 240 to 640). The addition of carrageenan effectively protected the enzyme activity of α-amylase during PEF treatment. When the mixed ratio of α-amylase to carrageenan was 10:1, they formed electrostatic complexes with a size of ~20 nm, and carrageenan inhibited the increase in surface hydrophobicity (<600) and aggregation (<40 nm) of α-amylase after five cycles of PEF treatment. This work clarifies the influence of co-existing polysaccharides on the intermediate state of proteins during PEF treatment and provides a strategy to modulate protein structure by adding polysaccharides during food processing.

Evaluating Enzymatic Productivity—The Missing Link to Enzyme Utility

Kinetic productivity analysis is critical to the characterization of enzyme catalytic performance and capacity. However, productivity analysis has been largely overlooked in the published literature. Less than 0.01% of studies which report on enzyme characterization present productivity analysis, despite the fact that this is the only measurement method that provides a reliable indicator of potential commercial utility. Here, we argue that reporting productivity data involving native, modified, and immobilized enzymes under different reaction conditions will be of immense value in optimizing enzymatic processes, with a view to accelerating biotechnological applications. With the use of examples from wide-ranging studies, we demonstrate that productivity is a measure of critical importance to the translational and commercial use of enzymes and processes that employ them. We conclude the review by suggesting steps to maximize the productivity of enzyme catalyzed reactions.

Molecular strategies to enhance stability and catalysis of extremophile-derived α-amylase using computational biology

α-Amylase is the most significant glycoside hydrolase having applications in various industries. It cleaves the α,1-4 glucosidic linkages of polysaccharides like starch, glycogen to yield a small polymer of glucose in α-anomeric configuration. α-Amylase is produced by all the three domains of life but microorganisms are preferred sources for industrial-scale production due to several advantages. Enormous studies and research have been done in this field in the past few decades. Still, it is requisite to work on enzyme stability and catalysis, as it loses its functionality in extreme. As the enzyme loses its structural and catalytic property under extreme environmental conditions, it is mandatory to confer some potential strategies for enhancing enzyme behaviour in such conditions. This limitation of an enzyme can be overcome up to some extent by extremophiles. They serve as an excellent source of α-amylase with outstanding features. This review is an attempt to encapsulate some structure-based strategies for improving enzyme behaviour thereby enabling researchers to selectively amend any of the strategies as per requirement during upstream and downstream processing for higher enzyme yield and stability. Thus, it will provide some cutting-edge strategies for tailoring α-amylase producing organism and enzyme with the help of several computational biology tools.

Computational Analysis of Thermal Adaptation in Extremophilic Chitinases: The Achilles' Heel in Protein Structure and Industrial Utilization

Understanding protein stability is critical for the application of enzymes in biotechnological processes. The structural basis for the stability of thermally adapted chitinases has not yet been examined. In this study, the amino acid sequences and X-ray structures of psychrophilic, mesophilic, and hyperthermophilic chitinases were analyzed using computational and molecular dynamics (MD) simulation methods. From the findings, the key features associated with higher stability in mesophilic and thermophilic chitinases were fewer and/or shorter loops, oligomerization, and less flexible surface regions. No consistent trends were observed between stability and amino acid composition, structural features, or electrostatic interactions. Instead, unique elements affecting stability were identified in different chitinases. Notably, hyperthermostable chitinase had a much shorter surface loop compared to psychrophilic and mesophilic homologs, implying that the extended floppy surface region in cold-adapted and mesophilic chitinases may have acted as a “weak link” from where unfolding was initiated. MD simulations confirmed that the prevalence and flexibility of the loops adjacent to the active site were greater in low-temperature-adapted chitinases and may have led to the occlusion of the active site at higher temperatures compared to their thermostable homologs. Following this, loop “hot spots” for stabilizing and destabilizing mutations were also identified. This information is not only useful for the elucidation of the structure–stability relationship, but will be crucial for designing and engineering chitinases to have enhanced thermoactivity and to withstand harsh industrial processing conditions

Microbial Alpha-Amylase Production: Progress, Challenges and Perspectives

Alpha-amylase reputes for starch modification by breaking of 1-4 glycosidic bands and is widely applied in different industrial sectors. Microorganisms express unique alpha-amylases with thermostable and halotolerant characteristics dependent on the microorganism’s intrinsic features. Likewise, genetic engineering methods are applied to produce enzymes with higher stability in contrast to wild types. As there are widespread application of α-amylase in industry, optimization methods like RSM are used to improve the production of the enzyme ex vivo. This study aimed to review the latest researches on the production improvement and stability of α-amylase.

Thermostabilization of VPR, a kinetically stable cold adapted subtilase, via multiple proline substitutions into surface loops

Protein stability is a widely studied topic, there are still aspects however that need addressing. In this paper we examined the effects of multiple proline substitutions into loop regions of the kinetically stable proteinase K-like serine protease VPR, using the thermostable structural homologue AQUI as a template. Four locations for proline substitutions were chosen to imitate the structure of AQUI. Variants were produced and characterized using differential scanning calorimetry (DSC), circular dichroism (CD), steady state fluorescence, acrylamide fluorescence quenching and thermal inactivation experiments. The final product VPR_ΔC_N3P/I5P/N238P/T265P was greatly stabilized which was achieved without any noticeable detrimental effects to the catalytic efficiency of the enzyme. This stabilization seems to be derived from the conformation restrictive properties of the proline residue in its ability to act as an anchor point and strengthen pre-existing interactions within the protein and allowing for these interactions to prevail when thermal energy is applied to the system. In addition, the results underline the importance of the synergy between distant local protein motions needed to result in stabilizing effects and thus giving an insight into the nature of the stability of VPR, its unfolding landscape and how proline residues can infer kinetic stability onto protein structures.

Structural effect of amine N-oxides on the facilitation of α-glucosidase-catalyzed hydrolysis reactions

Activation and stabilization of enzymes is an important issue in their industrial application. We recently reported that synthetic betaines, derived from cellular metabolites, structure-dependently increased the activity and stability of various enzymes including hydrolases, oxidases, and synthetases simply by mixing them into the reaction buffer. In this report, we focus on amine N-oxides, which are similarly important metabolites in cells with a highly polarized N-oxide bond, and investigate their enzyme stabilization and activation behavior. It was revealed that synthetic amine N-oxides structure-dependently activate α-glucosidase-catalyzed hydrolysis reactions similarly to betaines. The subsequent comparison of the kinetic parameters, the optimal concentration range for activation, and the maximal activity, suggested that amine N-oxides facilitate hydrolysis reactions via the same mechanism as betaines, because no differences were confirmed. However, the enzyme stabilization effect of amine N-oxides was slightly superior to that of betaines and the temporal stability of the enzyme in aqueous solutions was higher in the low amine N-oxide concentration range. The rheological properties, CD spectra, and dynamic fluorescence quenching experiments suggested that the suppression of unfavorable conformational perturbation was related to the difference in the hydration environments provided by the surrounding water molecules. Thus, we clarified that amine N-oxides facilitate enzyme reactions as a result of their similarity to betaines and provide a superior stabilizing effect for enzymes. Amine N-oxides show potential for application in enzyme storage and long-term reactions.

Improved expression, purification and characterization of VPR, a cold active subtilisin-like serine proteinase and the effects of calcium on expression and stability

Cloning into a pET 11a vector, followed by high-level expression of the cold adapted subtilase, VPR, utilizing the rhamnose titratable T7 system of Lemo21, resulted in a dramatic increase of soluble protein compared to the older system used. Expression optimization clearly shows the importance of calcium in the medium after induction, both for stability of the proteinase and cell health. Characterization of the purified enzyme obtained in a redesigned purification protocol which removed apparent RNA contaminants, resulted in a significantly higher value for k_cat than previously reported. The new recombinant protein exhibited slightly lower stability against thermal denaturation and thermal inactivation. Our results also indicate that two of the calcium binding sites have apparent binding constants in the mM range. Binding of calcium to the weaker of those two sites only affects resistance of the enzyme against irreversible thermal inactivation. Differential scanning calorimetry revealed a non-two-state denaturation process, with indication of presence of intermediates caused by unfolding of calcium binding motifs.

How to calculate thermostability of enzymes using a simple approach

Determination of thermostability of enzymes is of prime importance for their successful industrial applications and, yet, the published data has often been incompletely analyzed to assess the suitability of enzymes. It is possible to determine meaningful thermostability parameters from the routinely acquired data through a straightforward method that is not only more informative but also provides a means to compare thermostability of enzymes from different sources. Here, we describe a simple, effective, and economical way to determine enzyme thermostability. In our opinion, including this method in Biochemistry and Molecular Biology curricula will encourage students to include thermostability analysis in their future work, leading to a more meaningful approach to evaluate and compare enzymes. Furthermore, as the method requires minimum specialized equipment, the analysis will be particularly suitable for labs that cannot afford expensive setup. © 2018 by The International Union of Biochemistry and Molecular Biology, 46:398-402, 2018.

Increased yield of β-glucosidase-catalyzed hydrolysis reactions in the presence of betaine-type metabolite analog

β-Glucosidases (EC 3.2.1.21), abundant enzymes distributed in animals, plants and microorganism, has been generating lots of attentions for bioethanol production from cellulosic biomass. In this study, using three different origins of β-glucosidases, glucose productivity of β-glucosidase-catalyzed hydrolysis reactions in the presence of synthetic betaine-type metabolite analog (2-N,N,N-tri-n-butylammonium) acetate, was investigated. By the addition of the analog, the hydrolysis yields for all β-glucosidases was highly improved from 4-13 to 64-100 %. To understand the factors affecting on the yield enhancements, the kinetic parameters, inhibition constants of end-product and temporal stability of β-glucosidases were compared. As a result, enhancement of the yields is mainly related to the increase in the temporal stability of β-glucosidases in the presence of the analog. The present findings lead to not only improve the glucose productivity of β-glucosidase-catalyzed hydrolysis reaction toward bioethanol production but also apply to a new stabilization method for various unstable enzymes.

α-Amylase: an enzyme specificity found in various families of glycoside hydrolases

α-Amylase (EC 3.2.1.1) represents the best known amylolytic enzyme. It catalyzes the hydrolysis of α-1,4-glucosidic bonds in starch and related α-glucans. In general, the α-amylase is an enzyme with a broad substrate preference and product specificity. In the sequence-based classification system of all carbohydrate-active enzymes, it is one of the most frequently occurring glycoside hydrolases (GH). α-Amylase is the main representative of family GH13, but it is probably also present in the families GH57 and GH119, and possibly even in GH126. Family GH13, known generally as the main α-amylase family, forms clan GH-H together with families GH70 and GH77 that, however, contain no α-amylase. Within the family GH13, the α-amylase specificity is currently present in several subfamilies, such as GH13_1, 5, 6, 7, 15, 24, 27, 28, 36, 37, and, possibly in a few more that are not yet defined. The α-amylases classified in family GH13 employ a reaction mechanism giving retention of configuration, share 4-7 conserved sequence regions (CSRs) and catalytic machinery, and adopt the (β/α)8-barrel catalytic domain. Although the family GH57 α-amylases also employ the retaining reaction mechanism, they possess their own five CSRs and catalytic machinery, and adopt a (β/α)7-barrel fold. These family GH57 attributes are likely to be characteristic of α-amylases from the family GH119, too. With regard to family GH126, confirmation of the unambiguous presence of the α-amylase specificity may need more biochemical investigation because of an obvious, but unexpected, homology with inverting β-glucan-active hydrolases.

Thermostable mutant variants of Bacillus sp. 406 α-amylase generated by site-directed mutagenesis

Several mutations are known to increase the thermostability of α-amylase of B. licheniformis and other α-amylases. Site-directed mutagenesis was used to introduce similar mutations into the sequence of the α-amylase gene from mesophilic Bacillus sp. 406. The influence of the mutations on thermostability of the enzyme was studied. It was shown that the Gly211Val and Asn192Phe substitutions increased the half-inactivation temperature (Tm) of the enzyme from 51.94±0.45 to 55.51±0.59 and 58.84±0.68°C respectively, in comparison to the wild-type enzyme. The deletion of Arg178-Gly179 (dRG) resulted in an increase of Tm of the α-amylase to 71.7±1.73°C. The stabilising effect of mutations was additive. When combined they increase the Tm of the wild-type amylase by more than 26°C. Thermostability rates of the triple mutant are close to the values which are typical for industrial heat-stable α-amylases, and its ability to degrade starch at 75°C was considerably increased. The present research confirmed that the Gly211Val, Asn192Phe and dRG mutations could play a significant role in thermostabilization of both mesophilic and thermophilic α-amylases.

Kinetic and thermodynamic characterization of the functional properties of a hybrid versatile peroxidase using isothermal titration calorimetry: Insight into manganese peroxidase activation and lignin peroxidase inhibition

Isothermal titration calorimetry (ITC) was developed for measuring lignin peroxidase (LiP) and manganese peroxidase (MnP) activities of versatile peroxidase (VP) from Bjerkandera adusta. Developing an ITC approach provided an alternative to colorimetric methods that enabled reaction kinetics to be accurately determined. Although VP from Bjerkandera adjusta is a hybrid enzyme, specific conditions of [Mn+2] and pH were defined that limited activity to either LiP or MnP activities, or enabled both to be active simultaneously. MnP activity was found to be more efficient than LiP activity, with activity increasing with increasing concentrations of Mn+2. These properties of MnP were explained by a second metal binding site involved in homotropic substrate (Mn+2) activation. The activation of MnP was also accompanied by a decrease in both activation energy and substrate (Mn) affinity, reflecting a flexible enzyme structure. In contrast to MnP activity, LiP activity was inhibited by high dye (substrate) concentrations arising from uncompetitive substrate inhibition caused by substrate binding to a site distinct from the catalytic site. Our study provides a new level of understanding about the mechanism of substrate regulation of catalysis in VP from B. adjusta, providing insight into a class of enzyme, hybrid class II peroxidases, for which little experimental data is available.

Expanding LAGLIDADG endonuclease scaffold diversity by rapidly surveying evolutionary sequence space

LAGLIDADG homing endonucleases (LHEs) are a family of highly specific DNA endonucleases capable of recognizing target sequences ≈ 20 bp in length, thus drawing intense interest for their potential academic, biotechnological and clinical applications. Methods for rational design of LHEs to cleave desired target sites are presently limited by a small number of high-quality native LHEs to serve as scaffolds for protein engineering-many are unsatisfactory for gene targeting applications. One strategy to address such limitations is to identify close homologs of existing LHEs possessing superior biophysical or catalytic properties. To test this concept, we searched public sequence databases to identify putative LHE open reading frames homologous to the LHE I-AniI and used a DNA binding and cleavage assay using yeast surface display to rapidly survey a subset of the predicted proteins. These proteins exhibited a range of capacities for surface expression and also displayed locally altered binding and cleavage specificities with a range of in vivo cleavage activities. Of these enzymes, I-HjeMI demonstrated the greatest activity in vivo and was readily crystallizable, allowing a comparative structural analysis. Taken together, our results suggest that even highly homologous LHEs offer a readily accessible resource of related scaffolds that display diverse biochemical properties for biotechnological applications.

Biotechnological uses of enzymes from psychrophiles

The bulk of the Earth's biosphere is cold (e.g. 90% of the ocean's waters are ≤ 5°C), sustaining a broad diversity of microbial life. The permanently cold environments vary from the deep ocean to alpine reaches and to polar regions. Commensurate with the extent and diversity of the ecosystems that harbour psychrophilic life, the functional capacity of the microorganisms that inhabitat the cold biosphere are equally diverse. As a result, indigenous psychrophilic microorganisms provide an enormous natural resource of enzymes that function effectively in the cold, and these cold‐adapted enzymes have been targeted for their biotechnological potential. In this review we describe the main properties of enzymes from psychrophiles and describe some of their known biotechnological applications and ways to potentially improve their value for biotechnology. The review also covers the use of metagenomics for enzyme screening, the development of psychrophilic gene expression systems and the use of enzymes for cleaning.