Impact of cofactor-binding loop mutations on thermotolerance and activity of E. coli transketolase

Improvement of thermostability in engineered enzymes can allow biocatalysis on substrates with poor aqueous solubility. Denaturation of the cofactor-binding loops of Escherichia coli transketolase (TK) was previously linked to the loss of enzyme activity under conditions of high pH or urea. Incubation at temperatures just below the thermal melting transition, above which the protein aggregates, was also found to anneal the enzyme to give an increased specific activity. The potential role of cofactor-binding loop instability in this process remained unclear. In this work, the two cofactor-binding loops (residues 185–192 and 382–392) were progressively mutated towards the equivalent sequence from the thermostable Thermus thermophilus TK and variants assessed for their impact on both thermostability and activity. Cofactor-binding loop 2 variants had detrimental effects on specific activity at elevated temperatures, whereas the H192P mutation in cofactor-binding loop 1 resulted in a two-fold improved stability to inactivation at elevated temperatures, and increased the critical onset temperature for aggregation. The specific activity of H192P was 3-fold and 19-fold higher than that for wild-type at 60 °C and 65 °C respectively, and also remained 2.7-4 fold higher after re-cooling from pre-incubations at either 55 °C or 60 °C for 1 h. Interestingly, H192P was also 2-times more active than wild-type TK at 25 °C. Optimal activity was achieved at 60 °C for H192P compared to 55 °C for wild type. These results show that cofactor-binding loop 1, plays a pivotal role in partial denaturation and aggregation at elevated temperatures. Furthermore, a single rigidifying mutation within this loop can significantly improve the enzyme specific activity, as well as the stability to thermal denaturation and aggregation, to give an increased temperature optimum for activity.     

Novel S-enantioselective lipase TALipB from Trichosporon asahii MSR54: Heterologous expression,characterization, conformational stability and homology modeling

A novel lipase encoding gene, TALipB from Trichosporon asahii MSR54 was heterologously expressed in Escherichia coli using three vectors, pET22b, pET28a & pEZZ18. The three recombinant proteins, viz. C-hexahistidine fused HLipB, N and C-hexahistidine fused HLipBH and ZZ-fused ZZLipB were purified using affinity chromatography. All the three enzymes were mid to long fatty acyl chain selective on p-NP esters and S-enantioselective irrespective of tags. HLipB had lowest activation energy (3.5 Kcal mol⁻¹) and highest catalytic efficiency (254 mM⁻¹ min⁻¹) on p-NP caprate followed by HLipBH and ZZLipB. However, ZZLipB demonstrated best pH stability (pH 6–10), thermostability (t_1/2 of 50 min at 70 °C) and stability toward the denaturant Guanidium chloride (300 mM). Far-UV CD and fluorescence studies confirmed the role of N-terminal ZZ-tag in stabilizing the protein by altering its secondary and tertiary structures. All the three proteins were thiol activated. ZZLipB required higher concentration of β-mercaptoethanol as compared to the other two proteins to attain similar velocity. This indicated the involvement of additional disulfide bonds in its conformational stability. In silico analysis suggested low sequence identity of the enzyme with the available database but a close structural homology with Candida antarctica lipase B (CALB) was revealed by PHYRE². MULTALIN with CALB predicted the active site residues (Ser137–Asp228–His261) which were confirmed by superimposition and site directed mutagenesis.     

Biochemical stability and molecular dynamic characterization of Aspergillus fumigatus cystathionine γ-lyase in response to various reaction effectors

Cystathionine γ-lyase (CGL) is a key enzyme in the methionine–cysteine cycle in all living organisms forming cysteine, α-ketobutyrate and ammonia via homocysteine and cystathionine intermediates. Although, human and plant CGLs have been extensively studied at the molecular and mechanistic levels, there has been little work on the molecular and catalytic properties of fungal CGL. Herein, we studied in detail for the first time the molecular and catalytic stability of Aspergillus fumigatus CGL, since conformational instability, inactivation and structural antigenicity are the main limitations of the PLP-dependent enzymes on various therapeutic uses. We examined these properties in response to buffer compositions, stabilizing and destabilizing agents using Differential Scanning Fluorometery (DSF), steady state and gel-based fluorescence of the intrinsic hydrophobic core, stability of internal aldimine linkage and catalytic properties. The activity of the recombinant A. fumigatus CGL was 13.8 U/mg. The melting temperature (T_m) of CGL in potassium phosphate buffer (pH 7.0–8.0) was 73.3 °C, with ∼3 °C upshifting in MES and sodium phosphate buffers (pH 7.0). The conformational thermal stability was increased in potassium phosphate, sodium phosphate and MES buffers, in contrast to Tris–HCl, HEPES (pH 7.0) and CAPS (pH 9.0–10.0). The thermal stability and activity of CGL was slightly increased in the presence of trehalose and glycerol that might be due to hydration of the enzyme backbone, unlike the denaturing effect of GdmCl and urea. Modification of surface CGL glutamic and aspartic acids had no significant effect on the enzyme conformational and catalytic stability. Molecular modeling and dynamics simulations unveil the high conformational stability of the overall scaffold of CGL with high flexibility at the non-structural regions. CGL structure has eight buried Trp residues, which are reoriented to the enzyme surface and get exposed to the solvent under perturbation of destabilizers. Furthermore, electrostatic calculations of selected snapshots of CGL 3D structure under different experimental conditions showed a remarkable differences on the polarity of the enzyme surface.     

Protein engineering of Bacillus acidopullulyticus pullulanase for enhanced thermostability using in silico data driven rational design methods

Thermostability has been considered as a requirement in the starch processing industry to maintain high catalytic activity of pullulanase under high temperatures. Four data driven rational design methods (B-FITTER, proline theory, PoPMuSiC-2.1, and sequence consensus approach) were adopted to identify the key residue potential links with thermostability, and 39 residues of Bacillus acidopullulyticus pullulanase were chosen as mutagenesis targets. Single mutagenesis followed by combined mutagenesis resulted in the best mutant E518I-S662R-Q706P, which exhibited an 11-fold half-life improvement at 60 °C and a 9.5 °C increase in T_m. The optimum temperature of the mutant increased from 60 to 65 °C. Fluorescence spectroscopy results demonstrated that the tertiary structure of the mutant enzyme was more compact than that of the wild-type (WT) enzyme. Structural change analysis revealed that the increase in thermostability was most probably caused by a combination of lower stability free-energy and higher hydrophobicity of E518I, more hydrogen bonds of S662R, and higher rigidity of Q706P compared with the WT. The findings demonstrated the effectiveness of combined data-driven rational design approaches in engineering an industrial enzyme to improve thermostability.     

Relationship between the magnitude of IgE production in mice and conformational stability of the house dust mite allergen,Der p 2

BackgroundProtein antigens are degraded by endosomal protease in antigen presentation cell. T cells recognize peptides derived from antigen proteins bound to class II major histocompatibility complex molecules. We previously reported that an increase in the conformational stability of an antigen depressed its immunogenicity. However, there is little information on antigens with differences in molecular properties such as net charges and molecular weight.MethodsDenaturation experiments against guanidine hydrochloride. The serum IgE levels to protein antigens at 35 days after the first immunization analyzed using ELISA.ResultsThe Der p 2 mutations in which Ile13 is mutated to Ala (I13A) and Ala122 is mutated to Ile (A122I) were shown to have lower and higher conformational stability than the wild-type, respectively, by denaturation experiments. The amount of IgE production by the less stable I13A mutant was higher and that of the stable A122I mutant was lower than that of the wild-type.ConclusionOur results suggest that the increased conformational stability of Der p 2 depressed the IgE production in mice.General significanceThese findings should provide a milestone for the engineering of allergen vaccines.     

Exploring single-domain antibody thermostability by molecular dynamics simulation

Abstract

Single-domain antibodies also known as nanobodies are recombinant antigen-binding domains that correspond to the heavy-chain variable region of camelid antibodies. Previous experimental studies showed that the nanobodies have stable and active structures at high temperatures. In this study, the thermal stability and dynamics of nanobodies have been studied by employing molecular dynamics simulation at different temperatures. Variations in root mean square deviation, native contacts, and solvent-accessible surface area of the nanobodies during the simulation were calculated to analyze the effect of different temperatures on the overall conformation of the nanobody. Then, the thermostability mechanism of this protein was studied through calculation of dynamic cross-correlation matrix, principal component analyses, native contact analyses, and root mean square fluctuation. Our results manifest that the side chain conformation of some residues in the complementarity-determining region 3 (CDR3) and also the interaction between α-helix region of CDR3 and framework2 play a critical role to stabilize the protein at a high temperature.

Communicated by Ramaswamy H. Sarma     

Stabilization of Escherichia coli uridine phosphorylase by evolution and immobilization

Mutation and immobilization techniques were applied to uridine phosphorylase (UP) from Escherichia coli in order to enhance its thermal stability and hence productivity in a biocatalytic reaction. UP was evolved by iterative saturation mutagenesis. Compared to the wild type enzyme, which had a temperature optimum of 40 °C and a half-life of 9.89 h at 60 °C, the selected mutant had a temperature optimum of 60 °C and a half-life of 17.3 h at 60 °C. Self-immobilization of the native UP as a Spherezyme showed a 3.3 fold increase in thermostability while immobilized mutant enzyme showed a 4.4 fold increase in thermostability when compared to native UP. Combining UP with the purine nucleoside phosphorylase from Bacillus halodurans allows for synthesis of 5-methyluridine (a pharmaceutical intermediate) from guanosine and thymine in a one-pot transglycosylation reaction. Replacing the wild type UP with the mutant allowed for an increase in reaction temperature to 65 °C and increased the reaction productivity from 10 to 31 g l⁻¹ h⁻¹.     

Engineering a high-performance,metagenomic-derived novel xylanase with improved soluble protein yield and thermostability

The novel termite gut metagenomic-derived GH11 xylanase gene xyl7 was expressed in Escherichia coli BL21, and the purified XYL7 enzyme exhibited high specific activity (6340 U/mg) and broad pH active range of 5.5–10.0. Directed evolution was employed to enhance the thermostability of XYL7; two mutants (XYL7-TC and XYL7-TS) showed a 250-fold increase in half-life at 55 °C, with a 10 °C increase in optimal temperature compared to that of wild-type XYL7. A truncated enzyme (XYL7-Tr3) acquired by protein engineering showed similar catalytic properties as the wild-type, with a tenfold increase in soluble protein yield by the mutant. The reducing sugar produced by XYL7-TC was about fourfold greater than that produced by their parents when incubated with xylan at 60 °C for 4 h. The engineered novel xylanase exhibited superior enzymatic performance and showed promise as an excellent candidate for industrial application due to its high specific activity, stability and soluble protein yield.     

Applications of nanobodies in plant science and biotechnology

Key message

Present review summarizes the current applications of nanobodies in plant science and biotechnology, including plant expression of nanobodies, plant biotechnological applications, nanobody-based immunodetection, and nanobody-mediated resistance against plant pathogens.

Abstract

Nanobodies (Nbs) are variable domains of heavy chain-only antibodies (HCAbs) isolated from camelids. In spite of their single domain structure, nanobodies display many unique features, such as small size, high stability, and cryptic epitopes accessibility, which make them ideal for sophisticated applications in plants and animals. In this review, we summarize the current applications of nanobodies in plant science and biotechnology, focusing on nanobody expression in plants, plant biotechnological applications, determination of plant toxins and pathogens, and nanobody-mediated resistance against plant pathogens. Prospects and challenges of nanobody applications in plants are also discussed.

     

Size-dependent studies of macromolecular crowding on the thermodynamic stability,structure and functional activity of proteins: in vitro and in silico approaches

BackgroundThe environment inside cells in which proteins fold and function are quite different from that of the dilute buffer solutions often used during in vitro experiments. The presence of large amounts of macromolecules of varying shapes, sizes and compositions makes the intracellular milieu extremely crowded.Scope of reviewThe overall concentration of macromolecules ranges from 50 to 400 g l^− 1, and they occupy 10–40% of the total cellular volume. These differences in solvent conditions and the level of crowdedness resulting in excluded volume effects can have significant consequences on proteins' biophysical properties. A question that arises is: how important is it to examine the roles of shape, size and composition of macromolecular crowders in altering the biological properties of proteins? This review article aims at focusing, gathering and summarizing all of the research investigations done by means of in vitro and in silico approaches taking into account the size-dependent influence of the crowders on proteins' properties.Major conclusionsAltogether, the internal architecture of macromolecular crowding environment including size, shape and concentration of crowders, appears to be playing an extremely important role in causing changes in the biological processes. Most often the small sized crowders have been found more effective crowding agents. However, thermodynamic stability, structure and functional activity of proteins have been governed by volume exclusion as well as soft (chemical) interactions.General significanceThe article provides an understanding of importance of internal architecture of the cellular environment in altering the biophysical properties of proteins.     

Recombinant human sperm-specific glyceraldehyde-3-phosphate dehydrogenase: Structural basis for enhanced stability

Sperm-specific glyceraldehyde-3-phosphate dehydrogenase (GAPDS) is bound to the fibrous sheath of the sperm flagellum through the hydrophobic N-terminal domain of the enzyme molecule. Expression of human GAPDS in E.coli cells yields inactive and insoluble protein. Presumably, the N-terminal domain prevents correct folding of the full-length recombinant enzyme. To obtain GAPDS in a soluble and active form, a recombinant enzyme lacking in 68 amino acids of the N-terminal domain (dN-GAPDS) was expressed in E.coli cells. Purified dN-GAPDS was shown to be a protein of 9.3 nm in diameter (by dynamic light scattering), which is close to the size of the muscle tetrameric glyceraldehyde-3-phosphate dehydrogenase (8.6 nm). The catalytic properties of the protein differed a little from those of the muscle glyceraldehyde-3-phoshate dehydrogenase. However, compared to muscle glyceraldehyde-3-phoshate dehydrogenase, dN-GAPDS exhibited enhanced thermostability (the transition midpoints values are 60.8 and 67.4 °C, respectively) and was much more resistant towards action of guanidine hydrochloride (inactivation constants are 2.45 ± 0.018 and 0.118 ± 0.008 min^? 1, respectively). The enhanced stability of dN-GAPDS is likely to be related to some specific features of the GAPDS structure compared to that of the muscle enzyme: 1) reduced number of solvent-exposed salt bridges; 2) 2 additional buried salt bridges; and 3) 6 additional proline residues in GAPDS meeting the “proline rule”. It is assumed that high stability of the sperm-specific GAPDS is of importance for the efficiency of fertilization.     

Transrectal implantation and stability of gold markers in prostate bed for salvage radiotherapy of macroscopic recurrences

Background and purposeThe objective of the study was to verify the stability of gold markers in the prostatic bed (PB) during salvage radiotherapy.Material and methodsSeven patients, diagnosed with a macroscopic nodule visible on MRI, underwent targeted MRI-guided biopsies. Three gold markers were implanted into the PB close to the relapsing nodule for CT/MRI fusion. A dose of 60 Gy was delivered using IMRT to the PB followed by a dose escalation up to 72 Gy to the macroscopic nodule. Daily anterior and left-lateral kV-images were acquired for repositioning. The coordinates of the center of each marker were measured on the two kV-images. The distance variations (Dvar) of the markers in the first session and the subsequent ones were compared.ResultsNo marker was lost during treatment. The average distance between markers was 7.8 mm. The average Dvar was 0.8 mm, in absolute value. A total of 380/528 (72%) Dvar were ⩽1 mm. A Dvar greater than 2 mm was observed in 5.7% of measurements, with a maximum value of 4.8 mm.ConclusionsDespite the absence of the prostate, the implantation of gold markers in the PB remains feasible, with Dvar often less than 2 mm, and could be used to develop new approaches of salvage focal radiotherapy on the macroscopic relapse after prostatectomy.     

Postural stability in subjects with temporomandibular disorders and healthy controls: A comparative assessment

Purpose of the studyThe influence of the stomatognathic apparatus on body posture is a continuously discussed topic with contrasting results. The aim of this study is to analyze differences in postural stability between subjects with and without myogenous TMD.Methods25 subjects affected by myogenous TMD according with DC/TMD (6 males, 19 females; mean age 31.75 ± 6.68 years) and a healthy control group of 19 subjects (4 Males, 15 Females; mean age 27.26 ± 3.85 years) were enrolled in the study.Both groups underwent a posturo-stabilometric force platform exam under different mandibular and visual conditions. Sway area and sway velocity of the COP (Center Of foot Pressure) posturo-stabilometric parameters were evaluated and compared applying Mann-U-Whitney statistical test.ResultsThe sway area and sway velocity parameters resulted statistically significantly higher in the TMD group (sway area p < 0.01; sway velocity p < 0.05) in mandibular maximum intercuspation and rest positions with eyes open.ConclusionsThis study demonstrates a significant difference in body postural stability between subjects with myogenous TMD and healthy controls. In particular, sway area and sway velocity postural parameters are increased in these subjects.     

Purification and characterization of a solvent stable aminopeptidase from Pseudomonas aeruginosa: Cloning and analysis of aminopeptidase gene conferring solvent stability

Aminopeptidase from a solvent tolerant strain Pseudomonas aeruginosa PseA was purified and studied for its biochemical and molecular characteristics. Ion-exchange chromatography resulted in 11.9-fold purification and 38% recovery of the 56 kDa enzyme. The enzyme was found to be stable over a pH range of 6.0–8.0 and appreciably thermostable up to 70 °C. PseA aminopeptidase exhibited K_m of 3.02 mM and V_max of 6.71 μmol/mg/min towards l-Leu-p-nitroanilide. Remarkable stability in both hydrophilic and hydrophobic solvents makes PseA aminopeptidase unique. Partial N-terminal sequence of enzyme showed exact match with probable aminopeptidase of P. aeruginosa PAO1, coded by gene pepB. Polymerase chain reaction amplified the 1611-bp open reading frame encoding a 57.51 kDa, 536 amino acid PseA PepB polypeptide. The deduced PseA PepB protein sequence contained a 24-residue signal peptide (2.57 kDa) followed by a 1.28 kDa propeptide and a mature product of 500 residues. Search for conserved domain in PseA aminopeptidase explored its place in zinc-metallopeptidase family. Primary sequence analysis showed the hydrophobic inclination of the protein; and the 3D structure modeling elucidated the presence of a high content of hydrophobic residues on its surface probably imparting solvent stability to it. The enzyme might find potential applications in non-aqueous enzymology due to its marked thermostability and striking solvent stability.     

C-Terminal proline-rich sequence broadens the optimal temperature and pH ranges of recombinant xylanase from Geobacillus thermodenitrificans C5

Efficient utilization of hemicellulose entails high catalytic capacity containing xylanases. In this study, proline rich sequence was fused together with a C-terminal of xylanase gene from Geobacillus thermodenitrificans C5 and designated as GthC5ProXyl. Both GthC5Xyl and GthC5ProXyl were expressed in Escherichia coli BL21 host in order to determine effect of this modification. The C-terminal oligopeptide had noteworthy effects and instantaneously extended the optimal temperature and pH ranges and progressed the specific activity of GthC5Xyl. Compared with GthC5Xyl, GthC5ProXyl revealed improved specific activity, a higher temperature (70 °C versus 60 °C) and pH (8 versus 6) optimum, with broad ranges of temperature and pH (60–80 °C and 6.0–9.0 versus 40–60 °C and 5.0–8.0, respectively). The modified enzyme retained more than 80% activity after incubating in xylan for 3 h at 80 °C as compared to wild −type with only 45% residual activity. Our study demonstrated that proper introduction of proline residues on C-terminal surface of xylanase family might be very effective in improvement of enzyme thermostability. Moreover, this study reveals an engineering strategy to improve the catalytic performance of enzymes.     

Thermal stability of starch degrading enzymes of teff (Eragrostis tef) malt during isothermal mashing

Thermal stability of starch degrading enzymes varies from one source to another. This research was aimed to study thermal stability of starch degrading enzymes of teff malt. Isothermal mashing at temperatures ranging between 40 and 75 °C with sampling in 15 min interval for a total of 90 min was conducted. The study showed that deactivation rate constants of alpha- and beta-amylases ranged from 0.0003 to 0.0409 min^?1, and 0.002 to 0.032 min^?1, respectively. Rate of deactivation of limit dextrinase was not significant at temperatures lower than 60 °C but showed high deactivation at higher temperatures with rate constants ranging from 0.02 to 0.1 min^?1. The thermal deactivation energies of alpha-amylase, beta-amylase, and limit dextrinase were found to be 148, 82, and 144 kJ/mol, respectively. The present findings have significant applications in commercial processes where determination of the upper temperature limits for these enzymes is required.     

Improved production of 2-keto-3-deoxy-d-glycero-galactononulosonic acid (KDN) using FastPrep-CLEAs

FastPrep cross-linked enzyme aggregates of N-acetylneuraminate aldolase from Staphylococcus carnosus (ScNAL-FpCLEAs) were prepared in order to improve the synthesis of 2-keto-3-deoxy-d-glycero-galactononulosonic acid (KDN), an important building block for therapeutic glycolipids and a possible marker for human prostate cancer. ScNAL-FpCLEAs showed improved thermostability compared with the free enzyme, doubling its half-life at 60 °C. When the effect of substrate ratio (pyruvate:d-mannose) and temperature on the yield of KDN was studied at its optimum pH (pH 7.0), 90% conversion in only 8 h was reached in the presence of 0.6 M d-mannose and 1.2 M pyruvate at 37 °C. This is the highest conversion described to date for enzymatic KDN synthesis. In addition, ScNAL-FpCLEAs exhibited enhanced catalytic activity and stability and could be recycled 10 times with no loss of activity. These results suggest the biotechnological potential of using FastPrepCLEAs to obtain valuable biocatalysts.     

Aggregation of human serum albumin during a thermal viral inactivation step

A terminal pasteurization step has been used for some plasma-derived protein products such as human serum albumin (HSA), which consists of heating the protein in solution at 60 °C for 10 h. Native and denaturing SDS-PAGE and dynamic light scattering were used to follow the stability of HSA during this process. It appears that a thermally unstable fraction, comprised primarily of haptoglobin, is involved in the formation of soluble aggregates of HSA. Therefore, it appears that aggregation during heat treatment is not due to conformational instability of HSA itself, but arises from unfolding of a thermally labile protein impurity. As haptoglobin aggregates, it entraps some HSA, which is present at much higher concentrations. This study emphasizes that, in a complex mixture of naturally occurring proteins, one thermally labile species can trigger aggregation of more stable proteins.     

Application of recombinant Bacillus subtilis γ-glutamyltranspeptidase to the production of l-theanine

l-Theanine, which has seen increasing use in the functional food industry, can be prepared via enzymatic synthesis using γ-glutamyltranspeptidase (GGT; EC 2.3.2.2). In this study, the GGT from Bacillus subtilis 168 was cloned and expressed as a secreted protein using Escherichia coli BL21(DE3). The enzymatic properties of the GGT and the optimal conditions for the enzymatic synthesis of l-theanine were investigated in detail. The activity of the enzyme was optimal at pH 10; the optimal temperature was 50 °C. Desirable pH stability was observed between pH 5 and pH 12, and adequate thermostability was seen at 50 °C. In 5 h at 37 °C, the enzyme converted 200 mM l-glutamine and 2.2 M ethylamine to l-theanine with a final yield of 78%. Yields of l-theanine decreased to 58% when using 500 mM Gln and 45% when using 1 M Gln. The yield of l-theanine obtained at high substrate concentration provides the basis for the industrial-scale production of l-theanine.     

Thermal-aggregation suppression of proteins by a structured PEG analogue: Importance of denaturation temperature for effective aggregation suppression

Development of protein stabilizing reagents, that suppress aggregation and assist refolding, is an important issue in biochemical technology related with the synthesis and preservation of therapeutic or other functional proteins. In the precedent research, we have developed a structured poly(ethylene glycol) (PEG) analogue with triangular geometry, which turns into a dehydrated state above ca. 60 °C. Focusing on this rather lower dehydration temperature than that of conventional linear PEGs, a capability of the triangle-PEG to stabilize proteins under thermal stimuli was studied for citrate synthase, carbonic anhydrase, lysozyme and phospholipase. Variable temperature high-tension voltage and circular dichroism spectroscopic studies on the mixtures of these proteins and the triangle-PEG showed that the triangle-PEG stabilizes carbonic anhydrase, lysozyme and phospholipase that exhibit denaturation temperatures higher than 60 °C, while substantially no stabilization was observed for citrate synthase that denatures below 60 °C. Hence, the dehydrated triangle-PEG likely interacts with partially unfolded proteins through the hydrophobic interaction to suppress protein aggregation.