Preparation and characterization of multipoint yeast D-amino acid oxidase mutants with improved stability and activity

D-amino acid oxidase (DAAO) is an FAD-containing oxidoreductase that stereospecifically oxidases D-amino acids to produce α-keto-acids, an ammonium ion, and hydrogen peroxide. The most important biotechnological process involving DAAO is the production of 7-amino cephalospranic acid (7-ACA) from cephalosporin C. The reaction product, 7-ACA, is then used as a precursor for the synthesis of cephalosporin antibiotics of different generations. We previously obtained mutant DAAOs from the yeast Trigonopsis variabilis (TvDAAO). The mutants with point amino acid substitutions were characterized by either an increased thermal stability or improved catalytic properties in the oxidation of cephalosporin C. In the present study, we obtained two new mutant TvDAAOs with two and four amino acid substitutions, respectively. The catalytic constants of these mutant TvDAAOs for the oxidation of cephalosporin C were 1.8 and 4 times higher than the respective parameter of the wild-type enzyme (wt-TvDAAO). The combination of substitutions increased the thermal stabilities of both mutant TvDAAOs by a factor of 2–3 as compared with the wt- TvDAAO.     

Rational Design of Practically Important Enzymes

Majority of native enzymes are poorly applicable for practical usage: that is why different methods of enzyme modification are used to obtain the biocatalysts with appropriate characteristics. Development of genome sequencing and various modern approaches in protein engineering allow one to identify protein of interest and to improve the enzyme properties for a particular process. This review describes the results on development of novel biocatalysts based on bioinformatics and rational design. New genes encoding formate dehydrogenase (FDH) from bacterium Staphylococcus aureus, yeasts Ogataea parapolymorpha and Saccharomyces cerevisiae and moss Physcomitrella patens (SauFDH, OpaFDH, SceFDH and PpaFDH, respectively), have been cloned. New FDHs were produced in the active form and characterized. SauFDH was shown to have at least 2-fold higher catalytic constant than other known FDHs. OpaFDH has catalytic parameters as good as those for soy FDH mutant forms, and in addition, is more thermostable. Apo- and holo-forms of SauFDH have been crystallized. Mutation of two Cys residues in Pseudomonas sp.101 enzyme (PseFDH) yields enzyme preparations with improved kinetic parameters and enhanced thermal and chemical stability. New generation of PseFDH preparations with the coenzyme specificity changed from NAD⁺ to NADP⁺ have been obtained. The effect of ionic liquids on the catalytic properties and thermal stability of six wild-type recombinant FDHs, and a number of their mutants, have been studied. In case of D-amino acid oxidase (DAAO), single-point mutations have been combined to create multi-point mutants. The introduced amino acid replacements have been shown to exert an additive effect, improving both kinetic parameters and increasing thermal and chemical stability. DAAO genes from Hansenula polymorpha yeast have been cloned. α-Amino acid ester hydrolase (AEH) gene has been cloned and expressed in the active form in E. coli. Structural modeling has been performed and the effectiveness in amino beta-lactams synthesis studied. The structure of a single-chain penicillin acylase from Alcaligenes faecalis (scAfPA) has been modeled and two variants of scAfPA gene was generated by PCR. Both variants have been expressed in E. coli, isolated and characterized. Catalytic properties of scAfPA were slightly better than those of its natural heterodimer.     

Mutant d-amino acid oxidase with higher catalytic efficiency toward d-amino acids with bulky side chains

d-Amino acid oxidase from the yeast Trigonopsis variabilis (TvDAAO) is widely used in fine organic synthesis, including the preparation of unnatural l-amino acids and α-keto acids. The analysis of the three-dimensional structure of TvDAAO was carried out with the aim of producing the enzyme specific to d-amino acids with bulky side chains. The analysis revealed the residue Phe54 at the entrance to the active site, which controls the substrate access to this site. The residue Phe54 was replaced by residues Ala, Ser, and Tyr. The cultivation of recombinant E. coli strains expressing TvDAAO mutants showed that the mutein with the Phe54Ala substitution had very low stability. Thus, the inactivation of the enzyme occured within 10 min after the cell disruption. The Phe54Ser TvDAAO and Phe54Tyr TvDAAO mutants were obtained as homogeneous preparations, and their thermal stability and catalytic properties were investigated. The introduction of Phe54Ser and Phe54Tyr substitutions resulted in additional stabilization of the protein macromolecule compared to the wild-type TvDAAO. Thus, the half-inactivation time for the mutant enzymes at 54 °C increased by a factor of 1.5 and 2, respectively. As in the case of wild-type TvDAAO, the thermal inactivation of the muteins proceeds via a two-step dissociative mechanism. The introduction of mutations led to a strong change in the substrate specificity profile. The mutants have no activity toward a series of d-amino acids (Phe54Ser TvDAAO toward d-Ala, d-Ser, d-Val, and d-Thr; Phe54Tyr TvDAAO toward d-Ser, d-Tyr, d-Thr, and d-Lys). The catalytic efficiency (the k _cat/K _M ratio) of the Phe54Ser TvDAAO mutant toward d-amino acids with bulky side chains (d-Lys, d-Asn, d-Phe, d-Tyr, d-Trp, and d-Leu) increased from 2.4 to 7.3 times.     

The role of residues Arg169 and Arg220 in intersubunit interactions of yeast D-amino acid oxidase

D-Amino acid oxidase from the yeast Trigonopsis variabilis (EC 1.4.3.3, TvDAAO) exists as a dimer consisting of two identical subunits. The dimeric structure of the enzyme is stabilized by 12 (six pairs) hydrogen bonds, the residues Arg169 and Arg220 of each subunit being involved in eight hydrogen bonds. The Arg169Glu and Arg(169,220)Ala mutants of TvDAAO were prepared. Both mutant enzymes were expressed in E. coli cells as insoluble but catalytically active inclusion bodies. The introduction of amino acid substitutions at the intersubunit interface resulted in a change in the substrate specificity profile and a strong decrease in thermal stability.     

Engineering the properties of D-amino acid oxidases by a rational and a directed evolution approach

D-amino acid oxidase (DAAO) is a FAD-containing flavoprotein that dehydrogenates the D-isomer of amino acids to the corresponding imino acids, coupled with the reduction of FAD. The cofactor then reoxidizes on molecular oxygen and the imino acid hydrolyzes spontaneously to the alpha-keto acid and ammonia. In vitro DAAO displays broad substrate specificity, acting on several neutral and basic D-amino acids: the most efficient substrates are amino acids with hydrophobic side chains. D-aspartic acid and D-glutamic acid are not substrates for DAAO. Through the years, it has been the subject of a number of structural, functional and kinetic investigations. The most recent advances are represented by site-directed mutagenesis studies and resolution of the 3D-structure of the enzymes from pig, human and yeast. The two approaches have given us a deeper understanding of the structure-function relationships and promoted a number of investigations aimed at the modulating the protein properties. By a rational and/or a directed evolution approach, DAAO variants with altered substrate specificity (e.g., active on acidic or on all D-amino acids), increased stability (e.g., stable up to 60 degrees C), modified interaction with the flavin cofactor, and altered oligomeric state were produced. The aim of this paper is to provide an overview of the most recent research on the engineering of DAAOs to illustrate their new intriguing properties, which also have enabled us to pursue new biotechnological applications.     

Optimization of HPLC technique for determining catalytic parameters of D-amino acid oxidase on cephalosporin C

Approximately half of cephalosporin antibiotics of different generations are produced from 7-aminocephalosporanic acid, which to date is prepared by organic synthesis. Instead of organic synthesis, a two-step enzymatic process is gradually being developed. The first step is enzymatic oxidation of natural antibiotic cephalosporin C by D-amino acid oxidase (DAAO). Yeast enzymes are used for this purpose due to the highest activity on cephalosporin C. The standard technique of determining the activity of D-amino acid oxidase is based on determining the concentration of released hydrogen peroxide using horseradish peroxidase. During cephalosporin C oxidation, hydrogen peroxide is involved in the spontaneous nonenzymatic reaction with the intermediate product. Thus, monitoring the substrate consumption with high-performance liquid chromatography (HPLC) is the most correct way to determine the activity. In this paper, we have optimized the HPLC technique of determining the cephalosporin C concentration during its oxidation with D-amino acid oxidase in the reaction mixture. Using the optimized technique, we have determined the catalytic parameters for wild-type and mutant D-amino acid oxidase on cephalosporin C.     

The 3D-structural modeling of yeast D-amino acid oxidase

D-amino acid oxidase from the yeast Trigonopsis variabilis (TvDAAO) is used in the pharmaceutical industry and fine organic synthesis but for future practical applications new mutant forms of the enzyme with improved stability and catalytic properties are needed. Experiments on the crystallization of TvDAAO have been carried out for the last three decades without any success. For protein engineering of the enzyme using a rational design approach a model 3D-structure of TvDAAO was built using the homology modeling method. Cys108 and Cys298 residues were proposed for site-directed mutagenesis after analysis of the enzyme model structure.     

Purification and Analytical Application of <Emphasis Type="Italic">Vigna mungo</Emphasis> Chitinase for Determination of Total Fungal Load of Stored Cereals

Chitinases are glycosyl hydrolases that catalyze the hydrolysis of β-(1,4)-glycosidic bonds in chitin, the major structural polysaccharide presented in the cuticle and gut peritrophic matrix of insects. Two aspartate residues (D143, D145) and one tryptophan (W146) in the Lymantria dispar chitinase are highly conserved residues observed within the second conserved motif of the family 18 chitinase catalytic region. In this study, a chitinase cDNA, LdCht5, was cloned from L. dispar, and the roles of the three residues were investigated using site-directed mutagenesis and substituting them with three other amino acids. Seven mutant proteins, D143E, D145E, W146G, D143E/D145E, D143E/W146G, D145E/W146G, and D143E/D145E/W146G, as well as the wild-type enzyme, were produced using the baculovirus-insect cell line expression system. The enzymatic and kinetic properties of these mutant enzymes were measured using the oligosaccharide substrate MU-(GlcNAc)₃. Among the seven mutants, the D145E, D143E/D145E, and D145E/W146G mutations kept some extant catalytic activity toward MU-(GlcNAc)₃, while the D143E, W146G, D143E/W146G, and D143E/D145E/W146G mutant enzymes were inactivated. Compared with the mutant enzymes, the wild-type enzyme had higher values of k _cat and k _cat / K _m . A study of the multiple point mutations in the second conserved catalytic region would help to elucidate the role of the critical residues and their relationships.     

Synthesis of amino acid conjugates of glycyrrhizic acid using <Emphasis Type="Italic">N</Emphasis>-hydroxyphthalimide and <Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>'-dicyclohexylcarbodiimide

Synthesis of amino acid conjugates of glycyrrhizic acid with the use of N-hydroxyphthalimide, N,N'-dicyclohexylcarbodiimide, and tert-butyl esters of L-amino acids (valine, isoleucine, phenylalanine, and methionine) was performed followed by deprotection with trifluoroacetic acid. The target amino acid conjugates were isolated by column chromatography on silica gel in 40–45% yield. The structure of the prepared compounds was confirmed by IR and ¹³C NMR spectroscopy.     

Analysis of the Racemization of Tryptophan

Diastereoisomers of L- and D-tryptophan were formed with a chiral reagent, 1-thio-β-D-glucose tetraacetate and o-phthaldialdehyde, and were separated from the derivatives of the other amino acids that occur in food proteins on an achiral column by high performance liquid chromatography. Mercaptoethanesulfonic acid that is used as an agent for hydrolyzing proteins made the derivatization with o-phthaldialdehyde and 1-thio-β-D-glucose tetraacetate impossible. On the other hand the reaction was completed in the presence of p-toluenesulfonic acid, but the oxidative losses during hydrolysis were significant. During boiling, the racemization of tryptophan can be detected after 12 h above pH 9, but the rate of conversion was lower than expected (<1%). The decrease of L-tryptophan after 24 h was 2–5% depending on pH. Besides racemization, other reactions, e.g. oxidative deterioration may play a role in the loss of L-tryptophan.     

Direct profiling of the phospholipid composition of adult <Emphasis Type="Italic">Caenorhabditis elegans</Emphasis> using whole-body imaging mass spectrometry

A protocol for the direct analysis of the phospholipid composition in the whole body of adult soil nematode, Caenorhabditis elegans (C. elegans), was developed, which combined freeze-cracking of the exoskeletal cuticle and matrix-assisted laser desorption/ionization-imaging mass spectrometry (MALDI-IMS). Biomolecules in the m/z range from 700 to 900 were more effectively detected in the freeze-cracked than from simple frozen adult nematode bodies. Different distribution of biomolecules was observed in a nematode body when the matrix was applied with a sublimation deposition method. The whole-body IMS technique was applied on genetically deficient mutant C. elegans to combine whole-body lipidomics and genetics, by comparing the fatty acid compositions, especially of the phosphatidylcholine (PC) species, between the wild-type and fat-1 mutants, which lack the gene encoding an n-3 fatty acid desaturase. A significant reduction of PC(20:5/20:5) and PC(20:4/20:5) and a marked increase of PC(20:4/20:4), PC(20:3/20:4), and PC(20:3/20:3) were detected in the fat-1 mutants in positive ion mode. In addition, phospholipid compositions other than PCs were analyzed in negative ion mode. A loss of a possible phosphatidylinositol (PI) with 18:0/20:5 and a compensative accumulation of putative PI(18:0/20:4) were detected in the fat-1 mutants. In conclusion, the whole-body MALDI-IMS technique is useful for the profiling of multiple biomolecules in C. elegans in both intra- and inter-individual levels.     

Comparative sequence analysis and mutagenesis of Ethylene Forming Enzyme (EFE) 2-oxoglutarate/Fe(II)-dependent dioxygenase homologs

Background

Ethylene is one of the most used chemical monomers derived from non-renewable sources and we are investigating the possibility of producing it in yeast via the ethylene forming enzyme (EFE) from Pseudomonas syringae. To enable engineering strategies to improve the enzyme, it is necessary to identify the regions and amino acid residues involved in ethylene formation.

Results

We identified the open reading frame for the EFE homolog in Penicillium digitatum and also showed its capability of mediating ethylene production in yeast. The sequence of the EFE homologs from P.digitatum and P. syringae was compared to that of the non-functional EFE-homolog from Penicillium chrysogenum and ten amino acids were found to correlate with ethylene production. Several of these amino acid residues were found to be important for ethylene production via point mutations in P. syringae EFE. The EFE homolog from P. chrysogenum was engineered at 10 amino acid residues to mimic the P. syringae EFE, but this did not confer ethylene producing capability.Furthermore, we predicted the structure of EFE by homology to known structures of 2-oxoglutarate/Fe(II) dependent dioxygenases. Three of the amino acids correlating with ethylene production are located in the predicted 2-oxoglutarate binding domain. A protein domain specific for the EFE-class was shown to be essential for activity. Based on the structure and alanine substitutions, it is likely that amino acids (H189, D191 and H268) are responsible for binding the Fe(II) ligand.

Conclusion

We provide further insight into the structure and function of the ethylene forming (EFE) - subclass of 2-oxoglutarate/Fe(II) dependent dioxygenases. We conclude that residues in addition to the 10 identified positions implicated in ethylene production by sequence comparison, are important for determining ethylene formation. We also demonstrate the use of an alternative EFE gene. The data from this study will provide the basis for directed protein engineering to enhance the ethylene production capability and properties of EFE.

     

A comparative study of the structure and properties of β-galactosidases

A comparative study of β-galactosidase amino acid sequences of E. coli and another four out of 11 microorganisms selected at the first stage was performed. It was shown that the functional amino acid residues in the catalytic domain and the ligand environment of the magnesium cation for all five sequences are identical. The mechanism of the catalytic action of E. coli and K. lactis β-galactosidases was investigated by the method of nucleophilic competition. It was shown that the mechanism of the effects of nucleophilic agents is kinetically identical both enzymes: the presence of methanol or butanediols affects the stage of degalactosylation; the presence of magnesium cations promotes the activity of both β-galactosidases; and the mechanisms of the thermal inactivation of E. coli and K. lactis β-galactosidases are different.     

Synthesis and conformational analysis of 6-[N,N-bis(dihydroxyphosphorylmethyl)amino]methyl-2-hydroxy-2-oxido-1,4,2-oxazaphosphorinane-4-methylphosphonic acid by NMR spectroscopy

The Kabachnik—Fields methylphosphorylation of 1,3-diaminopropan-2-ol affords a mixture of 1,3-diamino-2-hydroxypropane-N,N,N′,N′-tetrakismethylphosphonic acid and its intramolecular cyclic ester. Subsequent heating of this mixture led to the thermal dehydration of the acid with the 1,4,2-oxazaphosphorinane ring closure and the formation of 6-[N,N-bis(dihydroxyphosphorylmethyl)amino]methyl-2-hydroxy-2-oxido-1,4,2-oxazaphosphorinane4-methylphosphonic acid. A predominant chair conformation of the formed six-membered heterocycle was inferred from the data of 2D homonuclear (¹H, ¹H; J-resolved) and heteronuclear (¹H, ¹³C; HSQC, HMBC) NMR correlation spectra.     

Thermodynamic functions of the mixing of methacrylic acid in organic solvents

The saturated vapor pressure over solutions of methacrylic acid is measured tensimetrically in acetonitrile, benzene, hexane, 1,2-dichloroethane, and acetic acid is measured tensimetrically at 290–350 K. The composition of equilibrium phases, the activity coefficients of the components, and the thermodynamic functions of the mixing (H ^E , G ^E , S ^E ) of the investigated solutions are calculated from the temperature dependence data.     

A complete evaluation of thermal and oxidative stability of chia oil

Chia (Salvia hispanica L.) seed oil is the richest natural source of α-linolenic acid, an n ? 3 polyunsaturated fatty acid (ω-3 PUFA), contributing to its use as functional and nutraceutical food in large part of Latin America. However, a food with such fatty acid composition could be highly susceptible to lipid oxidation. Thus, the present study was conducted to determine the thermal and oxidative stability of chia oil by various methods. Rancimat method was used to evaluate the effect of synthetic and natural antioxidants in the oxidative stability. Pressurized differential scanning calorimetry (PDSC), Schaal test and ¹H NMR spectroscopy were used to assess the thermal stability. The effect of frying temperature and/or heating time on fatty acid composition was assessed by ¹H NMR. The results show that tert-butylhydroquinone (TBHQ) and a mixture of TBHQ and rosemary extract were effective in increasing the oxidative stability of chia oil. Concerning the storage conditions, PDSC, Schaal test and ¹H NMR data showed that chia oil is stable at 60 °C; hence, there is no need for special storage conditions. PDSC and ¹H NMR results indicate that chia oil cannot be used in cooking and frying, because at high temperatures severe degradation of the unsaturated groups and loss of the nutritional properties of the oil occur.     

Synthesis and crystal structures of two silver(I) complexes derived from 2-amino-6-methylpyridine with nicotinic acid and isonicotinic acid

The reaction of Ag₂O and 2-amino-6-methylpyridine (AMP) with nicotinic acid (HNA) and isonicotinic acid (HINA), respectively, afforded two silver(I) complexes, [Ag₂(NA)₂(AMP)₂] _n (I) and [Ag₂(INA)₂(AMP)₂] _n (II). Both complexes were characterized by elemental analyses and X-ray single-crystal diffraction. Complex I is a pyridine-3-carboxylate bridged polynuclear silver(I) complex, in which the Ag atom is in a tetrahedral geometry, while complex II is a pyridine-4-carboxylate bridged polynuclear silver(I) complex, in which the Ag atom is in a distorted T-shaped geometry. The crystal of I is monoclinic: space group P2₁/c, a = 8.079(2), b = 17.150(3), c = 8.912(2) Å, β = 98.106(2)°, V = 1222.5(5) ų, Z = 4. The crystal of II is monoclinic: space group P2₁/c, a = 7.225(1), b = 12.049(1), c = 15.053(2) Å, β = 102.050(1)°, V = 1281.6(3) ų, Z = 4.     

Silicon-containing dimethylphosphoric acid amides

α-Silylmethylamines MeNHCH₂SiMen(OMe)_3?n (n=0, 2) were involved into Todd-Atherton reaction with (MeO)₂P(O)H giving N-methyl-N-trimethoxysilylmethyl-and N-methyl-N-dimethyl-(methoxy)silylmethylamides of dimethylphosphoric acid. A reaction of these compounds with BF₃·Et₂O led to the formation of the corresponding N-methyl-N-trifluoro-and N-methyl-N-(dimethyl)fluorosilylmethylamides of dimethylphosphoric acid. (MeO)₂P(O)N(Me)CH₂SiF₃ existed as an (O-Si)-chelate with a pentacoordinate silicon due to the occurrence of a rare and unstudied intramolecular coordinating interaction P=O → Si.     

Evaluating the role of a trypsin inhibitor from soap nut <Emphasis Type="Italic">(Sapindus trifoliatus L. Var. Emarginatus)</Emphasis> seeds against larval gut proteases,its purification and characterization

Background

The defensive capacities of plant protease Inhibitors (PI) rely on inhibition of proteases in insect guts or those secreted by microorganisms; and also prevent uncontrolled proteolysis and offer protection against proteolytic enzymes of pathogens.

Methods

An array of chromatographic techniques were employed for purification, homogeneity was assessed by electrophoresis. Specificity, Ki value, nature of inhibition, complex formation was carried out by standard protocols. Action of SNTI on insect gut proteases was computationally evaluated by modeling the proteins by threading and docking studies by piper using Schrodinger tools.

Results

We have isolated and purified Soap Nut Trypsin Inhibitor (SNTI) by acetone fractionation, ammonium sulphate precipitation, ion exchange and gel permeation chromatography. The purified inhibitor was homogeneous by both gel filtration and polyacrylamide gel electrophoresis (PAGE). SNTI exhibited a molecular weight of 29 kDa on SDS-PAGE, gel filtration and was negative to Periodic Acid Schiff’s stain. SNTI inhibited trypsin and pronase of serine class. SNTI demonstrated non-competitive inhibition with a Ki value of 0.75?±?0.05×10-10 M. The monoheaded inhibitor formed a stable complex in 1:1 molar ratio. Action of SNTI was computationally evaluated on larval gut proteases from Helicoverpa armigera and Spodoptera frugiperda. SNTI and larval gut proteases were modeled and docked using Schrodinger software. Docking studies revealed strong hydrogen bond interactions between Lys10 and Pro71, Lys299 and Met80 and Van Der Waals interactions between Leu11 and Cys76amino acid residues of SNTI and protease from H. Armigera. Strong hydrogen bonds were observed between SNTI and protease of S. frugiperda at positions Thr79 and Arg80, Asp90 and Gly73, Asp2 and Gly160 respectively.

Conclusion

We conclude that SNTI potentially inhibits larval gut proteases of insects and the kinetics exhibited by the protease inhibitor further substantiates its efficacy against serine proteases.

     

Ambazone salt with p-aminobenzoic acid

In this study, we obtained a novel salt of ambazone (AMB) with p-aminobenzoic acid (PABA) that exhibits improved solubility and antibacterial activity. The salt was produced by solvent-drop grinding and characterized by powder X-ray diffraction, thermal analysis and Fourier transform infrared spectroscopy. The salt nature of the new form was confirmed by infrared spectroscopy based on the characteristic vibrational band of the protonated amino group. Based on the X-ray powder diffraction data, the compound crystallizes in the triclinic P_-1 space group with the following unit cell parameters: a = 14.294 Å, b = 9.162 Å, c = 8.777 Å, α = 95.90°, β = 100.63°, γ = 91.73°. Thermal analysis reveals the thermal events and different decomposition steps of this solid form as compared to the starting compounds. Powder dissolution measurements showed solubility improvement compared with pure ambazone of 2 and 3.3 times in water and phosphate buffer, respectively. Antibacterial tests showed higher activity of the salt to Gram-negative Escherichia coli and Salmonella bacteria as compared to AMB and PABA. The study demonstrates that the pharmaceutical salt of ambazone with p-aminobenzoic acid (AMB–PABA) can be a possible alternative to ambazone in the treatment of infections with Gram-negative bacteria.