Loop engineering of amadoriase II and mutational cooperativity

Amadori compounds and their cross-linked products have been implicated in diabetic complications and some age-related diseases. Fructosyl amine oxidases (FAOXs) are a family of enzymes that can cleave the amadori compounds. However, the natural enzymes are only active on small substrates (fructosyl amino acids or dipeptides), which limits the therapeutic and diagnostic applications of these enzymes. In this study, amadoriase II, a member of the FAOX family from Aspergillus fumigatus was engineered to broaden its substrate range using a modified combinatorial active site saturation testing approach. The two loops at the entrance of the substrate channel were targeted. Saturation mutagenesis was carried out to search for hot-spot sites, followed by pairwise mutagenesis and subsequent combination of active mutations. Five sites on the loops were found to be critical for accessibility for two model bulky substrates, fructosyl adamantanamine and fructosyl-polylysine (3–13 lysines). Two best mutants (with three and five mutations, respectively) were obtained, with a specific activity toward the model substrates 20.6-fold and 16.8-fold that of the wild-type, respectively. Deconvolution experiments revealed the cooperativity of the mutations.     

Alteration of substrate selectivity through mutation of two arginine residues in the binding site of amadoriase II from Aspergillus sp

Amadoriases I and II are deglycation isoenzymes from Aspergillus sp. of potential relevance for treatment of diabetic complications resulting from excessive protein glycation. Amadoriase II has a preference for anionic substrate with a K(m) of 0.23 and 2.53 mM for fructosylglycine and fructosylpropylamine, respectively. In contrast, the corresponding K(m) values for amadoriase I are 9.75 and 0.023 mM, respectively. Chemical modification of amadoriase II with p-hydroxyphenylglyoxal, a specific arginine-modifying reagent, resulted in an inhibition of enzyme activity toward fructosylglycine, while having less effect on the enzymatic activity toward fructosylpropylamine. Peptide mapping and subsequent mass spectrometry analysis suggest that Arg(112) is one of the sites of p-hydroxyphenylglyoxal modification. Sequence alignment between amadoriase I and amadoriase II revealed that two glutamic acids in amadoriase I align to Arg(112) and Arg(114) in amadoriase II. Site-directed mutation of amadoriase II (R112E, R114E) resulted in reversal of the enzymatic activities toward fructosylglycine and fructosylpropylamine. Our results suggested that Arg(112) and Arg(114) are responsible for the high affinity of amadoriase II toward anionic substrates and determine the substrate selectivity of the enzyme.     

Kinetic studies, mechanism, and substrate specificity of amadoriase I from Aspergillus sp.

Amadoriase is a flavoenzyme that catalyzes the oxidative deglycation of Amadori products (fructosyl amino acids or aliphatic amines) to yield free amine, glucosone, and hydrogen peroxide. The mechanism of action of amadoriase I from Aspergillus sp. has been investigated by stopped-flow kinetic studies using fructosyl propylamine and O(2) as substrates in 10 mM Tris HCl, pH 7.9, 4 degrees C. Using both substrate analogues and fast kinetic techniques, the active configuration of the substrate was found to be the beta-pyranose form. Stopped-flow studies showed that the reductive half-reaction is triphasic and generates intermediates that absorb at long wavelengths and is consistent either with (i) the reaction of the substrate with the flavin followed by iminium deprotonation or hydrolysis and then product release or with (ii) the formation of flavin reduction intermediates (carbanion equivalents or adducts), followed by product release. The rate of product release after flavin reduction is lower than the aerobic turnover rate, 14.4 s(-1), suggesting that it is not involved in the catalytic cycle and that reoxidation of the reduced enzyme occurs in the E(red)-product complex. In the oxidative half-reaction, the reduced flavin is oxidized by O(2) in a single phase. The observed rate constant has a linear dependence on oxygen concentration, giving a bimolecular rate constant of 4.9 x 10(4) M(-1) s(-1) in the absence of product, and 3.6 x 10(4) M(-1) s(-1) when the product is bound. The redox potentials of amadoriase have been measured at pH 7.0, 25 degrees, giving values of +48 and -52 mV for the oxidized enzyme/anionic semiquinone and anionic semiquinone/reduced enzyme couples, respectively.     

Crystal structure of the deglycating enzyme fructosamine oxidase (amadoriase II)

Fructosamine oxidases (FAOX) catalyze the oxidative deglycation of low molecular weight fructosamines (Amadori products). These proteins are of interest in developing an enzyme to deglycate proteins implicated in diabetic complications. We report here the crystal structures of FAOX-II from the fungi Aspergillus fumigatus, in free form and in complex with the inhibitor fructosyl-thioacetate, at 1.75 and 1.6A resolution, respectively. FAOX-II is a two domain FAD-enzyme with an overall topology that is most similar to that of monomeric sarcosine oxidase. Active site residues Tyr-60, Arg-112 and Lys-368 bind the carboxylic portion of the fructosamine, whereas Glu-280 and Arg-411 bind the fructosyl portion. From structure-guided sequence comparison, Glu-280 was identified as a signature residue for FAOX activity. Two flexible surface loops become ordered upon binding of the inhibitor in a catalytic site that is about 12A deep, providing an explanation for the very low activity of FAOX enzymes toward protein-bound fructosamines, which would have difficulty accessing the active site. Structure-based mutagenesis showed that substitution of Glu-280 and Arg-411 eliminates enzyme activity. In contrast, modification of other active site residues or of amino acids in the flexible active site loops has little effect, highlighting these regions as potential targets in designing an enzyme that will accept larger substrates.     

Engineering of protease variants exhibiting altered substrate specificity

By using an improved genetic screening system, variants of the HAV 3CP protease which exhibit altered P2 specificity were obtained. We randomly mutated the His145, Lys146, Lys147, and Leu155 residues that constitute the S2 pocket of 3CP and then isolated variants that preferred substrates with Gln over the original Thr at the P2 position using a yeast-based screening method. One of the isolated variants cleaved the Gln-containing peptide substrate more efficiently in vitro, proving the efficiency of our method in isolating engineered proteases with desired substrate selectivity.     

Rational redesign of the 4-chlorobenzoate binding site of 4-chlorobenzoate: coenzyme a ligase for expanded substrate range

Environmental aromatic acids are transformed to chemical energy in bacteria that possess the requisite secondary pathways. Some of these pathways rely on the activation of the aromatic acid by coenzyme A (CoA) thioesterification catalyzed by an aromatic acid: CoA ligase. Adaptation of such pathways to the bioremediation of man-made pollutants such as polychlorinated biphenyl (PCB) and dichlorodiphenyltrichloroethane (DDT) requires that the chlorinated benzoic acid byproduct that is formed be able to be eliminated by further degradation. To take advantage of natural benzoic acid degrading pathways requiring initial ring activation by thioesterification, the pathway aromatic acid:CoA ligase must be an effective catalyst with the chlorinated benzoic acid. This study, which focuses on the 4-chlorobenzoate:CoA ligase (CBL) of the 4-monochlorobiphenyl degrading bacterium Alcaligenes sp. strain ALP83, was carried out to determine if the 4-chlorobenzoate binding site of this enzyme can be transformed by rational design to recognize the chlorobenzoic acids formed in the course of breakdown of other environmental PCB congeners. The fundamental question addressed in this study is whether it is possible to add or subtract space from the substrate-binding pocket of this ligase (to complement the topology of the unnatural aromatic substrate) without causing disruption of the ligase catalytic machinery. Herein, we report the results of a substrate specificity analysis that, when interpreted within the context of the X-ray crystal structures, set the stage for the rational design of the ligase for thioesterification of two PCB-derived chlorobenzoic acids. The ligase was first optimized to catalyze CoA thioesterification of 3,4-dichlorobenzoic acid, a poor substrate, by truncating Ile303, a large hydrophobic residue that packs against the ring meta-C(H) group. The structural basis for the approximately 100-fold enhancement in the rate of 3,4-dichlorobenzoate thioesterification catalyzed by the I303A and I303G CBL mutants was validated by determination of the crystal structure of the 3,4-dichlorobenzoate-bound enzymes. Determinations of the structures of I303 mutant complexes of 3-chlorobenzoate, a very poor substrate, revealed nonproductive binding as a result of the inability of the substrate ring C(4)H group to fill the pocket that binds the C(4)Cl group of the native substrate. The C(4)Cl pocket of the CBL I303A mutant was then reduced in size by strategic amino acid replacement. A 54-fold improvement in catalytic efficiency was observed for the CBL F184W/I303A/V209T triple mutant. The results of this investigation are interpreted as evidence that the plasticity of the ligase catalytic scaffold is sufficient to allow expansion of substrate range by rational design. The combination of structural and kinetic analyses of the constructed mutants proved to be an effective approach to engineering the ligase for novel substrates.     

Retuning Rieske-type oxygenases to expand substrate range

Rieske-type oxygenases are promising biocatalysts for the destruction of persistent pollutants or for the synthesis of fine chemicals. In this work, we explored pathways through which Rieske-type oxygenases evolve to expand their substrate range. BphAE(p4), a variant biphenyl dioxygenase generated from Burkholderia xenovorans LB400 BphAE(LB400) by the double substitution T335A/F336M, and BphAE(RR41), obtained by changing Asn(338), Ile(341), and Leu(409) of BphAE(p4) to Gln(338), Val(341), and Phe(409), metabolize dibenzofuran two and three times faster than BphAE(LB400), respectively. Steady-state kinetic measurements of single- and multiple-substitution mutants of BphAE(LB400) showed that the single T335A and the double N338Q/L409F substitutions contribute significantly to enhanced catalytic activity toward dibenzofuran. Analysis of crystal structures showed that the T335A substitution relieves constraints on a segment lining the catalytic cavity, allowing a significant displacement in response to dibenzofuran binding. The combined N338Q/L409F substitutions alter substrate-induced conformational changes of protein groups involved in subunit assembly and in the chemical steps of the reaction. This suggests a responsive induced fit mechanism that retunes the alignment of protein atoms involved in the chemical steps of the reaction. These enzymes can thus expand their substrate range through mutations that alter the constraints or plasticity of the catalytic cavity to accommodate new substrates or that alter the induced fit mechanism required to achieve proper alignment of reaction-critical atoms or groups.     

An expanded conformation of single-ring GroEL-GroES complex encapsulates an 86 kDa substrate

Electron cryomicroscopy reveals an unprecedented conformation of the single-ring mutant of GroEL (SR398) bound to GroES in the presence of Mg-ATP. This conformation exhibits a considerable expansion of the folding cavity, with approximately 80% more volume than the X-ray structure of the equivalent cis cavity in the GroEL-GroES-(ADP)(7) complex. This expanded conformation can encapsulate an 86 kDa heterodimeric (alphabeta) assembly intermediate of mitochondrial branched-chain alpha-ketoacid dehydrogenase, the largest substrate ever observed to be cis encapsulated. The SR398-GroES-Mg-ATP complex is found to exist as a mixture of standard and expanded conformations, regardless of the absence or presence of the substrate. However, the presence of even a small substrate causes a pronounced bias toward the expanded conformation. Encapsulation of the large assembly intermediate is supported by a series of electron cryomicroscopy studies as well as the protection of both alpha and beta subunits of the substrate from tryptic digestion.     

Evolutionary domain fusion expanded the substrate specificity of the transmembrane electron transporter DsbD

Modular organization of proteins has been postulated as a widely used strategy for protein evolution. The multidomain transmembrane protein DsbD catalyzes the transfer of electrons from the cytoplasm to the periplasm of Escherichia coli. Most bacterial species do not have DsbD, but instead their genomes encode a much smaller protein, CcdA, which resembles the central hydrophobic domain of DsbD. We used reciprocal heterologous complementation assays between E.coli and Rhodobacter capsulatus to show that, despite their differences in size and structure, DsbD and CcdA are functional homologs. While DsbD transfers reducing potential to periplasmic protein disulfide bond isomerases and to the cytochrome c thioreduction pathway, CcdA appears to be involved only in cytochrome c biogenesis. Our findings strongly suggest that, by the acquisition of additional thiol-redox active domains, DsbD expanded its substrate specificity.     

Reaction design for evaluation of the substrate range of hydrolases

Biocatalytic acylation reactions involving 24 alcohols, 8 acyl donors and 6 hydrolases were analysed using an original method. The reaction outcome was determined by semi-automated semi-automated solid-phase microextraction and GC/MS (SPME-GC/MS) allowing rapid evaluation of the success rate of each enzyme. Using Candida antarctica Lipase B (CALB), in 36% of the cases (46 reactions) quantitative conversion of the starting alcohol was observed, with an average isolated yield of 96%. The platform was then used to screen other enzymes with the CALB non-reacting substrates, allowing the design and optimisation of some efficient enzymatic reactions. Modification of the odour profile of rose essential oils by enzymatic treatment was also carried out.     

Reaction design for evaluation of the substrate range of hydrolases

Biocatalytic acylation reactions involving 24 alcohols, 8 acyl donors and 6 hydrolases were analysed using an original method. The reaction outcome was determined by semi-automated semi-automated solid-phase microextraction and GC/MS (SPME-GC/MS) allowing rapid evaluation of the success rate of each enzyme. Using Candida antarctica Lipase B (CALB), in 36% of the cases (46 reactions) quantitative conversion of the starting alcohol was observed, with an average isolated yield of 96%. The platform was then used to screen other enzymes with the CALB non-reacting substrates, allowing the design and optimisation of some efficient enzymatic reactions. Modification of the odour profile of rose essential oils by enzymatic treatment was also carried out.     

Engineered jadomycin analogues with altered sugar moieties revealing JadS as a substrate flexible O-glycosyltransferase

Applied Microbiology and Biotechnology - Glycosyltransferases (GTs)-mediated glycodiversification studies have drawn significant attention recently, with the goal of generating bioactive compounds...     

Evidence for a widely expanded humpback whale calving range along the Western Australian coast

The recognized calving grounds of humpback whales (Megaptera novaeangliae) that breed along the Western Australian coast (Breeding Stock D) extend along the Kimberley coast between Camden Sound and Broome (15°–18°S). However, there are reports of neonates further south, suggesting that the calving areas may be poorly defined. During aerial photogrammetric research in 2013 and 2015, we sighted large numbers of humpback whale calves along North West Cape (21°47′–22°43′S). We estimated the minimum relative calf abundance to be 463–603 in 2013 and 557–725 in 2015. We categorized the calves as either neonate or post neonate according to their color and size. The majority of calves sighted in both years (85% in 2013; 94% in 2015) were neonates. Our observations indicate that a minimum of approximately 20% (17.1%–24.3%) of the expected number of calves of this population are born near, or south of, North West Cape. We thus demonstrate that the calving grounds for the Breeding Stock D population extend south from Camden Sound in the Kimberley (15°S) to at least North West Cape (22°43′S), 1,000 km southwest of the currently recognized calving area.     

Minimal methylated substrate and extended substrate range of Escherichia coli AlkB protein,a 1-methyladenine-DNA dioxygenase

The Escherichia coli AlkB protein, and two human homologs ABH2 and ABH3, directly demethylate 1-methyladenine and 3-methylcytosine in DNA. They couple Fe(II)-dependent oxidative demethylation of these damaged bases to decarboxylation of alpha-ketoglutarate. Here, we have determined the kinetic parameters for AlkB oxidation of 1-methyladenine in poly(dA), short oligodeoxyribonucleotides, nucleotides, and nucleoside triphosphates. Methylated poly(dA) was the preferred AlkB substrate of those tested. The oligonucleotide trimer d(Tp1meApT) and even 5'-phosphorylated 1-me-dAMP were relatively efficiently demethylated, and competed with methylated poly(dA) for AlkB activity. A polynucleotide structure was clearly not essential for AlkB to repair 1-methyladenine effectively, but a nucleotide 5' phosphate group was required. Consequently, 1-me-dAMP(5') was identified as the minimal effective AlkB substrate. The nucleoside triphosphate, 1-me-dATP, was inefficiently but actively demethylated by AlkB; a reaction with 1-me-ATP was even slower. E. coli DNA polymerase I Klenow fragment could employ 1-me-dATP as a precursor for DNA synthesis in vitro, suggesting that demethylation of alkylated deoxynucleoside triphosphates by AlkB could have biological significance. Although the human enzymes, ABH2 and ABH3, demethylated 1-methyladenine residues in poly(dA), they were inefficient with shorter substrates. Thus, ABH3 had very low activity on the trimer, d(Tp1meApT), whereas no activity was detected with ABH2. AlkB is known to repair methyl and ethyl adducts in DNA; to extend this substrate range, AlkB was shown to reduce the toxic effects of DNA damaging agents that generate hydroxyethyl, propyl, and hydroxypropyl adducts.     

Evolution of flight morphology in a butterfly that has recently expanded its geographic range

Individuals colonizing unoccupied habitats typically possess characters associated with increased dispersal and, in insects, colonization success has been related to flight morphology. The speckled wood butterfly, Pararge aegeria, has undergone recent major expansions in its distribution: in the north of its range, P. aegeria has colonized many areas in north and east England, and in the south, it was first recorded on Madeira in 1976. We examined morphological traits associated with flight and reproduction in the northern subspecies tircis, and in the southern subspecies aegeria, from sites colonized about 20 years ago in northern England and on Madeira, respectively. Investment in flight was measured as relative wing area and thorax mass, and investment in reproduction as relative abdomen mass. All measurements were from individuals reared in a common environment and there were significant family effects in most of the variables measured. Compared with individuals from sites continuously occupied in recent history, colonizing individuals were larger (adult live mass). In the subspecies tircis, colonizing individuals also had relatively larger thoraxes and lower wing aspect ratios indicating that evolutionary changes in flight morphology may be related to colonization. However, sex by site interactions in analyses of thorax mass and abdomen mass suggest different selection pressures on flight morphology between the sexes in relation to colonization. Overall, the subspecies aegeria was smaller (adult live mass) and had a relatively larger thorax and wings, and smaller abdomen than subspecies tircis. Evolutionary changes in flight morphology and dispersal rate may be important determinants of range expansion, and may affect responses to future climate change. Received: 1 March 1999 / Accepted: 30 June 1999     

Alteration of the substrate range of haloalkane dehalogenase by site-directed mutagenesis

We attempted to expand the range of chlorinated solvents degraded by Xanthobacter autotrophicus GJ10 to include trichloroethylene by the rational modification of the enzyme haloalkane dehalogenase. The amino acids Phe164, Asp170, Phe172 and Trp175 were individually replaced with alanine by site-directed mutagenesis. All substitutions produced enzymes with lower than wild type activity with 1,2-dichloroethane. The Phe164Ala and Asp170Ala mutants were 3 and 2 times more active than was the wild type enzyme in dechlorinating 1,6-dichlorohexane. The Asp170Ala mutant resembled the wild type enzyme in its relative activity against longer chain substrates. No mutant was active with trichloroethylene.     

An engineered viral protease exhibiting substrate specificity for a polyglutamine stretch prevents polyglutamine-induced neuronal cell death

Background

Polyglutamine (polyQ)-induced protein aggregation is the hallmark of a group of neurodegenerative diseases, including Huntington''s disease. We hypothesized that a protease that could cleave polyQ stretches would intervene in the initial events leading to pathogenesis in these diseases. To prove this concept, we aimed to generate a protease possessing substrate specificity for polyQ stretches.

Methodology/Principal Findings

Hepatitis A virus (HAV) 3C protease (3CP) was subjected to engineering using a yeast-based method known as the Genetic Assay for Site-specific Proteolysis (GASP). Analysis of the substrate specificity revealed that 3CP can cleave substrates containing glutamine at positions P5, P4, P3, P1, P2′, or P3′, but not substrates containing glutamine at the P2 or P1′ positions. To accommodate glutamine at P2 and P1′, key residues comprising the active sites of the S2 or S1′ pockets were separately randomized and screened. The resulting sets of variants were combined by shuffling and further subjected to two rounds of randomization and screening using a substrate containing glutamines from positions P5 through P3′. One of the selected variants (Var26) reduced the expression level and aggregation of a huntingtin exon1-GFP fusion protein containing a pathogenic polyQ stretch (HttEx1(97Q)-GFP) in the neuroblastoma cell line SH-SY5Y. Var26 also prevented cell death and caspase 3 activation induced by HttEx1(97Q)-GFP. These protective effects of Var26 were proteolytic activity-dependent.

Conclusions/Significance

These data provide a proof-of-concept that proteolytic cleavage of polyQ stretches could be an effective modality for the treatment of polyQ diseases.     

A unique cellular myosin II exhibiting differential expression in the cerebral cortex

Clones possessing inserts of brain myosin II have been obtained by screening a rat brain cDNA expression library with a polyclonal antibody, raised against myosin II from the mouse neuroblastoma cell line, Neuro-2A. A partial sequence comprising the 3' coding and non-coding regions of the myosin message has been determined which is markedly different from other myosin sequences. The derived amino-acid sequence comprises the C-terminal 90 amino acids: VSS(PO4)LKNKLRRGDLPFVVTRRLVRKGTLELS(PO4)DDDDESKASLINETQPPQCLDQQ LDQQ LDQLFNWPVNAGCVCGWGVEQTQGEEAVHKCRT(CO2H). This sequence encompasses regions homologous to both the casein kinase II and protein kinase C heavy-chain phosphorylation sites. The non-helical "tail-piece" is considerably longer (an additional 39 amino acid residues) than found in other myosins. Northern blot analysis demonstrates this myosin II message to be unique to cerebral cortex, with no expression in all other non-cortical brain regions and peripheral tissues tested. Our results suggest functional diversity for myosin II isozymes within the brain.     

Stilbenoids of Kobresia nepalensis (Cyperaceae) exhibiting DNA topoisomerase II inhibition

Resveratrol oligomers, nepalensinol A, B and C, were isolated from the stem of Kobresia nepalensis (Cyperaceae). The structures were established on the basis of chemical properties and spectroscopic evidence including 2D NMR spectroscopic analysis. Nepalensinol A, B and C showed a potent inhibitory effect on topoisomerase II - stronger than etoposide (VP-16), a topoisomerase II inhibitor used as an anti-cancer drug. Nepalensinol B, in particular, exhibited the most potent activity with an IC₅₀ of 0.02 μg/ml.