Role of glutamine-169 in the substrate recognition of human aminopeptidase B

Background

Aminopeptidase B (EC 3.4.11.6, APB) preferentially hydrolyzes N-terminal basic amino acids of synthetic and peptide substrates. APB is involved in the production and maturation of peptide hormones and neurotransmitters such as miniglucagon, cholecystokinin and enkephalin by cleaving N-terminal basic amino acids in extended precursor proteins. Therefore, the specificity for basic amino acids is crucial for the biological function of APB.

Methods

Site-directed mutagenesis and molecular modeling of the S1 site were used to identify amino acid residues of the human APB responsible for the basic amino acid preference and enzymatic efficiency.

Results

Substitution of Gln169 with Asn caused a significant decrease in hydrolytic activity toward the fluorescent substrate Lys-4-methylcoumaryl-7-amide (MCA). Substantial retardation of enzyme activity was observed toward Arg-MCA and substitution with Glu caused complete loss of enzymatic activity of APB. Substitution with Asn led to an increase in IC₅₀ values of inhibitors that interact with the catalytic pocket of APB. The EC₅₀ value of chloride ion binding was also found to increase with the Asn mutant. Gln169 was required for maximal cleavage of the peptide substrates. Molecular modeling suggested that interaction of Gln169 with the N-terminal Arg residue of the substrate could be bridged by a chloride anion.

Conclusion

Gln169 is crucial for obtaining optimal enzymatic activity and the unique basic amino acid preference of APB via maintaining the appropriate catalytic pocket structure and thus for its function as a processing enzyme of peptide hormones and neurotransmitters.     

Structure/Function Relationships of Adipose Phospholipase A2 Containing a Cys-His-His Catalytic Triad

Adipose phospholipase A₂ (AdPLA or Group XVI PLA₂) plays an important role in the onset of obesity by suppressing adipose tissue lipolysis. As a consequence, AdPLA-deficient mice are resistant to obesity induced by a high fat diet or leptin deficiency. It has been proposed that AdPLA mediates its antilipolytic effects by catalyzing the release of arachidonic acid. Based on sequence homology, AdPLA is part of a small family of acyltransferases and phospholipases related to lecithin:retinol acyltransferase (LRAT). To better understand the enzymatic mechanism of AdPLA and LRAT-related proteins, we solved the crystal structure of AdPLA. Our model indicates that AdPLA bears structural similarity to proteins from the NlpC/P60 family of cysteine proteases, having its secondary structure elements configured in a circular permutation of the classic papain fold. Using both structural and biochemical evidence, we demonstrate that the enzymatic activity of AdPLA is mediated by a distinctive Cys-His-His catalytic triad and that the C-terminal transmembrane domain of AdPLA is required for the interfacial catalysis. Analysis of the enzymatic activity of AdPLA toward synthetic and natural substrates indicates that AdPLA displays PLA₁ in addition to PLA₂ activity. Thus, our results provide insight into the enzymatic mechanism and biochemical properties of AdPLA and LRAT-related proteins and lead us to propose an alternate mechanism for AdPLA in promoting adipose tissue lipolysis that is not contingent on the release of arachidonic acid and that is compatible with its combined PLA₁/A₂ activity.     

Black soybean extract can attenuate thrombosis through inhibition of collagen-induced platelet activation

Many clinical trials have demonstrated the beneficial effects of soybean (Glycine max) on general cardiovascular health. Among a variety of soybeans, black soybean is known to display diverse biological activities superior to those of yellow and green soybeans, such as in antioxidant, anti-inflammatory and anticancer activities. However, few studies have been directed on the effect of black soybean on cardiovascular function. In this study, we aimed to investigate the effect of black soybean extract (BB) on platelet activation, a key contributor to thrombotic diseases. In freshly isolated human platelets, BB has shown potent inhibitory activity on collagen-induced platelet aggregation, while yellow soybean extract had marginal activity only. BB also attenuated serotonin secretion and P-selectin expression, which are important factors for the platelet–tissue interaction along with thromboxane A₂ formation. These in vitro results were further confirmed in an ex vivo platelet aggregation measurement and in vivo venous thrombosis model where oral administration of BB reduced collagen-induced platelet aggregation and FeCl₃-induced thrombus formation significantly. A potential active ingredient for antiplatelet effects of BB was isolated and identified to be adenosine through bioassay-directed fractionation and NMR and ESI-MS analyses. These results indicate that black soybean can be a novel dietary supplement for the prevention of cardiovascular risks and the improvement of blood circulation.     

Selecting the signals for a brain-machine interface

Brain-machine interfaces are being developed to assist paralyzed patients by enabling them to operate machines with recordings of their own neural activity. Recent studies show that motor parameters, such as hand trajectory, and cognitive parameters, such as the goal and predicted value of an action, can be decoded from the recorded activity to provide control signals. Neural prosthetics that use simultaneously a variety of cognitive and motor signals can maximize the ability of patients to communicate and interact with the outside world. Although most studies have recorded electroencephalograms or spike activity, recent research shows that local field potentials (LFPs) offer a promising additional signal. The decode performances of LFPs and spike signals are comparable and, because LFP recordings are more long lasting, they might help to increase the lifetime of the prosthetics.     

Determination of catalase activity using chromogenic probe involving iso-nicotinicacidhydrazide and pyrocatechol

A biocatalatic pathway involving chromogenic probe has been proposed for the determination of catalase activity by means of iso-nicotinicacidhydrazide (INH) and pyrocatechol (PC). The assay is based on the enzymatic consumption of hydrogen peroxide using INH-PC system. The response of the catalase activity was ascertained by the rate of the reaction involving 14.10 mM H₂O₂. On addition of H₂O₂, INH-PC indicator system formed a chromogenic product with absorbance maxima at 490 nm. Hence the activity of catalase was directly measured by the chromogenic response in the formation of the coupled product. The catalase assay was elaborated by the kinetic response of the INH-PC system. The linearity of the catalase activity and H₂O₂ was in the range 0.2-7.0 units and 1.76-7.0 mM, respectively in 3 ml solution. The catalytic efficiency and catalytic power were calculated. The Michaelis-Menten constant of INH, PC and H₂O₂ were found to be 0.344, 0.176 and 8.82 mM, respectively. The indicator reaction was applied in the determination of catalase activity in mycelia mats and culture media.     

Molecular properties of the glucosaminidase AcmA from Lactococcus lactis MG1363: Mutational and biochemical analyses

The major autolysin AcmA of Lactococcus lactis ssp. cremoris MG1363 is a modular protein consisting of an N-terminal signal sequence, a central enzymatic region (glu_acma as a glucosaminidase), and a C-terminal cell-recognition domain (LysM123). glu_acma (about 160 amino acids) belongs to the glycoside hydrolase (GH) 73 family, and the two acidic residues E128 and D153 have been thought to be catalytically important. In this study, amino-acid substitution analysis of AcmA was first carried out in the Escherichia coli system. Point mutations E94A, E94Q, E128A, D153A, and Y191A markedly reduced cell-lytic activity (3.8%, 1.1%, 4.2%, 4.8%, and 2.4%, respectively), whereas E128Q and D153N retained significant residual activities (32.1% and 44.0%, respectively). On the other hand, Y191F and Y191W mutations retained high activities (66.2% and 46.0%, respectively). These results showed that E94 (rather than E128 and D153) and the aromatic residue Y191 probably play important roles in catalysis of AcmA. Together with mutational analysis of another GH73 glucoaminidase Glu_atlwm from the Staphylococcus warneri M autolysin Atl_WM, these results suggested that the GH73 members cleave a glycosidic bond via a substrate-assisted mechanism, as postulated in the GH20 members. AcmA and Glu_atlwm were purified from E. coli recombinant cells, and their enzymatic properties were studied.     

Chemical profiling of the deacetylase activity of acetyl xylan esterase A (AxeA) variants on chitooligosaccharides using hydrophilic interaction chromatography-mass spectrometry

Chitosan oligosaccharides (oligomers of (GlcNAc)_x(GlcN)_y) are used in the pharmaceutical, cosmetic and food industries and are reported to have therapeutic benefits. However, it is unknown whether their biological activity depends on the degree of deacetylation or the sequence of residues within the oligomer. We report here the development of a random mutagenesis method for directed evolution of Streptomyces lividans acetyl xylan esterase (AxeA), which we previously showed is able to deacetylate chitinous substrate, in order to obtain chitooligosaccharides with well-defined structural properties. A colorimetric assay was used to pre-screen libraries for p-nitrophenol acetate hydrolysis activity and an HPLC-UV absorbance assay was optimized to subsequently screen for deacetylase activity toward hexa-N-acetyl-glucosamine substrate (GlcNAc)₆. Native AxeA and two variants displaying > 50% deacetylation of the oligohexamer substrate after reaction at 50 °C for 24 h in diluted culture supernatant were then selected for detailed analysis of the enzymatic products. A HILIC (hydrophilic interaction chromatography)-mode LC method was developed for profiling the deacetylated chitooligosaccharide products and HILIC-MS/MS sequencing revealed that ca. 30 different deacetylation products ranging from (GlcNAc)₅(GlcN)₁ to (GlcNAc)₁(GlcN)₅ and isomers thereof were produced. The AxeA variants produced, on average, 26% more unique products than the native enzyme; however, none were able to fully deacetylate the substrate to make (GlcN)₆. The long term goal of this multidisciplinary approach is to improve the activity of chitosan oligosaccharides to an industrially applicable level.     

Endogenous generation of sulfur dioxide in rat tissues

While sulfur dioxide (SO₂) has been previously known for its toxicological effects, it is now known to be produced endogenously in mammals from sulfur-containing amino acid l-cysteine. l-cysteine is catalyzed by cysteine dioxygenase (CDO) to l-cysteinesulfinate, which converts to β-sulfinylpyruvate through transamination by aspartate aminotransferase (AAT), and finally spontaneously decomposes to pyruvate and SO₂. The present study explored endogenous SO₂ production, and AAT and CDO distribution in different rat tissue. SO₂ content was highest in stomach, followed by tissues in the right ventricle, left ventricle, cerebral gray matter, pancreas, lung, cerebral white matter, renal medulla, spleen, renal cortex and liver. AAT activity and AAT1 mRNA expression were highest in the left ventricle, while AAT1 protein expression was highest in the right ventricle. AAT2 and CDO mRNA expressions were both highest in liver tissue. AAT2 protein expression was highest in the renal medulla, but CDO protein expression was highest in liver tissue. In all tissues, AAT1 and AAT2 were mainly distributed in the cytoplasm rather than the nucleus. These observed differences among tissues endogenously generating SO₂ and associated enzymes are important in implicating the discovery of SO₂ as a novel endogenous signaling molecule.     

Light-regulated nuclear localization of phytochromes

Phytochrome is a soluble protein that regulates various responses of plants to light. Not all but most of the phytochrome responses are accompanied by changes in the pattern of gene expression. Upon light activation, phytochrome is imported into the nucleus by the nuclear localization activity of the carboxy-terminal half of the molecule. In darkness, the amino-terminal chromophoric domain suppresses this activity to retain the molecule in the cytoplasm. In the nucleus, light-activated phytochrome forms speckles whose biological function remains unclear.     

Use of Enzymatic Biosensors to Quantify Endogenous ATP or H2O2 in the Kidney

Enzymatic microelectrode biosensors have been widely used to measure extracellular signaling in real-time. Most of their use has been limited to brain slices and neuronal cell cultures. Recently, this technology has been applied to the whole organs. Advances in sensor design have made  possible the measuring of cell signaling in blood-perfused in vivo kidneys. The present protocols list the steps needed to measure ATP and H₂O₂ signaling in the rat kidney interstitium. Two separate sensor designs are used for the ex vivo and in vivo protocols. Both types of sensor are coated with a thin enzymatic biolayer on top of a permselectivity layer to give fast responding, sensitive and selective biosensors. The permselectivity layer protects the signal from the interferents in biological tissue, and the enzymatic layer utilizes the sequential catalytic reaction of glycerol kinase and glycerol-3-phosphate oxidase in the presence of ATP to produce H₂O₂. The set of sensors used for the ex vivo studies further detected analyte by oxidation of H₂O₂ on a platinum/iridium (Pt-Ir) wire electrode. The sensors for the in vivo studies are instead based on the reduction of H₂O₂ on a mediator coated gold electrode designed for blood-perfused tissue. Final concentration changes are detected by real-time amperometry followed by calibration to known concentrations of analyte. Additionally, the specificity of the amperometric signal can be confirmed by the addition of enzymes such as catalase and apyrase that break down H₂O₂ and ATP correspondingly. These sensors also rely heavily on accurate calibrations before and after each experiment. The following two protocols establish the study of real-time detection of ATP and H₂O₂ in kidney tissues, and can be further modified to extend the described method for use in other biological preparations or whole organs.     

Quantitative imaging of rhizosphere pH and CO2 dynamics with planar optodes

Background and Aims

Live imaging methods have become extremely important for the exploration of biological processes. In particular, non-invasive measurement techniques are key to unravelling organism–environment interactions in close-to-natural set-ups, e.g. in the highly heterogeneous and difficult-to-probe environment of plant roots: the rhizosphere. pH and CO₂ concentration are the main drivers of rhizosphere processes. Being able to monitor these parameters at high spatio-temporal resolution is of utmost importance for relevant interpretation of the underlying processes, especially in the complex environment of non-sterile plant–soil systems. This study introduces the application of easy-to-use planar optode systems in different set-ups to quantify plant root–soil interactions.

Methods

pH- and recently developed CO₂-sensors were applied to rhizobox systems to investigate roots with different functional traits, highlighting the potential of these tools. Continuous and highly resolved real-time measurements were made of the pH dynamics around Triticum turgidum durum (durum wheat) roots, Cicer arietinum (chickpea) roots and nodules, and CO₂ dynamics in the rhizosphere of Viminaria juncea.

Key Results

Wheat root tips acidified slightly, while their root hair zone alkalized their rhizosphere by more than 1 pH unit and the effect of irrigation on soil pH could be visualized as well. Chickpea roots and nodules acidified the surrounding soil during N₂ fixation and showed diurnal changes in acidification activity. A growing root of V. juncea exhibited a large zone of influence (mm) on soil CO₂ content and therefore on its biogeochemical surrounding, all contributing to the extreme complexity of the root–soil interactions.

Conclusions

This technique provides a unique tool for future root research applications and overcomes limitations of previous systems by creating quantitative maps without, for example, interpolation and time delays between single data points.     

Structural aspects of the distinct biochemical properties of glutaredoxin 1 and glutaredoxin 2 from Saccharomyces cerevisiae

Glutaredoxins (Grxs) are small (9-12 kDa) heat-stable proteins that are ubiquitously distributed. In Saccharomyces cerevisiae, seven Grx enzymes have been identified. Two of them (yGrx1 and yGrx2) are dithiolic, possessing a conserved Cys-Pro-Tyr-Cys motif. Here, we show that yGrx2 has a specific activity 15 times higher than that of yGrx1, although these two oxidoreductases share 64% identity and 85% similarity with respect to their amino acid sequences. Further characterization of the enzymatic activities through two-substrate kinetics analysis revealed that yGrx2 possesses a lower K_M for glutathione and a higher turnover than yGrx1. To better comprehend these biochemical differences, the pK_a of the N-terminal active-site cysteines (Cys27) of these two proteins and of the yGrx2-C30S mutant were determined. Since the pK_a values of the yGrx1 and yGrx2 Cys27 residues are very similar, these parameters cannot account for the difference observed between their specific activities. Therefore, crystal structures of yGrx2 in the oxidized form and with a glutathionyl mixed disulfide were determined at resolutions of 2.05 and 1.91 Å, respectively. Comparisons of yGrx2 structures with the recently determined structures of yGrx1 provided insights into their remarkable functional divergence. We hypothesize that the substitutions of Ser23 and Gln52 in yGrx1 by Ala23 and Glu52 in yGrx2 modify the capability of the active-site C-terminal cysteine to attack the mixed disulfide between the N-terminal active-site cysteine and the glutathione molecule. Mutagenesis studies supported this hypothesis. The observed structural and functional differences between yGrx1 and yGrx2 may reflect variations in substrate specificity.     

Determination of the Amino Acid Sequence of a New Phospholipase A<Subscript>2</Subscript> (MIDCA1) Isolated from <Emphasis Type="Italic">Micrurus dumerilii carinicauda</Emphasis> Venom

A new Phospholipase A₂ (PLA₂) from Micrurus dumerilii carinicauda venom was isolated and its primary structure determined. This new PLA₂ showed a low enzymatic activity when compared with other PLA₂s and it is moderately basic with an isoelectric point of 8.0. Its amino acid sequence showed the presence of 120 amino acid residues and its sequence was: NLIQFLNMIQCTTPGREPLVAFANYGCYCGRGGSGTPVDELDRCCQVHDNCYDTAKKVFGCSPYFTMYSYDCSEGKLTCKDNNTKCKAAVCNCDRTAALCFAKAPYNDKNYKIDLTKRCQ. The structural model of MIDCA1, when compared with other strong neurotoxic PLA₂s, such as Naja naja, showed significant differences in the β-wing and neurotoxic sites, despite the high level of amino acid sequence similarity. These observations indicate a dissociation between the biological and catalytic activity of this new PLA₂, supporting the view that other regions of the protein are involved in the biological effects.     

牛流行热病毒糖蛋白G1抗原表位在毕赤酵母中的表达和抗原性鉴定

从包含牛流行热病毒G蛋白基因的质粒pMD-G中克隆G₁抗原表位区基因,亚克隆进表达载体pPIC9K,构建重组载体pPIC9K-G₁,线性化后电转化毕赤酵母GS115,通过G418压力和PCR法筛选阳性重组酵母进行诱导表达。经SDS-PAGE、脱糖基化分析、Western blot、ELISA、兔体免疫实验和特异性分析,表明该基因在GS115中表达并进行了适度的糖基化,表达蛋白有良好的生物学活性和特异性,可作为包被抗原,开发ELISA诊断试剂盒。     

牛流行热病毒糖蛋白G1抗原表位在毕赤酵母中的表达和抗原性鉴定

从包含牛流行热病毒G蛋白基因的质粒pMD-G中克隆G₁抗原表位区基因,亚克隆进表达载体pPIC9K,构建重组载体pPIC9K-G₁,线性化后电转化毕赤酵母GS115,通过G418压力和PCR法筛选阳性重组酵母进行诱导表达。经SDS-PAGE、脱糖基化分析、Western blot、ELISA、兔体免疫实验和特异性分析,表明该基因在GS115中表达并进行了适度的糖基化,表达蛋白有良好的生物学活性和特异性,可作为包被抗原,开发ELISA诊断试剂盒。     

Replacement or exclusion of the B-branch bacteriopheophytin in the purple bacterial reaction centre: The HB cofactor is not required for assembly or core function of the Rhodobacter sphaeroides complex

All of the membrane-embedded cofactors of the purple bacterial reaction centre have well-defined functional or structural roles, with the exception of the bacteriopheophytin (H_B) located approximately half-way across the membrane on the so-called inactive- or B-branch of cofactors. Sequence alignments indicate that this bacteriochlorin cofactor is a conserved feature of purple bacterial reaction centres, and a pheophytin is also found at this position in the Photosystem-II reaction centre. Possible structural or functional consequences of replacing the H_B bacteriopheophytin by bacteriochlorophyll were investigated in the Rhodobacter sphaeroides reaction centre through mutagenesis of residue Leu L185 to His (LL185H). Results from absorbance spectroscopy indicated that the LL185H mutant assembled with a bacteriochlorophyll at the H_B position, but this did not affect the capacity of the reaction centre to support photosynthetic growth, or change the kinetics of charge separation along the A-branch of cofactors. It was also found that mutation of residue Ala M149 to Trp (AM149W) caused the reaction centre to assemble without an H_B bacteriochlorin, demonstrating that this cofactor is not required for correct assembly of the reaction centre. The absence of a cofactor at this position did not affect the capacity of the reaction centre to support photosynthetic growth, or the kinetics of A-branch electron transfer. A combination of X-ray crystallography and FTIR difference spectroscopy confirmed that the H_B cofactor was absent in the AM149W mutant, and that this had not produced any significant disturbance of the adjacent ubiquinol reductase (Q_B) site. The data are discussed with respect to possible functional roles of the H_B bacteriopheophytin, and we conclude that the reason(s) for conservation of a bacteriopheophytin cofactor at this position in purple bacterial reaction centres are likely to be different from those underlying conservation of a pheophytin at the analogous position in Photosystem-II.