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Dissolved organic matter (DOM) degradation in freshwater rivers and streams plays a major role in the global carbon cycle. However, little is known about how the source and composition of riverine DOM contribute to the production of greenhouse gases, especially in high-latitude areas with a large proportion of carbon-rich peatlands. Here, we conducted for the first time the combination of molecular-level characterization of terrestrially derived DOM and the potential carbon dioxide (CO2) production measurements in pristine subarctic rivers of Finnish Lapland. 21-day incubation studies were conducted with water samples taken from two rivers differing in DOM content during spring and fall 2018. The changes in the DOM concentration and molecular composition, as well as the CO2 production, were measured. The DOM molecular characterization was carried out using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Our results demonstrate efficient mineralization of dissolved organic carbon (DOC) into CO2 in mineral soil associated clearwater river during the incubation, while significantly lower CO2 production per DOC was observed in the brown-water river surrounded by peatlands. The limited degradability in the brown-water river was caused by a large number of terrestrial and aromatic compounds (i.e., highly unsaturated and phenolic compounds, condensed aromatics, and polyphenolics) from surrounding peatlands. In the clearwater river, the percentage of formulas assigned to aliphatics decreased over the incubation, indicating microbial utilization of biolabile DOM. This study highlights the importance of energy-rich, biolabile molecular compounds and the contribution of clearwater systems in the DOM degradation dynamics of subarctic catchments.

Along with the evidence and analyses expounded on in this book, this chapter provides conclusions and suggestions concerning policy implications. These are based on a perspective that calls attention to the need for a holistic approach to look at the nexus of forests, the bioeconomy and climate change. Moreover, it is emphasised that, given the different uses of forests and the scarcity of forest resources, it makes sense to try to find ways to maximise synergies and minimise trade-offs between the different usages of forests. The forest-based sector contributes to climate-change mitigation via three channels––forests are a carbon sink, forest-based products can substitute for fossil-based products, and these products can store carbon for up to centuries. However, achieving these mitigation potentials in the future depends on forests being made resilient to the changing climate. Therefore, mitigation and adapting forests to climate change are married, both needing to be advanced simultaneously. Globally and in the EU, around 80–90% of the CO2 emissions originate from the use of coal, oil and natural gas. Consequently, the core issue in the fight against climate change is the phasing out of fossil-based products. Reaching this goal will not be possible without substituting also forest-based bioproducts for the purposes we are using oil, coal and gas for today. In the EU, this implies paying more attention to the need to develop new innovations in the forest bioeconomy, improve the resource efficiency and circularity of the bioproducts already available, and monitor the environmental sustainability of the bioeconomy.

The tree bark represents an abundant but currently underutilized forest biomass side stream. In this work, temperature-programmed slow pyrolysis with fractional condensation was used for thermochemical conversion of the bark obtained from three short rotation tree species, aspen, goat willow, and rowan. Heating was performed in three stages, drying (135 °C), torrefaction (275 °C), and pyrolysis (350 °C), and the resulting vapors were condensed at 120, 70, and 5 °C, producing nine liquid fractions. An additional fraction was collected in the pyrolysis stage at 0 °C. The obtained liquid fractions were characterized in terms of their yields and bulk chemistry (i.e., CHNOS content, water content, pH, and total acid number) as well as their molecular level chemistry by high-resolution mass spectrometry. The highest liquid yields were obtained for the fractions condensed at 70 °C. The water content varied considerably, being the highest for the drying fractions (>96%) and the lowest for the pyrolysis fractions obtained at 120 °C (0.1-2%). Considerable compositional differences were observed between the liquid fractions. While the drying fractions contained mostly some dissolved phenolics, the torrefaction fractions contained more sugaric compounds. In contrast, the pyrolysis fractions were enriched lipids (e.g., suberinic fatty acids and their derivatives) and alicyclic/aromatic hydrocarbons. These fractions could be further refined into different platforms and/or specialty chemicals. Thus, slow pyrolysis with fractional condensation offers a potential route for the valorization of tree bark residues from forest industry.

International audience; Seven cloud water samples were collected from May to October 2018 at the Puy de Dôme station (PUY) in France and analyzed by positive-ion atmospheric pressure photoionization [(+)APPI] Fourier transform ion cyclotron resonance mass spectrometry. The assigned formulas (ranging from 3,865 to 6,380) were attributed using the multidimensional stoichiometric constraint classification of Rivas-Ubach et al. (2018, https://doi.org.10.1021/acs.analchem.8b00529) to six main categories (RUCs): LipidC, ProteinC, Amino-sugarC, CarbohydrateC, NucleotideC, and OxyaromaticC. Back trajectories were calculated by the computing atmospheric trajectory tool (CAT) model to obtain information on the air mass history. Partial least square regressions were performed using chemical data, CAT back-trajectory calculations and FT-ICR MS data to analyze the environmental variability of the organic sample composition. ProteinC is correlated with the continental surface for air masses transported within the boundary layer, and Amino-sugarC is strongly correlated with acetate, NO3- and NH4+, suggesting Anthropogenic sources for amino sugars and proteins. LipidC is correlated with the sea surface for air masses transported within the free troposphere, confirming the long-range transport of marine biogenic sources. Concerning Oxy-aromaticC, given the correlations with oxidants and pollutants, as well as anti-correlations with local influence, we proposed a mechanism of oxidation from remote anthropogenic sources.

The state of the world’s managed forests is determined by the societal demands for wood resources and other ecosystem services. The forest-based sector is experiencing a number of structural changes, which makes the task of looking ahead important, but challenging. One of the main trends in the forest-based industries is diversification. On one hand, this refers to the emergence of new factors influencing the demand for forest-based products, which leads to substitution between forest-based products and alternative products. On the other hand, it refers to new market opportunities for forest-based industries in, for example, the construction, textiles, packaging, biochemicals and biofuels markets. As the importance of some of the traditional forest-based industries, such as communication papers, is declining, and new opportunities are simultaneously emerging, the sector will not necessarily be dominated by single sectors in the long term. However, research illuminating the possible impacts of the expected structural changes of the forest-based sector remains scarce. The uncertainties in the future outlook of the forest-based sector also imply great uncertainties in the demand for roundwood globally, and by extension, the extent of trade-offs between different ecosystem services and land uses.

Groundwater : : journal of the Association of Ground-Water Scientists and Engineers, a division of the National Ground Water Association (2021). doi:10.1111/gwat.13087, Published by Wiley-Blackwell, Oxford [u.a.]

Journal of cell science 133(19), jcs239202 (1-15) - (2020). doi:10.1242/jcs.239202, Integrin activation and clustering by talin are early steps of cell adhesion. Membrane-bound talin head domain and kindlin bind to the �� integrin cytoplasmic tail, cooperating to activate the heterodimeric integrin, and the talin head domain induces integrin clustering in the presence of Mn$^{2+}$. Here we show that kindlin-1 can replace Mn2+ to mediate ��3 integrin clustering induced by the talin head, but not that induced by the F2���F3 fragment of talin. Integrin clustering mediated by kindlin-1 and the talin head was lost upon deletion of the flexible loop within the talin head F1 subdomain. Further mutagenesis identified hydrophobic and acidic motifs in the F1 loop responsible for ��3 integrin clustering. Modeling, computational and cysteine crosslinking studies showed direct and catalytic interactions of the acidic F1 loop motif with the juxtamembrane domains of ��- and ��3-integrins, in order to activate the ��3 integrin heterodimer, further detailing the mechanism by which the talin���kindlin complex activates and clusters integrins. Moreover, the F1 loop interaction with the ��3 integrin tail required the newly identified compact FERM fold of the talin head, which positions the F1 loop next to the inner membrane clasp of the talin-bound integrin heterodimer., Published by Company of Biologists Limited, Cambridge

Fast pyrolysis oil (FPO) produced from short-rotation willow was characterized by using high-resolution Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry and various bulk chemical analyses. The pyrolysis experiments were carried out on a bench-scale bubbling fluidized bed pyrolysis reactor operating at the temperature of 500 °C. The resulting pyrolysis oil was a single-phase liquid with relatively low oxygen content and had pH and total acid number values of 3.0 and 129 mg/g, respectively. A wealth of compositional information of the willow FPO was obtained using FT-ICR MS in combination with electrospray ionization (ESI) and atmospheric-pressure photoionization (APPI) techniques. While ESI preferentially ionized acidic extractives, small phenolics and anhydrosugars, APPI ionized clearly larger compounds, including neutral lipophilic extractives, triterpenoids and high molecular mass pyrolytic lignin, most of which are beyond conventional gas chromatography–mass spectrometry analyses.

We present a novel crystal structure of the IlvD/EDD family enzyme, l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT, EC 4.2.1.25), which catalyzes the conversion of l-arabinonate to 2-dehydro-3-deoxy-L-arabinonate. The enzyme is a tetramer consisting of a dimer of dimers, where each monomer is composed of two domains. The active site contains a catalytically important [2Fe-2S] cluster and Mg2+ ion and is buried between two domains, and also at the dimer interface. The active site Lys129 was found to be carbamylated. Ser480 and Thr482 were shown to be essential residues for catalysis, and the S480A mutant structure showed an unexpected open conformation in which the active site was more accessible for the substrate. This structure showed the partial binding of L-arabinonate, which allowed us to suggest that the alkoxide ion form of the Ser480 side chain functions as a base and the [2Fe-2S] cluster functions as a Lewis acid in the elimination reaction.

Pharmaceutically active compounds (PhACs) are emerging pollutants causing serious challenges to wastewater treatment plants due to poor biodegradability. In this study, the enhanced removal of highly recalcitrant and commonly monitored PhACs, carbamazepine (CBZ) and diclofenac (DCF) by heterogeneous photocatalysis was investigated using 5% Ag2O/P-25 photocatalyst. The photocatalyst was characterized by scanning electron microscope (SEM-EDX), Brunauer-Emmett-Teller (BET), Fourier transfer infrared spectroscopy (FTIR) and UV–vis diffuse reflectance spectra (UV-DRS). The effects of catalyst dose, initial pollutants concentration, and mineralization during the photocatalytic degradation of PhACs were investigated. The matrix effect was assessed in deionized water (DW) and real membrane bioreactor effluent (RME). Optimal CBZ and DCF removals of 89.10% and 93.5%, respectively for 180 min of UV irradiation were achieved at catalyst dosage of 0.4 g L−1 in DW matrix. However, the optimal catalyst dosages for CBZ and DCF in RME matrix were increased by factor 2 and 1.5, respectively, to achieve the same degree of removal. Declining trends of removal rate were observed when initial concentrations of both the PhACs were increased under optimal catalyst dosages, and kinetics seem to fit the Langmuir-Hinshelwood model. Photo-induced holes and OH were the dominant oxidation species involved in the photocatalytic degradation of the PhACs. A plausible reusability of 5% Ag2O/P-25 photocatalyst was observed for both the PhACs. Moreover, various aromatic/aliphatic intermediates generated during the photodegradation CBZ were identified using fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometry, and a possible multi-step degradation pathway was proposed. Overall, the removal of PhACs using 5% Ag2O/P-25 photocatalyst showed promising results in real wastewater. Post-print / Final draft

Coinage metal cyanides efficiently react with a triphosphine. PPh2C6H4-PPh-C6H4PPh2 (P(3)). to give the complexes M(P(3))CN, where M = Cu (1), Ag (2), and Au (3), which can further interact with coordinatively unsaturated metal centers [M(P(3))](+) to give the homobimetallic [(P(3))M-CN-M(P(3))](+)X(-) [M = Cu (4a with X(-) = CF3SO3(-) and 4b with X(-) = BF4(-)), Ag (5)] or heterometallic [(P(3))Au-CN-Ag(P(3))](+) (6) species. Extension of this approach also provided the trinuclear complex [(P(3))Cu-NC-Au-CN-Cu(P(3))](+) (7). Compounds 1-5 were characterized in the solid state by X-ray crystallography. The NMR spectroscopic studies revealed that all of the complexes except 6 retain their structures in solution. The title compounds are luminescent in the solid state, with quantum yields ranging from 8 to 87%. The observed photoemission originates mainly from the metal-to-ligand charge-transfer states according to time-dependent density functional theory computational studies. The crystalline bimetallic Cu complexes 4a/4b demonstrate extremely high sensitivity of the emission intensity to molecular O2 (KSV1 = 639 atm(-1) and LOD = 0.010% for 3 times the signal-to-noise ratio).

Proceedings of the National Academy of Sciences of the United States of America 115(27), 7141 - 7146 (2018). doi:10.1073/pnas.1806668115, Cyanobacteria are important photosynthetic organisms inhabiting a range of dynamic environments. This phylum is distinctive among photosynthetic organisms in containing genes encoding uncharacterized cystathionine β-synthase (CBS)–chloroplast protein (CP12) fusion proteins. These consist of two domains, each recognized as stand-alone photosynthetic regulators with different functions described in cyanobacteria (CP12) and plants (CP12 and CBSX). Here we show that CBS–CP12 fusion proteins are encoded in distinct gene neighborhoods, several unrelated to photosynthesis. Most frequently, CBS–CP12 genes are in a gene cluster with thioredoxin A (TrxA), which is prevalent in bloom-forming, marine symbiotic, and benthic mat cyanobacteria. Focusing on a CBS–CP12 from Microcystis aeruginosa PCC 7806 encoded in a gene cluster with TrxA, we reveal that the domain fusion led to the formation of a hexameric protein. We show that the CP12 domain is essential for hexamerization and contains an ordered, previously structurally uncharacterized N-terminal region. We provide evidence that CBS–CP12, while combining properties of both regulatory domains, behaves different from CP12 and plant CBSX. It does not form a ternary complex with phosphoribulokinase (PRK) and glyceraldehyde-3-phosphate dehydrogenase. Instead, CBS–CP12 decreases the activity of PRK in an AMP-dependent manner. We propose that the novel domain architecture and oligomeric state of CBS–CP12 expand its regulatory function beyond those of CP12 in cyanobacteria., Published by National Acad. of Sciences, Washington, DC

Background Carbonic anhydrases (CAs) are ubiquitous, essential enzymes which catalyze the conversion of carbon dioxide and water to bicarbonate and H+ ions. Vertebrate genomes generally contain gene loci for 15–21 different CA isoforms, three of which are enzymatically inactive. CA VI is the only secretory protein of the enzymatically active isoforms. We discovered that non-mammalian CA VI contains a C-terminal pentraxin (PTX) domain, a novel combination for both CAs and PTXs. Methods We isolated and sequenced zebrafish (Danio rerio) CA VI cDNA, complete with the sequence coding for the PTX domain, and produced the recombinant CA VI–PTX protein. Enzymatic activity and kinetic parameters were measured with a stopped-flow instrument. Mass spectrometry, analytical gel filtration and dynamic light scattering were used for biophysical characterization. Sequence analyses and Bayesian phylogenetics were used in generating hypotheses of protein structure and CA VI gene evolution. A CA VI–PTX antiserum was produced, and the expression of CA VI protein was studied by immunohistochemistry. A knock-down zebrafish model was constructed, and larvae were observed up to five days post-fertilization (dpf). The expression of ca6 mRNA was quantitated by qRT-PCR in different developmental times in morphant and wild-type larvae and in different adult fish tissues. Finally, the swimming behavior of the morphant fish was compared to that of wild-type fish. Results The recombinant enzyme has a very high carbonate dehydratase activity. Sequencing confirms a 530-residue protein identical to one of the predicted proteins in the Ensembl database (ensembl.org). The protein is pentameric in solution, as studied by gel filtration and light scattering, presumably joined by the PTX domains. Mass spectrometry confirms the predicted signal peptide cleavage and disulfides, and N-glycosylation in two of the four observed glycosylation motifs. Molecular modeling of the pentamer is consistent with the modifications observed in mass spectrometry. Phylogenetics and sequence analyses provide a consistent hypothesis of the evolutionary history of domains associated with CA VI in mammals and non-mammals. Briefly, the evidence suggests that ancestral CA VI was a transmembrane protein, the exon coding for the cytoplasmic domain was replaced by one coding for PTX domain, and finally, in the therian lineage, the PTX-coding exon was lost. We knocked down CA VI expression in zebrafish embryos with antisense morpholino oligonucleotides, resulting in phenotype features of decreased buoyancy and swim bladder deflation in 4 dpf larvae. Discussion These findings provide novel insights into the evolution, structure, and function of this unique CA form., published version, peerReviewed

Tetranuclear AuI–FeII dimetallic and AuI–CuI–FeII trimetallic complexes bearing ferrocenyl (Fc) groups have been assembled by using two triphosphane ligands, namely, (PPh2CH2)2PPh (dpmp) and (PPh2)3CH (tppm). The compositions and structural type of the clusters are dependent on the stereochemistry of the P donor ligands. The complexes [tppmAu3Cu(C2R)3]PF6 [R = Fc (1) and 4-C6H4-Fc (2)] adopt a trigonal pyramidal {Au3Cu} arrangement of the coordinating metal core, whereas for the compounds with the linear triphosphane [Au4(dpmp)2(C2R)2](PF6)2 [R = Fc (3) and 4-C6H4-Fc (4)], a planar rhomboidal {Au4} framework was found. Clusters 1–4 were characterized by NMR spectroscopy and ESI-MS measurements. The solid-state structures of 1, 3, and 4 have been determined by X-ray crystallography. The electrochemical properties of 1–4 were studied and revealed redox processes attributed to the Fc functions. Oxidation of the Fc units in 1, 2, and 4 occurs independently. In 3, an electron transfer process mediated by the {Au4} metal core was observed.

Sarcosine dimethylglycine methyltransferase (EC 2.1.1.157) is an enzyme from the extremely halophilic anaerobic bacterium Halorhodospira halochoris. This enzyme catalyzes the twofold methylation of sarcosine to betaine, with S-­adenosylmethionine (AdoMet) as the methyl-group donor. This study presents the crystallization and preliminary X-ray analysis of recombinant sarcosine dimethylglycine methyltransferase produced in Escherichia coli. Mass spectroscopy was used to determine the purity and homogeneity of the enzyme material. Two different crystal forms, which initially appeared to be hexagonal and tetragonal, were obtained. However, on analyzing the diffraction data it was discovered that both crystal forms were pseudo-merohedrally twinned. The true crystal systems were monoclinic and orthorhombic. The monoclinic crystal diffracted to a maximum of 2.15 Å resolution and the orthorhombic crystal diffracted to 1.8 Å resolution.

A D1 Fab fragment containing the allergen-binding variable domains of the IgE antibody was characterized by ESI FT-ICR mass spectrometry and crystallized with bovine beta-lactoglobulin (BLG) using the hanging-drop vapour-diffusion method at 293 K. X-ray data suitable for structure determination were collected to 2.8 A resolution using synchrotron radiation. The crystal belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 67.0, b = 100.6, c = 168.1 A. The three-dimensional structure of the D1 Fab fragment-BLG complex will provide the first insight into IgE antibody-allergen interactions at the molecular level.

Lipocalins are one of the most important groups of inhalant animal allergens. The analysis of structural features of these proteins is important to get insights into their allergenicity. We have determined two different dimeric crystal structures for bovine dander lipocalin Bos d 2, which was earlier described as a monomeric allergen. The crystal structure analysis of all other determined lipocalin allergens also revealed oligomeric structures which broadly utilize inherent structural features of the β-sheet in dimer formation. According to the moderate size of monomer-monomer interfaces, most of these dimers would be transient in solution. Native mass spectrometry was employed to characterize quantitatively transient dimerization of two lipocalin allergens, Bos d 2 and Bos d 5, in solution.

Avidins are a family of proteins widely employed in biotechnology. We have previously shown that functional chimeric mutant proteins can be created from avidin and avidin-related protein 2 using a methodology combining random mutagenesis by recombination and selection by a tailored biopanning protocol (phage display). Here, we report the crystal structure of one of the previously selected and characterized chimeric avidin forms, A/A2-1. The structure was solved at 1.8 Å resolution and revealed that the protein fold was not affected by the shuffled sequences. The structure also supports the previously observed physicochemical properties of the mutant. Furthermore, we improved the selection and screening methodology to select for chimeric avidins with slower dissociation rate from biotin than were selected earlier. This resulted in the chimeric mutant A/A2-B, which showed increased thermal stability as compared to A/A2-1 and the parental proteins. The increased stability was especially evident at conditions of extreme pH as characterized using differential scanning calorimetry. In addition, amino acid sequence and structural comparison of the chimeric mutants and the parental proteins led to the rational design of A/A2-B I109K. This mutation further decreased the dissociation rate from biotin and yielded an increase in the thermal stability. Public Library of Science open access

In vitro toxicological studies together with atomistic molecular dynamics simulations show that occupational co-exposure with C-60 fullerene may strengthen the health effects of organic industrial chemicals. The chemicals studied are acetophenone, benzaldehyde, benzyl alcohol, m-cresol, and toluene which can be used with fullerene as reagents or solvents in industrial processes. Potential co-exposure scenarios include a fullerene dust and organic chemical vapor, or a fullerene solution aerosolized in workplace air. Unfiltered and filtered mixtures of C-60 and organic chemicals represent different co-exposure scenarios in in vitro studies where acute cytotoxicity and immunotoxicity of C-60 and organic chemicals are tested together and alone by using human THP-1-derived macrophages. Statistically significant co-effects are observed for an unfiltered mixture of benzaldehyde and C-60 that is more cytotoxic than benzaldehyde alone, and for a filtered mixture of m-cresol and C-60 that is slightly less cytotoxic than m-cresol. Hydrophobicity of chemicals correlates with co-effects when secretion of pro-inflammatory cytokines IL-1 beta and TNF-alpha is considered. Complementary atomistic molecular dynamics simulations reveal that C-60 co-aggregates with all chemicals in aqueous environment. Stable aggregates have a fullerene-rich core and a chemical-rich surface layer, and while essentially all C-60 molecules aggregate together, a portion of organic molecules remains in water.

The avidin protein family members are well known for their high affinity towards D-biotin and high structural stability. These properties make avidins valuable tools for a wide range of biotechnology applications. We have identified a new member of the avidin family in the zebrafish (Danio rerio) genome, hereafter called zebavidin. The protein is highly expressed in the gonads of both male and female zebrafish and in the gills of male fish, but our data suggest that zebavidin is not crucial for the developing embryo. Biophysical and structural characterisation of zebavidin revealed distinct properties not found in any previously characterised avidins. Gel filtration chromatography and native mass spectrometry suggest that the protein forms dimers in the absence of biotin at low ionic strength, but assembles into tetramers upon binding biotin. Ligand binding was analysed using radioactive and fluorescently labelled biotin and isothermal titration calorimetry. Moreover, the crystal structure of zebavidin in complex with biotin was solved at 2.4 Å resolution and unveiled unique ligand binding and subunit interface architectures; the atomic-level details support our physicochemical observations. Public Library of Science open access

Our previous microarray study showed that the non-specific cytotoxic cell receptor protein 1 (Nccrp1) transcript is significantly upregulated in the gastric mucosa of carbonic anhydrase IX (CA IX)-deficient (Car9(-/-)) mice. In this paper, we aimed to characterize human NCCRP1 and to elucidate its relationship to CA IX. Recombinant NCCRP1 protein was expressed in Escherichia coli, and a novel polyclonal antiserum was raised against the purified full-length protein. Immunocytochemistry showed that NCCRP1 is expressed intracellularly, even though it has previously been described as a transmembrane protein. Using bioinformatic analyses, we identified orthologs of NCCRP1 in 35 vertebrate genomes, and up to five paralogs per genome. These paralogs are FBXO genes whose protein products are components of the E3 ubiquitin ligase complexes. NCCRP1 proteins have no signal peptides or transmembrane domains. NCCRP1 has mainly been studied in fish and was thought to be responsible for the cytolytic function of nonspecific cytotoxic cells (NCCs). Our analyses showed that in humans, NCCRP1 mRNA is expressed in tissues containing squamous epithelium, whereas it shows a more ubiquitous tissue expression pattern in mice. Neither human nor mouse NCCRP1 expression is specific to immune tissues. Silencing CA9 using siRNAs did not affect NCCRP1 levels, indicating that its expression is not directly regulated by CA9. Interestingly, silencing NCCRP1 caused a statistically significant decrease in the growth of HeLa cells. These studies provide ample evidence that the current name, "non-specific cytotoxic cell receptor protein 1," is not appropriate. We therefore propose that the gene name be changed to FBXO50.

The extensive use of avidin and streptavidin in life sciences originates from the extraordinary tight biotin-binding affinity of these tetrameric proteins. Numerous studies have been performed to modify the biotin-binding affinity of (strept)avidin to improve the existing applications. Even so, (strept)avidin greatly favours its natural ligand, biotin. Here we engineered the biotin-binding pocket of avidin with a single point mutation S16C and thus introduced a chemically active thiol group, which could be covalently coupled with thiol-reactive molecules. This approach was applied to the previously reported bivalent dual chain avidin by modifying one binding site while preserving the other one intact. Maleimide was then coupled to the modified binding site resulting in a decrease in biotin affinity. Furthermore, we showed that this thiol could be covalently coupled to other maleimide derivatives, for instance fluorescent labels, allowing intratetrameric FRET. The bifunctional avidins described here provide improved and novel tools for applications such as the biofunctionalization of surfaces. Public Library of Science

BackgroundAllergen-mediated cross-linking of IgE antibodies bound to the FcεRI receptors on the mast cell surface is the key feature of the type I allergy. If an allergen is a homodimer, its allergenicity is enhanced because it would only need one type of antibody, instead of two, for cross-linking.Methodology/Principal FindingsAn analysis of 55 crystal structures of allergens showed that 80% of them exist in symmetric dimers or oligomers in crystals. The majority are transient dimers that are formed at high protein concentrations that are reached in cells by colocalization. Native mass spectrometric analysis showed that native allergens do indeed form transient dimers in solution, while hypoallergenic variants of them exist almost solely in the monomeric form. We created a monomeric Bos d 5 allergen and show that it has a reduced capability to induce histamine release.Conclusions/SignificanceThe results suggest that dimerization would be a very common and essential feature for allergens. Thus, the preparation of purely monomeric variants of allergens could open up novel possibilities for specific immunotherapy.

Two different types of approach were taken to improve the hydrolytic activity towards crystalline cellulose at elevated temperatures of Melanocarpus albomyces Cel7B (Ma Cel7B), a single-module GH-7 family cellobiohydrolase. Structure-guided protein engineering was used to introduce an additional tenth disulphide bridge to the Ma Cel7B catalytic module. In addition, a fusion protein was constructed by linking a cellulose-binding module (CBM) and a linker from the Trichoderma reesei Cel7A to the C terminus of Ma Cel7B. Both approaches proved successful. The disulphide bridge mutation G4C/M70C located near the N terminus, close to the entrance of the active site tunnel of Ma Cel7B, led to improved thermostability (ΔT m = 2.5°C). By adding the earlier found thermostability-increasing mutation S290T (ΔT m = 1.5°C) together with the disulphide bridge mutation, the unfolding temperature was increased by 4°C (mutant G4C/M70C/S290T) compared to that of the wild-type enzyme, thus showing an additive effect on thermostability. Both disulphide mutants had increased activity towards microcrystalline cellulose (Avicel) at 75°C, apparently solely because of their improved thermostability. The addition of a CBM also improved the thermostability (ΔT m = 2.5°C) and caused a clear (sevenfold) increase in the hydrolysis activity of Ma Cel7B towards Avicel at 70°C.

Carbonic anhydrase IX (CA IX) is an exceptional member of the CA protein family; in addition to its classical role in pH regulation, it has also been proposed to participate in cell proliferation, cell adhesion, and tumorigenic processes. To characterize the biochemical properties of this membrane protein, two soluble recombinant forms were produced using the baculovirus-insect cell expression system. The recombinant proteins consisted of either the CA IX catalytic domain only (CA form) or the extracellular domain, which included both the proteoglycan and catalytic domains (PG + CA form). The produced proteins lacked the small transmembrane and intracytoplasmic regions of CA IX. Stopped-flow spectrophotometry experiments on both proteins demonstrated that in the excess of certain metal ions the PG + CA form exhibited the highest catalytic activity ever measured for any CA isozyme. Investigations on the oligomerization and stability of the enzymes revealed that both recombinant proteins form dimers that are stabilized by intermolecular disulfide bond(s). Mass spectrometry experiments showed that CA IX contains an intramolecular disulfide bridge (Cys119-Cys299) and a unique N-linked glycosylation site (Asn309) that bears high mannose-type glycan structures. Parallel experiments on a recombinant protein obtained by a mammalian cell expression system demonstrated the occurrence of an additional O-linked glycosylation site (Thr78) and characterized the nature of the oligosaccharide structures. This study provides novel information on the biochemical properties of CA IX and may help characterize the various cellular and pathophysiological processes in which this unique enzyme is involved.

Background Acetaldehyde, the first metabolite of ethanol, can generate covalent modifications of proteins and cellular constituents. However, functional consequences of such modification remain poorly defined. In the present study, we examined acetaldehyde reaction with human carbonic anhydrase (CA) isozyme II, which has several features that make it a suitable target protein: It is widely expressed, its enzymatic activity can be monitored, its structural and catalytic properties are known, and it contains 24 lysine residues, which are accessible sites for aldehyde reaction. Results Acetaldehyde treatment in the absence and presence of a reducing agent (NaBH3(CN)) caused shifts in the pI values of CA II. SDS-PAGE indicated a shift toward a slightly higher molecular mass. High-resolution mass spectra of CA II, measured with and without NaBH3(CN), indicated the presence of an unmodified protein, as expected. Mass spectra of CA II treated with acetaldehyde revealed a modified protein form (+26 Da), consistent with a "Schiff base" formation between acetaldehyde and one of the primary NH2 groups (e.g., in lysine side chain) in the protein structure. This reaction was highly specific, given the relative abundance of over 90% of the modified protein. In reducing conditions, each CA II molecule had reacted with 9–19 (14 on average) acetaldehyde molecules (+28 Da), consistent with further reduction of the "Schiff bases" to substituted amines (N-ethyllysine residues). The acetaldehyde-modified protein showed decreased CA enzymatic activity. Conclusion The acetaldehyde-derived modifications in CA II molecule may have physiological consequences in alcoholic patients.

The pyrolysis of scrap tires is a very attractive strategy to valorize chemically these end-of-life wastes. The products of this step and any additional one, such as hydrotreating, are relatively complex in nature entangling the understanding and limiting the viability. In this work, we have investigated in detail the composition of a tire pyrolysis oil blended with light cycle oil (from a refinery) and its hydrotreated products using a bifunctional NiW/HY catalyst at 320-400 °C. We have applied a set of analytical techniques to assess the composition, namely simulated distillation, ICP, GC/FID-PFPD, GC × GC/MS, and APPI FT-ICR/MS. Our results show the strength of our analytical workflow to highlight the compositional similarities of this pyrolysis oil with the standard refinery streams. The main differences arise from the higher boiling point species (originated during the pyrolysis of tires) and relatively high concentration of oxygenates. These effects can be minimized by hydrotreating the feed which effectively removes heteroatomic compounds from the feed while boosting the quantity and quality of gasoline and diesel fractions.