Janne Jänis

Biochemical characterization of CA IX: one of the most active carbonic anhydrase isozymes

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.

Chemistry inside molecular containers in the gas phase

Inner-phase chemical reactions of guest molecules encapsulated in a macromolecular cavity give fundamental insight into the relative stabilization of transition states by the surrounding walls of the host, thereby modelling the situation of substrates in enzymatic binding pockets. Although in solution several examples of inner-phase reactions are known, the use of cucurbiturils as macrocyclic hosts and bicyclic azoalkanes as guests has now enabled a systematic mass spectrometric investigation of inner-phase reactions in the gas phase, where typically the supply of thermal energy results in dissociation of the supramolecular host-guest assembly. The results reveal a sensitive interplay in which attractive and repulsive van der Waals interactions between the differently sized hosts and guests need to be balanced with a constrictive binding to allow thermally activated chemical reactions to compete with dissociation. The results are important for the understanding of supramolecular reactivity and have implications for catalysis.

Zinc Coordination Spheres in Protein Structures

Zinc metalloproteins are one of the most abundant and structurally diverse proteins in nature. In these proteins, the Zn(II) ion possesses a multifunctional role as it stabilizes the fold of small zinc fingers, catalyzes essential reactions in enzymes of all six classes, or assists in the formation of biological oligomers. Previously, a number of database surveys have been conducted on zinc proteins to gain broader insights into their rich coordination chemistry. However, many of these surveys suffer from severe flaws and misinterpretations or are otherwise limited. To provide a more comprehensive, up-to-date picture on zinc coordination environments in proteins, zinc containing protein structures deposited in the Protein Data Bank (PDB) were analyzed in detail. A statistical analysis in terms of zinc coordinating amino acids, metal-to-ligand bond lengths, coordination number, and structural classification was performed, revealing coordination spheres from classical tetrahedral cysteine/histidine binding sites to more complex binuclear sites with carboxylated lysine residues. According to the results, coordination spheres of hundreds of crystal structures in the PDB could be misinterpreted due to symmetry-related molecules or missing electron densities for ligands. The analysis also revealed increasing average metal-to-ligand bond length as a function of crystallographic resolution, which should be taken into account when interrogating metal ion binding sites. Moreover, one-third of the zinc ions present in crystal structures are artifacts, merely aiding crystal formation and packing with no biological significance. Our analysis provides solid evidence that a minimal stable zinc coordination sphere is made up by four ligands and adopts a tetrahedral coordination geometry.

Improving the thermostability and activity of Melanocarpus albomyces cellobiohydrolase Cel7B.

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 (ΔTm = 2.5°C). By adding the earlier found thermostability-increasing mutation S290T (ΔTm = 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 (ΔTm = 2.5°C) and caused a clear (sevenfold) increase in the hydrolysis activity of Ma Cel7B towards Avicel at 70°C.

Transient dimers of allergens.

Background Allergen-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 Findings An 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/Significance The 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.

Highly Luminescent Octanuclear AuI–CuI Clusters Adopting Two Structural Motifs: The Effect of Aliphatic Alkynyl Ligands

Reactions of the homoleptic (AuC(2)R)(n) precursors with stoichiometric amount of diphosphine ligand PPh(2)C(6)H(4)PPh(2) (P^P) and Cu(+) ions lead to an assembly of a new family of bimetallic clusters [Au(6)Cu(2)(C(2)R)(6)(P^P)(2)](2+) (type I; R=9-fluorenolyl (1), diphenylmethanolyl (2), 2,6-dimethyl-4-heptanolyl (3), 1-cyclohexanolyl (4), Cy (5), tBu (6)). In the case of R=1-cyclohexanolyl, a structurally different complex [Au(6)Cu(2)(C(2)C(6)H(11)O)(6)(P^P)(3)](2+) (7, type II) could be obtained by treatment of 4 with one equivalent of the diphosphine, while for R=isopropanolyl only the latter type of cluster [Au(6)Cu(2)(C(2)C(3)H(7)O)(6)(P^P)(3)](2+) (8) was detected. Steric bulkiness of the alkynyl ligands and O···H-O hydrogen bonding are suggested to play an important role in stabilizing the type I and type II cluster structural motif, respectively. All the complexes exhibit intense photoluminescence in solution with emission parameters that depending on the geometrical arrangement of the octanuclear metal core. The clusters 1-4 and 6 show single emission band in a blue region (469-488 nm) with maximum quantum yield of 94% (4), while structurally different 7 and 8 emit yellow-orange (590 nm) with unity quantum efficiency. The theoretical DFT calculations of the electronic structures have been carried out to demonstrate that the metal-centered triplet emission within the heterometallic core plays a key role for the observed phosphorescence.

Microscale immobilized enzyme reactors in proteomics: Latest developments

Enzymatic digestion of proteins is one of the key steps in proteomic analyses. There has been a steady progress in the applied digestion protocols in the past, starting from conventional time-consuming in-solution or in-gel digestion protocols to rapid and efficient methods utilizing different types of microscale enzyme reactors. Application of such microreactors has been proven beneficial due to lower sample consumption, higher sensitivity and straightforward coupling with LC-MS set-ups. Novel stationary phases, immobilization techniques and device formats are being constantly developed and tested to optimize digestion efficiency of proteolytic enzymes. This review focuses on the latest developments associated with the preparation and application of microscale enzyme reactors for proteomics applications since 2008 onwards. A special attention has been paid to the discussion of different stationary phases applied for immobilization purposes.

Intensely luminescent homoleptic alkynyl decanuclear gold(I) clusters and their cationic octanuclear phosphine derivatives.

Treatment of Au(SC(4)H(8))Cl with a stoichiometric amount of hydroxyaliphatic alkyne in the presence of NEt(3) results in high-yield self-assembly of homoleptic clusters (AuC(2)R)(10) (R = 9-fluorenol (1), diphenylmethanol (2), 2,6-dimethyl-4-heptanol (3), 3-methyl-2-butanol (4), 4-methyl-2-pentanol (4), 1-cyclohexanol (6), 2-borneol (7)). The molecular compounds contain an unprecedented catenane metal core with two interlocked 5-membered rings. Reactions of the decanuclear clusters 1-7 with gold-diphosphine complex [Au(2)(1,4-PPh(2)-C(6)H(4)-PPh(2))(2)](2+) lead to octanuclear cationic derivatives [Au(8)(C(2)R)(6)(PPh(2)-C(6)H(4)-PPh(2))(2)](2+) (8-14), which consist of planar tetranuclear units {Au(4)(C(2)R)(4)} coupled with two fragments [AuPPh(2)-C(6)H(4)-PPh(2)(AuC(2)R)](+). The titled complexes were characterized by NMR and ESI-MS spectroscopy, and the structures of 1, 13, and 14 were determined by single-crystal X-ray diffraction analysis. The luminescence behavior of both Au(I)(10) and Au(I)(8) families has been studied, revealing efficient room-temperature phosphorescence in solution and in the solid state, with the maximum quantum yield approaching 100% (2 in solution). DFT computational studies showed that in both Au(I)(10) and Au(I)(8) clusters metal-centered Au → Au charge transfer transitions mixed with some π-alkynyl MLCT character play a dominant role in the observed phosphorescence.

DNA-Binding and -Bending Activities of SAP30L and SAP30 Are Mediated by a Zinc-Dependent Module and Monophosphoinositides

ABSTRACT Deacetylation of histones is carried out by a corepressor complex in which Sin3A is an essential scaffold protein. Two proteins in this complex, the Sin3A-associated proteins SAP30L and SAP30, have previously been suggested to function as linker molecules between various corepressors. In this report, we demonstrate new functions for human SAP30L and SAP30 by showing that they can associate directly with core histones as well as naked DNA. A zinc-coordinating structure is necessary for DNA binding, one consequence of which is bending of the DNA. We provide evidence that a sequence motif previously shown to be a nuclear localization signal is also a phosphatidylinositol (PI)-binding element and that binding of specific nuclear monophosphoinositides regulates DNA binding and chromatin association of SAP30L. PI binding also decreases the repression activity of SAP30L and affects its translocation from the nucleus to the cytoplasm. Our results suggest that SAP30L and SAP30 play active roles in recruitment of deacetylating enzymes to nucleosomes, and mediate key protein-protein and protein-DNA interactions involved in chromatin remodeling and transcription.

Stepwise 1D Growth of Luminescent Au(I)−Ag(I) Phosphine−Alkynyl Clusters: Synthesis, Photophysical, and Theoretical Studies

Reactions between the diphosphino-gold cationic complexes [Au(2)(PPh(2)-C(2)-(C(6)H(4))(n)-C(2)-PPh(2))(2)](2+) (n = 0, 1, 2, 3) and polymeric acetylides (AuC(2)Ph)(n) and (AgC(2)Ph)(n) lead to the formation of a new family of heterometallic clusters with the general formula [Au(8+2n)Ag(6+2n)(C(2)Ph)(8+4n)(PPh(2)C(2)(C(6)H(4))(n)C(2)PPh(2))(2)](2+), n = 0 (1), 1 (2), 2 (3), 3 (4). Compounds 1-4 were characterized in detail by NMR and ESI-MS spectroscopy. Complex 1 (n = 0) crystallizes in two forms (orange (1a) and yellow (1b)), one of which (1a) has been analyzed by X-ray crystallography. The luminescence behavior of 1-4 has been studied. Compounds 2 and 3 exhibited orange-red phosphorescence with quantitative quantum efficiency in both aerated and degassed CH(2)Cl(2), implying O(2)-independent phosphorescence due to efficient protection of the emitting chromophore center by the organic ligands. Complex 3 exhibits reasonable two-photon absorption (TPA) property with a cross section of σ ≈ 45 GM (800 nm), which is comparable to the value of commercially available TPA dyes such as coumarin 151. Computational studies have been performed to correlate the structural and photophysical features of the complexes studied. The metal-centered triplet emission within the heterometallic core is suggested to play a key role in the observed phosphorescence. The luminescence spectrum of 1 in CH(2)Cl(2) shows dual phosphorescence maximized at 575 nm (the P(1) band) and 770 nm (the P(2) band). Both P(1) and P(2) bands possess identical excitation spectra, i.e., the same ground-state origin, and the same relaxation dynamics throughout the temperature range of 298-200 K. The dual emission of 1 arises from fast structural fluctuation upon excitation, perhaps forming two geometry isomers, which exhibit distinctly different P(1) and P(2) bands. The scrambling dynamics might require large-amplitude motion and, hence, is hampered in rigid media, as evidenced by the single emission for 1a (610 nm) and 1b (570 nm) observed in solid.