Modelling the interdependence between the stoichiometry of receptor oligomerization and ligand binding for a coexisting dimer/tetramer receptor system

Many G protein-coupled receptors have been shown to exist as oligomers, but the oligomerization state and the effects of this on receptor function are unclear. For some G protein-coupled receptors, in ligand binding assays, different radioligands provide different maximal binding capacities. Here we have developed mathematical models for co-expressed dimeric and tetrameric species of receptors. We have considered models where the dimers and tetramers are in equilibrium and where they do not interconvert and we have also considered the potential influence of the ligands on the degree of oligomerization. By analogy with agonist efficacy, we have considered ligands that promote, inhibit or have no effect on oligomerization. Cell surface receptor expression and the intrinsic capacity of receptors to oligomerize are quantitative parameters of the equations. The models can account for differences in the maximal binding capacities of radioligands in different preparations of receptors and provide a conceptual framework for simulation and data fitting in complex oligomeric receptor situations.

Oligomerization of the cysteinyl-rich oligopeptidase EP24.15 is triggered by S-glutathionylation

Thimet oligopeptidase (EC 3.4.24.15; EP24.15) is a thiol-rich metallopeptidase ubiquitously distributed in mammalian tissues and involved in oligopeptide metabolism both within and outside cells. Fifteen Cys residues are present in the rat EP24.15 protein, seven are solvent accessible, and two are found inside the catalytic site cleft; no intraprotein disulfide is described. In the present investigation, we show that mammalian immunoprecipitated EP24.15 is S-glutathionylated. In vitro EP24.15 S-glutathionylation was demonstrated by the incubation of bacterial recombinant EP24.15 with oxidized glutathione concentration as low as 10 mu M. The in vitro S-glutathionylation of EP24.15 was responsible for its oxidative oligomerization to dimer and trimer complexes. EP24.15 immunoprecipitated from cells submitted to oxidative challenge showed increased trimeric forms and decreased S-glutathionylation compared to immunoprecipitated protein from control cells. Our present data also show that EP24.15 maximal enzymatic activity is maintained by partial S-glutathionylation, a mechanism that apparently regulates the protein oligomerization. Present results raise the possibility of an unconventional property of protein S-glutathionylation, inducing oligomerization by interprotein thiol-disulfide exchange. (c) 2007 Elsevier Inc. All rights reserved.

Analyzing glycerol-mediated protein oligomerization by electrospray ionization mass spectrometry

Glycerol is widely used as protein stabilizer, in both local and commercial preparations, so it has become necessary to develop methods for mass spectrometric analysis of protein preparations in the presence of glycerol. However, this stabilizing agent may cause signal suppression when present in high concentrations, and is also known to induce protein supercharging even at low concentrations. This work reports the,use of electrospray ionization (ESI) mass spectrometry to characterize glycerol-mediated protein oligomerization. this phenomenon seems to involve the formation of strong non-covalent interactions between protein and glycerol involving close contact between the monomers, leading to formation of protein oligomers adducted with glycerol molecules under the characteristic analytical conditions of the ESI interface. At high orders of oligomerization a lower number of glycerol molecules is required to maintain the high oligomeric states than for the dimers and trimers, and it is possible that for the higher oligomers the monomers become so close to one another that non-covalent bonds between the side chains of the amino acid residues in the proteins may be established. Copyright (C) 2005 John Wiley & Sons, Ltd.

Molecular adaptability of nucleoside diphosphate kinase b from trypanosomatid parasites: stability, oligomerization and structural determinants of nucleotide binding

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Highly selective nickel ethylene oligomerization catalysts based on sterically hindered tris(pyrazolyl)borate ligands

The reaction of TlTp' (Tp' = HB(3-mesitylpyrazolyl)(3)(-) (Tp(Ms)), HB(3-mesitylpyrazolyl)(2)(5-mesitylpyrazolyl)(-) (Tp(Ms)*)) with NiCl(2).6H(2)O affords Tp(Ms)NiCl (1) and Tp(Ms)*NiCl (2) in good yield. The compound 2 undergoes an isomerization process to form [{Tp(Ms)**}NiCl](2) (3) (Tp(Ms)** = HB(5-mesitylpyrazolyl)(2)(3-mesitylpyrazolyl)(-)) in 68% yield. Treatment of the tris(pyrazolyl)-borate nickel compounds 1 and 2 with alkylaluminum cocatalysts such as methylalumoxane (MAO) and trimethylaluminum (TMA) in toluene generates active catalysts for ethylene oligomerization. The compound 1 shows turnover frequencies in the range of (2.2-43.1) x 10(3) h(-1). Oligomerization reaction conditions can be adjusted that lead to selectivities as high as 81% for butene-1.

Purification of a PHA-Like chitin-binding protein from Acacia farnesiana seeds: A time-dependent oligomerization protein

A lectin-like protein from the seeds of Acacia farnesiana was isolated from the albumin fraction, characterized, and sequenced by tandem mass spectrometry. The albumin fraction was extracted with 0.5 M NaCl, and the lectin-like protein of A. farnesiana (AFAL) was purified by ion-exchange chromatography (Mono-Q) followed by chromatofocusing. AFAL agglutinated rabbit erythrocytes and did not agglutinate human ABO erythrocytes either native or treated with proteolytic enzymes. In sodium dodecyl sulfate gel electrophoresis under reducing and nonreducing conditions, AFAL separated into two bands with a subunit molecular mass of 35 and 50 kDa. The homogeneity of purified protein was confirmed by chromatofocusing with a pI=4.0+/-0.5. Molecular exclusion chromatography confirmed time-dependent oligomerization in AFAL, in accordance with mass spectrometry analysis, which confers an alteration in AFAL affinity for chitin. The protein sequence was obtained by a liquid chromatography quadrupole time-of-flight experiment and showed that AFAL has 68% and 63% sequence similarity with lectins of Phaseolus vulgaris and Dolichos biflorus, respectively.

Adsorption of silanes bearing nitrogenated Lewis bases on SiO 2/Si (100) model surfaces

The present paper describes the one-pot procedure for the formation of self-assembled thin films of two silanes on the model oxidized silicon wafer, SiO2/Si. SiO2/Si is a model system for other surfaces, such as glass, quartz, aerosol, and silica gel. MALDI-TOF MS with and without a matrix, XPS, and AFM have confirmed the formation of self-assembled thin films of both 3-imidazolylpropyltrimethoxysilane (3-IPTS) and 4-(N- propyltriethoxysilane-imino)pyridine (4-PTSIP) on the SiO2/Si surface after 30 min. Longer adsorption times lead to the deposition of nonreacted 3-IPTS precursors and the formation of agglomerates on the 3-IPTS monolayer. The formation of 4-PTSIP self-assembled layers on SiO2/Si is also demonstrated. The present results for the flat SiO2/Si surface can lead to a better understanding of the formation of a stationary phase for affinity chromatography as well as transition-metal-supported catalysts on silica and their relationship with surface roughness and ordering. The 3-IPTS and 4-PTSIP modified SiO2/Si wafers can also be envisaged as possible built-on-silicon thin-layer chromatography (TLC) extraction devices for metal determination or N-heterocycle analytes, such as histidine and histamine, with on-spot MALDI-TOF MS detection. © 2005 Elsevier Inc. All rights reserved.

The Cysteine-Rich Protein Thimet Oligopeptidase as a Model of the Structural Requirements for S-glutathiolation and Oxidative Oligomerization

Thimet oligopeptidase (EP24.15) is a cysteine-rich metallopeptidase containing fifteen Cys residues and no intra-protein disulfide bonds. Previous work on this enzyme revealed that the oxidative oligomerization of EP24.15 is triggered by S-glutathiolation at physiological GSSG levels (10-50 mu M) via a mechanism based on thiol-disulfide exchange. In the present work, our aim was to identify EP24.15 Cys residues that are prone to S-glutathiolation and to determine which structural features in the cysteinyl bulk are responsible for the formation of mixed disulfides through the reaction with GSSG and, in this particular case, the Cys residues within EP24.15 that favor either S-glutathiolation or inter-protein thiol-disulfide exchange. These studies were conducted by in silico structural analyses and simulations as well as site-specific mutation. S-glutathiolation was determined by mass spectrometric analyses and western blotting with anti-glutathione antibody. The results indicated that the stabilization of a thiolate sulfhydryl and the solvent accessibility of the cysteines are necessary for S-thiolation. The Solvent Access Surface analysis of the Cys residues prone to glutathione modification showed that the S-glutathiolated Cys residues are located inside pockets where the sulfur atom comes into contact with the solvent and that the positively charged amino acids are directed toward these Cys residues. The simulation of a covalent glutathione docking onto the same Cys residues allowed for perfect glutathione posing. A mutation of the Arg residue 263 that forms a saline bridge to the Cys residue 175 significantly decreased the overall S-glutathiolation and oligomerization of EP24.15. The present results show for the first time the structural requirements for protein S-glutathiolation by GSSG and are consistent with our previous hypothesis that EP24.15 oligomerization is dependent on the electron transfer from specific protonated Cys residues of one molecule to previously S-glutathionylated Cys residues of another one.

Aniline-1,4-benzoquinone as a model system for the characterization of products from aniline oligomerization in low acidic media

Increase in the pH medium of aniline polymerization is used for giving products of different morphologies, which are often wrongly attributed to PANI chains. Infrared and Raman spectroscopic data, supported by quantum chemical calculations, show that aniline-1,4-benzoquinone (AnBzq) is a model system for the characterization of the products of aniline oligomerization in low acidic media. The Raman spectra excited at different laser lines reveal the bichromophoric nature of AnBzq, whose absorption bands at 550 nm and 440 nm can be attributed to pi-pi* transitions of the delocalized benzoquinone and amino-phenyl moieties, respectively. (C) 2012 Elsevier B.V. All rights reserved.

Functional characterization and oligomerization of a recombinant xyloglucan-specific endo-beta-1,4-glucanase (GH12) from Aspergillus niveus

Xyloglucan is a major structural polysaccharide of the primary (growing) cell wall of higher plants. It consists of a cellulosic backbone (beta-1,4-linked glucosyl residues) that is frequently substituted with side chains. This report describes Aspergillus nidulans strain A773 recombinant secretion of a dimeric xyloglucan-specific endo-beta-1,4-glucanohydrolase (XegA) cloned from Aspergillus niveus. The ORF of the A. niveus xegA gene is comprised of 714 nucleotides, and encodes a 238 amino acid protein with a calculated molecular weight of 23.5 kDa and isoelectric point of 4.38. The optimal pH and temperature were 6.0 and 60 degrees C, respectively. XegA generated a xyloglucan-oligosaccharides (XGOs) pattern similar to that observed for cellulases from family GH12, i.e., demonstrating that its mode of action includes hydrolysis of the glycosidic linkages between glucosyl residues that are not branched with xylose. In contrast to commercial lichenase, mixed linkage beta-glucan (lichenan) was not digested by XegA, indicating that the enzyme did not cleave glucan beta-1,3 or beta-1,6 bonds. The far-UV CD spectrum of the purified enzyme indicated a protein rich in beta-sheet structures as expected for GH12 xyloglucanases. Thermal unfolding studies displayed two transitions with mid-point temperatures of 51.3 degrees C and 81.3 degrees C respectively, and dynamic light scattering studies indicated that the first transition involves a change in oligomeric state from a dimeric to a monomeric form. Since the enzyme is a predominantly a monomer at 60 degrees C. the enzymatic assays demonstrated that XegA is more active in its monomeric state. (c) 2012 Elsevier B.V. All rights reserved.

Staphylococcus aureus thiaminase II: oligomerization warrants proteolytic protection against serine proteases

Staphylococcus aureus TenA (SaTenA) is a thiaminase type II enzyme that catalyzes the deamination of aminopyrimidine, as well as the cleavage of thiamine into 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) and 5-(2-hydroxyethyl)-4-methylthiazole (THZ), within thiamine (vitamin B1) metabolism. Further, by analogy with studies of Bacillus subtilis TenA, SaTenA may act as a regulator controlling the secretion of extracellular proteases such as the subtilisin type of enzymes in bacteria. Thiamine biosynthesis has been identified as a potential drug target of the multi-resistant pathogen S. aureus and therefore all enzymes involved in the S. aureus thiamine pathway are presently being investigated in detail. Here, the structure of SaTenA, determined by molecular replacement and refined at 2.7 A ° resolution to an R factor of 21.6% with one homotetramer in the asymmetric unit in the orthorhombic space group P212121, is presented. The tetrameric state of wild-type (WT) SaTenA was postulated to be the functional biological unit and was confirmed by small-angle X-ray scattering (SAXS) experiments in solution. To obtain insights into structural and functional features of the oligomeric SaTenA, comparative kinetic investigations as well as experiments analyzing the structural stability of the WT SaTenA tetramer versus a monomeric SaTenA mutant were performed.

Synthesis and characterisation of photoreactive silanes for the self-assembly on functionalised silica surfaces

The aim of this thesis was to investigate novel techniques to create complex hierarchical chemical patterns on silica surfaces with micro to nanometer sized features. These surfaces were used for a site-selective assembly of colloidal particles and oligonucleotides. To do so, functionalised alkoxysilanes (commercial and synthesised ones) were deposited onto planar silica surfaces. The functional groups can form reversible attractive interactions with the complementary surface layers of the opposing objects that need to be assembled. These interactions determine the final location and density of the objects onto the surface. Photolithographically patterned silica surfaces were modified with commercial silanes, in order to create hydrophilic and hydrophobic regions on the surface. Assembly of hydrophobic silica particles onto these surfaces was investigated and finally, pH and charge effects on the colloidal assembly were analysed. In the second part of this thesis the concept of novel, "smart" alkoxysilanes is introduced that allows parallel surface activation and patterning in a one-step irradiation process. These novel species bear a photoreactive head-group in a protected form. Surface layers made from these molecules can be irradiated through a mask to remove the protecting group from selected regions and thus generate lateral chemical patterns of active and inert regions on the substrate. The synthesis of an azide-reactive alkoxysilane was successfully accomplished. Silanisation conditions were carefully optimised as to guarantee a smooth surface layer, without formation of micellar clusters. NMR and DLS experiments corroborated the absence of clusters when using neither water nor NaOH as catalysts during hydrolysis, but only the organic solvent itself. Upon irradiation of the azide layer, the resulting nitrene may undergo a variety of reactions depending on the irradiation conditions. Contact angle measurements demonstrated that the irradiated surfaces were more hydrophilic than the non-irradiated azide layer and therefore the formation of an amine upon irradiation was postulated. Successful photoactivation could be demonstrated using condensation patterns, which showed a change in wettability on the wafer surface upon irradiation. Colloidal deposition with COOH functionalised particles further underlined the formation of more hydrophilic species. Orthogonal photoreactive silanes are described in the third part of this thesis. The advantage of orthogonal photosensitive silanes is the possibility of having a coexistence of chemical functionalities homogeneously distributed in the same layer, by using appropriate protecting groups. For this purpose, a 3',5'-dimethoxybenzoin protected carboxylic acid silane was successfully synthesised and the kinetics of its hydrolysis and condensation in solution were analysed in order to optimise the silanisation conditions. This compound was used together with a nitroveratryl protected amino silane to obtain bicomponent surface layers. The optimum conditions for an orthogonal deprotection of surfaces modified with this two groups were determined. A 2-step deprotection process through a mask generated a complex pattern on the substrate by activating two different chemistries at different sites. This was demonstrated by colloidal adsorption and fluorescence labelling of the resulting substrates. Moreover, two different single stranded oligodeoxynucleotides were immobilised onto the two different activated areas and then hybrid captured with their respective complementary, fluorescent labelled strand. Selective hybridisation could be shown, although non-selective adsorption issues need to be resolved, making this technique attractive for possible DNA microarrays.

Oligomerization and protein-protein interactions of the sensory histidine kinase DcuS in Escherichia coli

DcuS is a membrane-integral sensory histidine kinase involved in the DcuSR two-component regulatory system in Escherichia coli by regulating the gene expression of C4-dicarboxylate metabolism in response to external stimuli. How DcuS mediates the signal transduction across the membrane remains little understood. This study focused on the oligomerization and protein-protein interactions of DcuS by using quantitative Fluorescence Resonance Energy Transfer (FRET) spectroscopy. A quantitative FRET analysis for fluorescence spectroscopy has been developed in this study, consisting of three steps: (1) flexible background subtraction to yield background-free spectra, (2) a FRET quantification method to determine FRET efficiency (E) and donor fraction (fD = [donor] / ([donor]+[acceptor])) from the spectra, and (3) a model to determine the degree of oligomerization (interaction stoichiometry) in the protein complexes based on E vs. fD. The accuracy and applicability of this analysis was validated by theoretical simulations and experimental systems. These three steps were integrated into a computer procedure as an automatic quantitative FRET analysis which is easy, fast, and allows high-throughout to quantify FRET accurately and robustly, even in living cells. This method was subsequently applied to investigate oligomerization and protein-protein interactions, in particular in living cells. Cyan (CFP) and yellow fluorescent protein (YFP), two spectral variants of green fluorescent protein, were used as a donor-acceptor pair for in vivo measurements. Based on CFP- and YFP-fusions of non-interacting membrane proteins in the cell membrane, a minor FRET signal (E = 0.06 ± 0.01) can be regarded as an estimate of direct interaction between CFP and YFP moieties of fusion proteins co-localized in the cell membrane (false-positive). To confirm if the FRET occurrence is specific to the interaction of the investigated proteins, their FRET efficiency should be clearly above E = 0.06. The oligomeric state of DcuS was examined both in vivo (CFP/YFP) and in vitro (two different donor-acceptor pairs of organic dyes) by three independent experimental systems. The consistent occurrence of FRET in vitro and in vivo provides the evidence for the homo-dimerization of DcuS as full-length protein for the first time. Moreover, novel interactions (hetero-complexes) between DcuS and its functionally related proteins, citrate-specific sensor kinase CitA and aerobic dicarboxylate transporter DctA respectively, have been identified for the first time by intermolecular FRET in vivo. This analysis can be widely applied as a robust method to determine the interaction stoichiometry of protein complexes for other proteins of interest labeled with adequate fluorophores in vitro or in vivo.