Characterization of N-terminal processing of group VIA phospholipase A<Subscript>2</Subscript> and of potential cleavage sites of amyloid precursor protein constructs by automated identification of signature peptides in LC/MS/MS analyses of proteolytic digests

Dysregulation of proteolytic processing of the amyloid precursor protein (APP) contributes to the pathogenesis of Alzheimer's Disease, and the Group VIA phospholipase A(2) (iPLA(2)beta) is the dominant PLA(2) enzyme in the central nervous system and is subject to regulatory proteolytic processing. We have identified novel N-terminal variants of iPLA(2)beta and previously unrecognized proteolysis sites in APP constructs with a C-terminal 6-myc tag by automated identification of signature peptides in LC/MS/MS analyses of proteolytic digests. We have developed a Signature-Discovery (SD) program to characterize protein isoforms by identifying signature peptides that arise from proteolytic processing in vivo. This program analyzes MS/MS data from LC analyses of proteolytic digests of protein mixtures that can include incompletely resolved components in biological samples. This reduces requirements for purification and thereby minimizes artifactual modifications during sample processing. A new algorithm to generate the theoretical signature peptide set and to calculate similarity scores between predicted and observed mass spectra has been tested and optimized with model proteins. The program has been applied to the identification of variants of proteins of biological interest, including APP cleavage products and iPLA(2)beta, and such applications demonstrate the utility of this approach.     

Modeling of serine protease prototype reactions with the flexible effective fragment potential quantum mechanical/molecular mechanical method

A complete cycle of chemical transformations for the serine protease prototype reaction is modeled following calculations with the flexible effective fragment quantum mechanical/molecular mechanical (QM/MM) method. The initial molecular model is based on the crystal structure of the trypsin–bovine pancreatic trypsin inhibitor complex including all atoms of the enzyme within approximately 15–18 Å of the oxygen center O of the catalytic serine residue. Several selections of the QM/MM partitioning are considered. Fractions of the side chains of the residues from the catalytic triad (serine, histidine and aspartic acid) and a central part of a model substrate around the C–N bond to be cleaved are included into the QM subsystem. The remaining part, or the MM subsystem, is represented by flexible chains of small effective fragments, whose potentials explicitly contribute to the Hamiltonian of the QM part, but the corresponding fragment–fragment interactions are described by the MM force fields. The QM/MM boundaries are extended over the C–C bonds of the peptides assigned to the QM subsystem in the enzyme, C–C and C–N bonds in model substrates. Multiple geometry optimizations have been performed by using the RHF/6-31G method in the QM part and OPLSAA or AMBER sets of MM parameters, resulting in a series of stationary points on the complex potential-energy surfaces. All structures generally accepted for the serine protease catalytic cycle have been located. Energies at the stationary points found have been recomputed at the MP2/6-31+G^* level for the QM part in the protein environment. Structural changes along the reaction path are analyzed with special attention to hydrogen-bonding networks. In the case of a model substrate selected as a short peptide CH₃(NHCO-CH₂)₂ – HN–CO–(CH₂–NHCO)CH₃ the computed energy profile for the acylation step shows too high activation energy barriers. The energetics of this rate-limiting step is considerably improved, if more realistic model for the substrate is considered, following the motifs of the ThrI11–GlyI12–ProI13-–CysI14–LysI15–AlaI16–ArgI17–IleI18–IleI19 sequence of the bovine pancreatic trypsin inhibitor.     

Electrochemical synthesis of Fe<Subscript>3</Subscript>O<Subscript>4</Subscript> nanoparticles in alkaline aqueous solutions containing complexing agents

Ultrafine magnetite particles are prepared through an electrochemical process, at room temperature, from an iron-based electrode immersed in an alkaline aqueous medium containing complexing compounds. XRD and chemical analysis indicate that the product is pure magnetite, Fe₃O₄. The size and morphology of the particles are studied by SEM. The magnetite nanoparticles present a magnetoresistance of almost 3%, at 300 K, under a magnetic field of 1 T. A reactive mechanism for the electrochemical process is proposed.     

Aminoalkylation with Aldehydes Mediated by Solid Lithium Perchlorate

Summary. The solid LiClO₄-mediated one-pot reaction of aldehydes with secondary amines and C nucleophiles afforded the corresponding aminoalkylation products in high yields. Unlike the previous reported procedure, the aminoalkylation of aldehyde was achieved in the presence of only 0.5 equivalents of solid lithium perchlorate in dichloromethane as the solvent with good to high yields at room temperature.     

The application of NMR and MS methods for detection of adulteration of wine,fruit juices,and olive oil. A review

This review covers two important techniques, high resolution nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS), used to characterize food products and detect possible adulteration of wine, fruit juices, and olive oil, all important products of the Mediterranean Basin. Emphasis is placed on the complementary use of SNIF-NMR (site-specific natural isotopic fractionation nuclear magnetic resonance) and IRMS (isotope-ratio mass spectrometry) in association with chemometric methods for detecting the adulteration.     

Influence of nonionic emulsifier included inside carboxylated polymer particles on the formation of multihollow structure by the alkali/cooling method

The influence of nonionic emulsifier, included inside styrene-methacrylic acid copolymer [P(S-MAA)] particles during emulsion copolymerization, on the formation of multihollow structure inside the particles via the alkali/cooling method (proposed by the authors) was examined in comparison to emulsifier-free particles. It was clarified that the nonionic emulsifier included inside the P(S-MAA) particles eased the formation of multihollow structure.Part CCL of the series studies on suspension and emulsion     

Unusual volumetric and hydration behavior of the catanionic system sodium undecenoate: sodecyltrimethylammonium bromide

Following the studies on the effect of double bonds in the surfactant hydrophobic tail on the formation of mixed surfactant aggregates, we studied the viscosity and density of the system Sodium 10-undecenoate (SUD)–decyltrimethylammonium bromide (DTAB)–water. We found that the partial molar volume (pmv) and intrinsic viscosity of both, micellised and unmicellised mixtures, are non-ideal, dependent on the mixture composition and related to structural changes in micelles. These phenomena are caused by the presence of the double bond at the distal extreme of the SUD molecule, which has some affinity with water by formation of hydrogen bonds. In particular, as far as we know, this is the first report on non-ideal behavior of the pmv in mixed micelles.     

The aqueous cationic system sodium undecenoate-dodecyltrimethylammonium bromide at low concentration

The aqueous sodium undecenoate (SUD) –dodecyltrimethylammonium bromide (DTAB) catanionic system was studied at low concentration. The system did not precipitate, even at a 1:1 SUD:DTAB proportion, but showed the formation of a coacervate in a range of surfactant mixture compositions. Micelles have a preferential composition of 0.37 mole fraction of SUD. This behavior is attributed to the presence of the double bond at the distal extreme of the SUD molecule, which can form hydrogen bonds with water. Consequently, the –CH=CH₂ group is situated at the interface between the hydrocarbon micelle core and water, reducing the interfacial free energy. Structural computations demonstrate that the mentioned SUD proportion produces complete coverage of the micelle surface by the double bonds.     

Hydrogels in aqueous phases of polyvinylalcohol (PVA), surfactants and clay minerals

Aqueous solutions of synthetic clay minerals have been studied in the presence of surfactants and water-soluble polyvinylalcohol (PVA). The PVAs (PVA 1, PVA 2) had a molecular weight of about 10⁵ Dalton and a degree of hydrolysis of 82%. The PVA-samples were surface active and lowered the surface tension to 43 mN/m. As a consequence of their amphiphilic nature the PVA molecules bind strongly to clay mineral particles. On saturation the clay mineral particles adsorb the fivefold weight of PVA of their own weight. It is concluded that the thickness of the adsorbed layers on both sides of the clay mineral is in the range of the hydrodynamic diameter of the PVA-coils in the bulk phase.When the clay mineral particles are not saturated with PVA, they act as cross-linking agents for the PVA. The whole systems are physically cross-linked and assume gel-like properties. Rheological measurements show that samples behave like soft matter with a yield stress value. All of them have a frequency independent storage modulus which is an order of magnitude larger than the loss modulus. The hydrogels become stronger as PVA concentration increases.Small amounts of cationic surfactants bind on the clay mineral. The interface of the clay mineral becomes more hydrophobic and the binding of the PVA on the clay mineral is strengthened. With rising concentration of the surfactant the surfactant molecules bind on PVA and the PVA becomes hydrophilic. As a consequence the PVA can no longer bind on the clay mineral and the gels transform to viscous and turbid solutions. Small amounts of cationic surfactants therefore stiffen the hydrogels while larger amounts cause phase separation and a solution with low viscosity. Anionic surfactants like SDS do not bind on the clay mineral, but strongly on the PVA. With increasing SDS concentration, the hydrogels become stiffer at first but thereafter they break and transform to viscous fluids.In PVA-solutions without the clay minerals both cationic and anionic surfactants bind to the PVAs in the aqueous solution. With increasing concentration of surfactant, the viscosities of the solutions pass over a maximum. In this respect the PVAs behave like hydrophobically modified water soluble polymers. The surfactants bind to the hydrophobic microdomain and thereby crosslink the polymer molecules. On saturation the polyvinyl alcohol with anionic surfactant become hydrophilic and the network character disappears to a certain extent.