Retention time prediction and protein identification

Proteins are commonly identified through enzymatic digestion and generation of short sequence tags or fingerprints of peptide masses by mass spectrometry. Separation methods, such as liquid chromatography and electrophoresis, are often used to fractionate complex protein or peptide mixtures and these separations also provide information on the different species, such as molecular weight and isoelectric point from electrophoresis and hydrophobicity in reversed-phase chromatography. These are also properties that can be predicted from amino acid sequences derived from genomic sequences and used in protein identification. This chapter reviews recently introduced methods based on retention time prediction to extract information from chromatographic separations and the applications to protein identification in organisms with small and large genomes. Novel data on retention time prediction of posttranslationally modified peptides is also presented.

Effects of high pressure on functional properties of soy protein

Simultaneous measurement of the effects of low soy protein concentration, pH and high pressure treatment at room temperature on solubility, emulsifying properties and rheological properties (loss modulus, G '') of soy protein isolate (SPI) were evaluated. Central composite rotatable designs (2(3)) were employed over two pH ranges (2.66-4.34 and 5.16-6.84) with SPI concentration (0.32-3.68%) and pressure (198-702 MPa) as the other independent variables. The surface responses were obtained for protein solubility, emulsifying activity index (EAI) and G ''. The samples with the highest effect on protein solubility, EAI and G '' values were evaluated, as well, by electrophoresis and free sulphydryl determination. The pH was the main factor that affected protein solubility, with solubility at a maximum at pH < 3 or pH > 6. Increasing SPI concentration and decreasing/increasing the pH away from the isoelectric point both caused a reduction in EAI. Loss modulus (G '') was found to increase with SPI concentration in both pH ranges. (c) 2006 Elsevier Ltd. All rights reserved.

The production, purification and characterisation of two novel alpha-D-mannosidases from Aspergillus phoenicis

1,6-alpha-D-Mannosidase from Aspergillits phoenicis was purified by anion-exchange chromatography, chromatofocussing and size-exclusion chromatography. The apparent molecular weight was 74 kDa by SDS-PAGE and 81 kDa by native-PAGE. The isoelectric point was 4.6. 1,6-alpha-D-Mannosidase had a temperature optimum of 60 degrees C, a pH optimum of 4.0-4.5. a K-m of 14 mM with alpha-D-Manp-(1 -> 6)-D-Manp as substrate. It was strongly inhibited by Mn2+ and did not need Ca2+ or any other metal cofactor of those tested. The enzyme cleaves specifically (1 -> 6)-linked mannobiose and has no activity towards any other linkages, p-nitrophenyl-alpha-D-mannopyranoside or baker's yeast mannan. 1,3(1,6)-alpha-D-Mannosidase from A. phoenicis was purified by anion-exchange chromatography, chromatofocus sing and size-exclusion chromatography. The apparent molecular weight was 97 kDa by SDS-PAGE and 110 kDa by native-PAGE. The 1,3(1,6)-alpha-D-mannosidase enzyme existed as two charge isomers or isoforms. The isoelectric points of these were 4.3 and 4.8 by isoelectric focussing. It cleaves alpha-D-Manp-(1 -> 3)-D-Manp 10 times faster than alpha-D-Manp-(1 -> 6)-D-Manp, has very low activity towards p-nitrophenyl-alpha-D-mannopyranoside and baker's yeast mannan, and no activity towards alpha-D-Manp-(1 -> 2)-D-Manp. The activity towards (1 -> 3)-linked mannobiose is strongly activated by 1 mM Ca2+ and inhibited by 10 mM EDTA, while (1 -> 6)-activity is unaffected, indicating that the two activities may be associated with different polypeptides. It is also possible that one polypeptide may have two active sites catalysing distinct activities. (c) 2005 Elsevier Ltd. All rights reserved.

First-dimension separation with the MicroRotoforTM cell prior to SDS-PAGE and LC-MS/MS analysis

Free-flow isoelectric focusing (IEF) is a gel-free method for separating proteins based on their isoelectric point (pl) in a liquid environment and in the presence of carrier ampholytes. this method has been used with the RotoforTM cell at the preparative scale to fractionate proteins from samples containing several hundred milligrams of protein; see the refeences listed in Bio-Rad bulletin 3152. the MicroRotofor cell applies the same method to much sl=maller protein samples without dilution, separating and recoverng milligram quantities of protein in a total volume of about 2 ml.

Bothrops insularis venomics: A proteomic analysis supported by transcriptomic-generated sequence data

A joint transcriptomic and proteomic approach employing two-dimensional electrophoresis, liquid chromatography and mass spectrometry was carried out to identify peptides and proteins expressed by the venom gland of the snake Bothrops insularis, an endemic species of Queimada Grande Island, Brazil. Four protein families were mainly represented in processed spots, namely metalloproteinase, serine proteinase, phospholipase A(2) and lectin. Other represented families were growth factors, the developmental protein G10, a disintegrin and putative novel bradykinin-potentiating peptides. The enzymes were present in several isoforms. Most of the experimental data agreed with predicted values for isoelectric point and M(r) of proteins found in the transcriptome of the venom gland. The results also support the existence of posttranslational modifications and of proteolytic processing of precursor molecules which could lead to diverse multifunctional proteins. This study provides a preliminary reference map for proteins and peptides present in Bothrops insularis whole venom establishing the basis for comparative studies of other venom proteomes which could help the search for new drugs and the improvement of venom therapeutics. Altogether, our data point to the influence of transcriptional and post-translational events on the final venom composition and stress the need for a multivariate approach to snake venomics studies. (c) 2009 Elsevier B.V. All rights reserved.

Thin films of xyloglucans for BSA adsorption

In this work. XG extracted from Tamarindus indica (XGT) and Copaifera langsdorffii (XGC) seeds were deposited onto Si wafers as thin films. The characteristics of XGT and XGC adsorbed layers were compared with a commercial XG sample (TKP, Tamarind kernel powder) by ellipsometry, and atomic force microscopy (AFM). Moreover, the adsorption of oxidized derivative of XGT (To60) onto amino-terminated Si wafers and the immobilization of bovine serum albumin (BSA) onto polysaccharides covered wafers, as a function of pH, were also investigated. The XG samples presented molar ratios Glc:Xyl:Gal of 2.4:2.1:1 (XGC) 2.8: 23: 1 (XGT) and 1.91.91 (TKP). The structure of XGT and XGC was determined by O-methy alditol acetate derivatization and showed similar features, but XGC confirmed the presence of more alpha-D-Xyl branches due to more beta-D-Gal ends. XGT deposited onto Si adsorbed as fibers and small entities uniformly distributed, as evidenced by AFM, while TPK and XGC formed larger aggregates. The thickness of To60 onto amino-terminated surface was similar to that determined for XGT onto Si wafers. A maximum in the adsorbed amount of BSA occurred close to its isoelectric point (5.5). These findings indicate that XGT and To60 are potential materials for the development of biomaterials and biotechnological devices. (C) 2008 Elsevier B.V. All rights reserved.

Interaction of giant extracellular Glossoscolex paulistus hemoglobin (HbGp) with zwitterionic surfactant N-hexadecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (HPS): Effects of oligomeric dissociation

The present work focuses on the interaction between the zwitterionic surfactant N-hexadecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (HPS) and the giant extracellular hemoglobin of Glossoscolex paulistus (HbGp). Electronic optical absorption, fluorescence emission and circular dichroism spectroscopy techniques, together with Gel-filtration chromatography, were used in order to evaluate the oligomeric dissociation as well as the autoxidation of HbGp as a function of the interaction with HPS. A peculiar behavior was observed for the HPS-HbGp interaction: a complex ferric species formation equilibrium was promoted, as a consequence of the autoxidation and oligomeric dissociation processes. At pH 7.0, HPS is more effective up to 1 mM while at pH 9.0 the surfactant effect is more intense above 1 mM. Furthermore, the interaction of HPS with HbGp was clearly less intense than the interaction of this hemoglobin with cationic (CTAC) and anionic (SDS) surfactants. Probably, this lower interaction with HPS is due to two factors: (i) the lower electrostatic attraction between the HPS surfactant and the protein surface ionic sites when compared to the electrostatic interaction between HbGp and cationic and anionic surfactants, and (ii) the low cmc of HPS, which probably reduces the interaction of the surfactant in the monomeric form with the protein. The present work emphasizes the importance of the electrostatic contribution in the interaction between ionic surfactants and HbGp. Furthermore, in the whole HPS concentration range used in this study, no folding and autoxidation decrease induced by this surfactant were observed. This is quite different from the literature data on the interaction between surfactants and tetrameric hemoglobins, that supports the occurrence of this behavior for the intracellular hemoglobins at low surfactant concentration range. Spectroscopic data are discussed and compared with the literature in order to improve the understanding of hemoglobin-surfactant interaction as well as the acid isoelectric point (pI) influence of the giant extracellular hemoglobins on their structure-activity relationship. (c) 2007 Elsevier B.V. All rights reserved.

Obtenção de dispersões de complexos polieletrolíticos à base de quitosana e poli(ácido metacrílico) e análise de adsorção de albumina bovina sérica

Dispersions composed of polyelectrolyte complexes based on chitosan and poly(methacrylic acid), PMAA, were obtained by the dropping method and template polymerization. The effect of molecular weight of PMAA and ionic strength on the formation of chitosan/poly(methacrylic acid), CS/PMAA, complexes was evaluated using the dropping method. The increase in molecular weight of PMAA inhibited the formation of insoluble complexes, while the increase in ionic strength first favored the formation of the complex followed by inhibiting it at higher concentrations. The polyelectrolyte complexation was strongly dependent on macromolecular dimensions, both in terms of molecular weight and of coil expansion/contraction driven by polyelectrolyte effect. The resultant particles from dropping method and template polymerization were characterized as having regions with different charge densities: chitosan predominating in the core and poly(methacrylic acid) at the surface, the particles being negatively charged, as a consequence. Albumin was adsorbed on templatepolymerized CS/PMAA complexes (after crosslinking with glutardialdehyde) and pH was controlled in order to obtain two conditions: (i) adsorption of positively charged albumin, and (ii) adsorption of albumin at its isoelectric point. Adsorption isotherms and zeta potential measurements showed that albumin adsorption was controlled by hydrogen bonding/van der Waals interactions and that brushlike structures may enhance adsorption of albumin on these particles

Structural and functional properties of Bp-LAAO, a new L-amino acid oxidase isolated from Bothrops pauloensis snake venom

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

Metallomic study on plasma samples from Nile tilapia using SR-XRF and GFAAS after separation by 2D PAGE: initial results

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

Purification, biochemical and functional characterization of miliin, a new thiol-dependent serine protease isolated from the latex of Euphorbia milii

Miliin, a new thiol-dependent serine protease purified from the latex of Euphorbia milii possesses a molecular weight of 79 kDa, an isoelectric point of 4.3 and is optimally active at 60 degrees C in the pH range of and 7.5-11.0. Activity tests indicate that milliin is a thiol-dependent serine protease.

NiTiO3 nanoparticles encapsulated with SiO2 prepared by sol-gel method

NiTiO3 (NTO) nanoparticles encapsulated with SiO2 were prepared by the sol-gel method resulting on core-shell structure. Changes on isoelectric point as a function of silica were evaluated by means of zeta potential. The NTO nanoparticles heat treated at 600 degrees C were characterized by X-ray diffraction, transmission electron microscopy (TEM) and energy dispersive X-ray analysis. TEM observations showed that the mean size of NTO is in the range of 2.5-42.5 nm while the thickness of SiO2 shell attained 1.5-3.5 nm approximately.

Expressão protéica diferencial entre plântulas apomíticas e zigóticas de citros

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

A rapid procedure for the isolation of the Lys-49 myotoxin II from Bothrops moojeni (caissaca) venom: Biochemical characterization, crystallization, myotoxic and edematogenic activity

A, M. Soares, V, M, Rodrigues, M. I. Homsi-Brandeburgo, M. H. Toyama, F, R, Lombardi, K. Arni and J. R, Giglio. A rapid procedure for the isolation of the Lys-49 myotoxin II from Bothrops moojeni (caissaca) venom: Biochemical characterization, crystallization, myotoxic and edematogenic activity. Toxicon 36, 503-514, 1998.-Bothrops moojeni snake venom was fractionated on a CM-Sepharose column which was previously equilibrated with 0.05 M ammonium bicarbonate buffer at pH 8.0 and subsequently eluted with an ammonium bicarbonate concentration gradient from 0.05 to 0.5 M at constant pH (8.0) and temperature (25 degrees C). The fraction which eluted last (M-VI) showed, after direct lyophilization, a single band by polyacrylamide gel electrophoresis (PAGE) and SDS-PAGE, indicating an approximate M,. of 14 000 and 77 000, in the presence and absence of dithiothreitol, respectively. Its amino acid composition revealed a high level of hydrophobic and basic amino acids as well as 13 half-cystine residues. Its isoelectric point and extinction coefficient (E-1.0cm(1.0mg/ml) at 278 nm and pH 7.0) were 8.2 and 1.170, respectively. M-VI was devoid of phospholipase A(2) (PLA(2)) activity on egg yolk, as well as of hemorrhagic, anticoagulant and coagulant activities, but could induce drastic necrosis on skeletal muscle fibres as well as rapid and transient edema on the rat paw. Its N-terminal sequence: SLFELGKMILQETGKNPAKSYGVYGCNCGVGGRGKPKDATDRCCYVHKCCYK.... revealed high homology with other Lys 49 PLA(2)-like myotoxins from other bothropic venoms. Orthorhombic crystals of M-VI? which diffracted to a maximal resolution of 1.6 Angstrom. were obtained and indicated the presence of a dimer in the asymmetrical unit. (C) 1998 Elsevier B.V. Ltd. All rights reserved.

Preparation of ceramic membranes from surface modified tin oxide nanoparticles

The preparation of crack-free SnO2 supported membranes requires the development of new strategies of synthesis capable to allow controlled changes of surface chemistry and to improve the processability of supported layers. In this way, the controlled modification of the SnO2 nanoparticle surface by adding capping molecules like Tiron(R) ((OH)(2)C6H2(SO3Na)(2)) during the sol-gel process was studied, aiming to obtain high performance membranes. Colloidal suspensions were prepared by hydrolyzing SnCl4.5H(2)O aqueous solution with NH4OH in presence of Tiron(R). The effect of the amount of Tiro(R) (from I to 20 wt.%) on the structural features of nanoparticles, powder redispersability and particle-solution interface properties was investigated by X-ray powder diffraction (XRPD), extended X-ray absorption fine structure (EXAFS), quasi-elastic light scattering and electrophoretic mobility measurements. XRPD and EXAFS results showed that the addition of Tiron(R) up to 20 wt.% to colloidal suspensions does not affect the crystallite size of SnO2 primary particles, determined around 2-3 nm. This value is comparable to the hydrodynamic size measured after redispersion of powder prepared with amount of Tiro(R) higher than 7.5 wt.%, indicating the absence of condensation reactions between primary particles after the initial precipitation step. As a consequence the powder with amount of Tiron(R) > 7.5 wt.%, can be fully redispersed in aqueous solution at pH greater than or equal to I I until a nanoparticle concentration of 6 vol.%. The electrophoresis measurements showed a decrease of the isoelectric point by increasing the amount of grafted Tiron(R) at the SnO2 nanoparticle surface, resulting in negatively charged particle-solution interface in all the studied pH range (2-11). These features govern the gelation process favoring the preparation of crack-free SnO2 supported membranes. The control exercised by Tiron(R) modifying agent in the aggregation process allows the fine-tuning of the porosity, from 0.124 to 0.065 cm(3) g(-1), and mean pore size, from 6.4 to 1.9 nm, as the amount of grafted molecules increases from 0 to 10 wt.%. In consequence, the membrane cut-off determined by filtration of polyethylene glycol standard solutions can be screened from 1500 to 3500 g mol(-1). (C) 2002 Elsevier B.V. B.V. All rights reserved.