Investigation of Interactions between Two Monoclonal Antibodies and SARS Virus with a Label-Free Protein Array

The investigation of interactions between two kinds of monoclonal antibodies and SARS virus with a label-free protein array technique were presented in this paper. The performance consists of three parts: a surface modification for ligand immobilization/surface, a protein array fabrication with an integrated microfluidic system for patterning, packaging and liquid handling, and a protein array reader of imaging ellipsometer. This revealed the technique could be used as an immunoassay for qualitative and quantitative detection as wen as kinetic analysis of biomolecule interaction.

The frequency of muscle protein polymorphism in Menidia menidia (Atherinidae) along the Atlantic coast

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PAnalyzer: A software tool for protein inference in shotgun proteomics

Background Protein inference from peptide identifications in shotgun proteomics must deal with ambiguities that arise due to the presence of peptides shared between different proteins, which is common in higher eukaryotes. Recently data independent acquisition (DIA) approaches have emerged as an alternative to the traditional data dependent acquisition (DDA) in shotgun proteomics experiments. MSE is the term used to name one of the DIA approaches used in QTOF instruments. MSE data require specialized software to process acquired spectra and to perform peptide and protein identifications. However the software available at the moment does not group the identified proteins in a transparent way by taking into account peptide evidence categories. Furthermore the inspection, comparison and report of the obtained results require tedious manual intervention. Here we report a software tool to address these limitations for MSE data. Results In this paper we present PAnalyzer, a software tool focused on the protein inference process of shotgun proteomics. Our approach considers all the identified proteins and groups them when necessary indicating their confidence using different evidence categories. PAnalyzer can read protein identification files in the XML output format of the ProteinLynx Global Server (PLGS) software provided by Waters Corporation for their MSE data, and also in the mzIdentML format recently standardized by HUPO-PSI. Multiple files can also be read simultaneously and are considered as technical replicates. Results are saved to CSV, HTML and mzIdentML (in the case of a single mzIdentML input file) files. An MSE analysis of a real sample is presented to compare the results of PAnalyzer and ProteinLynx Global Server. Conclusions We present a software tool to deal with the ambiguities that arise in the protein inference process. Key contributions are support for MSE data analysis by ProteinLynx Global Server and technical replicates integration. PAnalyzer is an easy to use multiplatform and free software tool.

Processing and characterization of soy protein-based materials

Las proteínas son biopolímeros con potenciales propiedades para aplicaciones en el campo de envases por su capacidad para formar films con buenas propiedades barrera en condiciones secas. Además, al ser biodegradables y provenir de recursos renovables, ofrecen importantes ventajas desde el punto de vista medioambiental y económico. Sin embargo, los films basados en proteínas son frágiles y presentan una baja resistencia a la humedad, por lo que se requiere su modificación para fabricar materiales útiles en las condiciones de servicio.El objetivo de esta tesis es reducir la absorción de humedad y simultáneamente mejorar las propiedades mecánicas de los materiales fabricados con proteína de soja. Para ello es necesaria la adición de sustancias que puedan interaccionar con los grupos polares de la proteína, reduciendo así su carácter hidrofílico y la absorción de humedad, y que a la vez puedan actuar como plastificantes, reduciendo la fragilidad del material fabricado. Además, las condiciones de procesado también influyen en las propiedades del material, por tanto, la optimización del procesado es otro de los objetivos de la tesis.Para poder conseguir la mejora de las propiedades del material y, en concreto, aquellas requeridas por el sector del envase, como son las propiedades mecánicas y la resistencia a la humedad, la tesis se ha centrado en tres áreas: plastificación por adición de glicerol; mezclado con sustancias naturales como gelatinas, ácidos, aceites y azúcares; y procesado por los métodos húmedo y seco.

New Oncogenic Drivers in Hepatocellular Carcinoma: Role of the RNA Binding Protein Hu antigen R

156 p. : graf.

A Computational Module Assembled from Different Protease Family Motifs Identifies PI PLC from Bacillus cereus as a Putative Prolyl Peptidase with a Serine Protease Scaffold

Proteolytic enzymes have evolved several mechanisms to cleave peptide bonds. These distinct types have been systematically categorized in the MEROPS database. While a BLAST search on these proteases identifies homologous proteins, sequence alignment methods often fail to identify relationships arising from convergent evolution, exon shuffling, and modular reuse of catalytic units. We have previously established a computational method to detect functions in proteins based on the spatial and electrostatic properties of the catalytic residues (CLASP). CLASP identified a promiscuous serine protease scaffold in alkaline phosphatases (AP) and a scaffold recognizing a beta-lactam (imipenem) in a cold-active Vibrio AP. Subsequently, we defined a methodology to quantify promiscuous activities in a wide range of proteins. Here, we assemble a module which encapsulates the multifarious motifs used by protease families listed in the MEROPS database. Since APs and proteases are an integral component of outer membrane vesicles (OMV), we sought to query other OMV proteins, like phospholipase C (PLC), using this search module. Our analysis indicated that phosphoinositide-specific PLC from Bacillus cereus is a serine protease. This was validated by protease assays, mass spectrometry and by inhibition of the native phospholipase activity of PI-PLC by the well-known serine protease inhibitor AEBSF (IC50 = 0.018 mM). Edman degradation analysis linked the specificity of the protease activity to a proline in the amino terminal, suggesting that the PI-PLC is a prolyl peptidase. Thus, we propose a computational method of extending protein families based on the spatial and electrostatic congruence of active site residues.

Surface Expression and Subunit Specific Control of Steady Protein Levels by the Kv7.2 Helix A-B Linker

12 p.