Search results for "protein structure"

Finding optimal finite biological sequences over finite alphabets: the OptiFin toolbox

2017

International audience; In this paper, we present a toolbox for a specific optimization problem that frequently arises in bioinformatics or genomics. In this specific optimisation problem, the state space is a set of words of specified length over a finite alphabet. To each word is associated a score. The overall objective is to find the words which have the lowest possible score. This type of general optimization problem is encountered in e.g 3D conformation optimisation for protein structure prediction, or largest core genes subset discovery based on best supported phylogenetic tree for a set of species. In order to solve this problem, we propose a toolbox that can be easily launched usin…

Gene symbol: f9.

2007

Structural and functional diversity of the lectin repertoire in teleost fish: Relevance to innate and adaptive immunity

2011

Protein–carbohydrate interactions mediated by lectins have been recognized as key components of innate immunity in vertebrates and invertebrates, not only for recognition of potential pathogens, but also for participating in downstream effector functions, such as their agglutination, immobilization, and complement-mediated opsonization and killing. More recently, lectins have been identified as critical regulators of mammalian adaptive immune responses. Fish are endowed with virtually all components of the mammalian adaptive immunity, and are equipped with a complex lectin repertoire. In this review, we discuss evidence suggesting that: (a) lectin repertoires in teleost fish are highly dive…

Polarity factor 'Frizzled' in the demosponge Suberites domuncula: identification, expression and localization of the receptor in the epithelium/pinac…

2003

Until recently, it was assumed that polarity and axis formation have evolved only in metazoan phyla higher than Cnidaria. One key molecule involved in the signal transduction causing tissue polarity is Frizzled, a seven-transmembrane receptor that is activated by the Wnt family of secreted proteins. We report the isolation and characterization of a Frizzled gene from the demosponge Suberites domuncula (Sd-Fz). The deduced polypeptide comprises all characteristic domains known from Frizzled receptors of higher metazoans. In situ hybridization studies show that Sd-Fz is expressed in cells close to the surface of the sponges and in the pinacocytes of some canals. Northern blot analysis demonst…

Pulsed Electric Field: Fundamentals and Effects on the Structural and Techno-Functional Properties of Dairy and Plant Proteins

2022

Dairy and plant-based proteins are widely utilized in various food applications. Several techniques have been employed to improve the techno-functional properties of these proteins. Among them, pulsed electric field (PEF) technology has recently attracted considerable attention as a green technology to enhance the functional properties of food proteins. In this review, we briefly explain the fundamentals of PEF devices, their components, and pulse generation and discuss the impacts of PEF treatment on the structure of dairy and plant proteins. In addition, we cover the PEF-induced changes in the techno-functional properties of proteins (including solubility, gelling, emulsifying, and foamin…

Biofilm formation byCandida albicansmutants for genes coding fungal proteins exhibiting the eight-cysteine-containing CFEM domain

2006

Several features and functions of a Candida albicans gene, PGA10 (also designated as RBT51), coding for a putative polypeptide species belonging to a subset of fungal proteins containing an eight-cysteine domain referred as CFEM (Common in several Fungal Extracellular Membrane proteins), are described. The ORF of the gene (ORF19.5674) encoded a protein of 250 amino acids, with a predicted molecular mass of 25.17 kDa. The product of the PGA10 gene also exhibited some features reminiscent of a class II-type hydrophobin. Deletion of PGA10 resulted in a cascade of pleiotropic effects, mostly affecting cell-surface-related properties. Thus, the null pga10Delta mutant displayed an increased sensi…

The tetrameric α-helical membrane protein GlpF unfolds via a dimeric folding intermediate.

2011

Many membrane proteins appear to be present and functional in higher-order oligomeric states. While few studies have analyzed the thermodynamic stability of α-helical transmembrane (TM) proteins under equilibrium conditions in the past, oligomerization of larger polytopic monomers has essentially not yet been studied. However, it is vital to study the folding of oligomeric membrane proteins to improve our understanding of the general mechanisms and pathways of TM protein folding. To investigate the folding and stability of the aquaglyceroporin GlpF from Escherichia coli, unfolding of the protein in mixed micelles was monitored by steady-state fluorescence and circular dichroism spectroscopy…

Determination of phosphorylation degrees in caseins by on-line gel electrophoresis coupled to ICP-SFMS

2007

The determination of the phosphorylation degree of proteins is essential in many biochemical fields. Besides mass spectrometric techniques elucidating the protein structure, ICP-MS has entered this research area as it provides excellent quantification capabilities. In this work the separation of the proteins has been carried out by gel electrophoresis on-line coupled to an ICP equipped with a double-focusing sector field-MS (ELEMENT 2). Based on the simultaneous detection of 32S+ and 31P+, this work presents an alternative approach to determining the phosphorylation degree of caseins. For the example of α- and β-casein the results obtained were in excellent agreement with the expected value…

Posttranslational N-glycosylation of the hepatitis B virus large envelope protein

2007

Abstract Background The addition of N-linked glycans to proteins is normally a cotranslational process that occurs during translocation of the nascent protein to the endoplasmic reticulum. Here, we report on an exception to this rule occurring on the hepatitis B virus (HBV) large L envelope protein that is a subject to co-plus posttranslational N-glycosylation. Results By using an improved detection system, we identified so far unrecognized, novel isoforms of L. Based on mutational analyses, the use of N-glycosylation inhibitors, and pulse-chase studies, we showed that these isoforms are due to posttranslational N-glycan addition to the asparagines 4 and 112 within the preS domain of L. Whi…

NAIP-deltaEx10-11: a novel splice variant of the apoptosis inhibitor NAIP differently expressed in drug-sensitive and multidrug-resistant HL60 leukem…

2002

Alterations of neuronal apoptosis inhibitory protein (NAIP), a member of the inhibitory of apoptosis protein (IAP) family of inhibitors of apoptosis, have been previously associated with different neurodegenerative disorders. This study indicated the existence of a novel NAIP splice variant. This isoform, NAIP-deltaEx10-11, was found in tumor cell lines of different origin and in normal adult brain. Analysis of the putative protein predicted that the NAIP variant lacks part of the third BIR domain as well as the COOH-terminal tail of regular NAIP. This might suggest that it is endowed with a reduced antiapoptotic activity. This view is supported by the fact that NAIP-deltaEx10-11 mRNA and p…