Using cellular fitness to map the structure and function of a major facilitator superfamily effluxer.

The major facilitator superfamily (MFS) effluxers are prominent mediators of antimicrobial resistance. The biochemical characterization of MFS proteins is hindered by their complex membrane environment that makes in vitro biochemical analysis challenging. Since the physicochemical properties of proteins drive the fitness of an organism, we posed the question of whether we could reverse that relationship and derive meaningful biochemical parameters for a single protein simply from fitness changes it confers under varying strengths of selection. Here, we present a physiological model that uses cellular fitness as a proxy to predict the biochemical properties of the MFS tetracycline efflux pump, TetB, and a family of single amino acid variants. We determined two lumped biochemical parameters roughly describing Km and Vmax for TetB and variants. Including in vivo protein levels into our model allowed for more specified prediction of pump parameters relating to substrate binding affinity and pumping efficiency for TetB and variants. We further demonstrated the general utility of our model by solely using fitness to assay a library of tet(B) variants and estimate their biochemical properties

Characterization of femtosecond laser written waveguides for integrated biochemical sensing

Fluorescence detection is known to be one of the most sensitive among the different optical sensing techniques. This work focuses on excitation and detection of fluorescence emitted by DNA strands labeled with fluorescent dye molecules that can be excited at a specific wavelength. Excitation occurs via optical channel waveguides written with femtosecond laser pulses applied coplanar with a microfluidic channel on a glass chip. The waveguides are optically characterized in order to facilitate the design of sensing structures which can be applied for monitoring the spatial separation of biochemical\ud species as a result of capillary electrophoresis

Electron microscopic and biochemical characterization of Fraction 1 protein

High resolution electron microscopy of Fraction I protein from plant leave

Activity and Process Stability of Purified Green Pepper (Capsicum annuum) Pectin Methylesterase

Pectin methylesterase (PME) from green bell peppers (Capsicum annuum) was extracted and purified by affinity chromatography on a CNBr-Sepharose-PMEI column. A single protein peak with pectin methylesterase activity was observed. For the pepper PME, a biochemical characterization in terms of molar mass (MM), isoelectric points (pI), and kinetic parameters for activity and thermostability was performed. The optimum pH for PME activity at 22 °C was 7.5, and its optimum temperature at neutral pH was between 52.5 and 55.0 °C. The purified pepper PME required the presence of 0.13 M NaCl for optimum activity. Isothermal inactivation of purified pepper PME in 20 mM Tris buffer (pH 7.5) could be described by a fractional conversion model for lower temperatures (55?57 °C) and a biphasic model for higher temperatures (58?70 °C). The enzyme showed a stable behavior toward high-pressure/temperature treatments. Keywords: Capsicum annuum; pepper; pectin methylesterase; purification; characterization; thermal and high-pressure stabilit

Mamey (Mammea americana L.) in Martinique Island : un patrimonio para ser valorizados

Introduction. Mamey (Mammea americana L., Clusiaceae) was present in Martini-que before the Spanish colonization. Its distribution area includes tropical America and the Carib-bean. A significant phenotypical diversity is observed on the island, with fruits of very uneven quality as well as various agronomic, pomological and biochemical characteristics. The aim of our work was to localize, identify and characterize trees considered of superior quality. Materials and methods. A survey carried out between April and September 2005 allowed the selection of 10 trees renowned by the people as bearing high-quality fruits. These fruits present a small number of seeds and nonadhesive pulp, and develop a sweet taste as well as a strong flavor. During the year 2006, pomological description and biochemical analysis (total soluble solids and total titrable acidity) were carried out on the fruits. Results and discussion. The biometric and biochemical characteristics measured were generally better than those cited in the literature. Some accessions stand out and present great assets for their promotion for the fresh market as well as for processing. Moreover, some tendencies emerged from the variability observed for a few characters: thus, the variability of the biochemical characteristics measured within one accession, as well as between accessions originating from the same land, is low. It is null for the seed adhesion to the pulp for fruits belonging to the same accession. Conclusion and perspectives. Our work is one of the first relating to identification and characterization of phenotypical diversity of the M. americana L. species, especially in Martinique Island. Our results are likely to pro-mote the development of a diversification network. Some highlighted trends suggest new research to be able to distinguish the role of the environmental versus genetic components in the performance of the phenotypes observed

Characterization of Aptamer-Protein Complexes by X-ray Crystallography and Alternative Approaches

Aptamers are oligonucleotide ligands, either RNA or ssDNA, selected for high-affinity binding to molecular targets, such as small organic molecules, proteins or whole microorganisms. While reports of new aptamers are numerous, characterization of their specific interaction is often restricted to the affinity of binding (KD). Over the years, crystal structures of aptamer-protein complexes have only scarcely become available. Here we describe some relevant technical issues about the process of crystallizing aptamer-protein complexes and highlight some biochemical details on the molecular basis of selected aptamer-protein interactions. In addition, alternative experimental and computational approaches are discussed to study aptamer-protein interactions.

Analysis of the molecular mobility of collagen and elastin in safe, atheromatous and aneurysmal aortas

Aim of the study : In this study, we propose to use a thermal technique, Differential Scanning Calorimetry (DSC) to follow the evolution of elastin and collagen in safe and pathological cardiovascular tissues. Patients and methods : The first part of this study deals with the analysis of the elastin network and associated proteins during ageing (from children to old persons) in aortic walls. The second part is devoted to the characterization of the collagenic phase in aneurysms. In both cases, physical data are correlated with biochemical analyses. Results and conclusion : For old persons aortas with atheromatous stades, elastin and associated proteins are found to interpenetrate to form a homogenous phase. Abdominal aortic aneurysms (AAA) are characterized by structural alterations of the aortic wall resulting from the degradation of elastic fibers and an increase of collagen/elastin ratio. Notable modifications are evidenced between collagen from control tissue and collagen from AAA, particularly concerning the thermal denaturation. Biochemical and thermal results are compatible with the increase of new collagen deposition and/or impairment of the collagen phase stability in the extracellular matrix of AAAs

An extra dimension in protein tagging by quantifying universal proteotypic peptides using targeted proteomics

The use of protein tagging to facilitate detailed characterization of target proteins has not only revolutionized cell biology, but also enabled biochemical analysis through efficient recovery of the protein complexes wherein the tagged proteins reside. The endogenous use of these tags for detailed protein characterization is widespread in lower organisms that allow for efficient homologous recombination. With the recent advances in genome engineering, tagging of endogenous proteins is now within reach for most experimental systems, including mammalian cell lines cultures. In this work, we describe the selection of peptides with ideal mass spectrometry characteristics for use in quantification of tagged proteins using targeted proteomics. We mined the proteome of the hyperthermophile Pyrococcus furiosus to obtain two peptides that are unique in the proteomes of all known model organisms (proteotypic) and allow sensitive quantification of target proteins in a complex background. By combining these 'Proteotypic peptides for Quantification by SRM' (PQS peptides) with epitope tags, we demonstrate their use in co-immunoprecipitation experiments upon transfection of protein pairs, or after introduction of these tags in the endogenous proteins through genome engineering. Endogenous protein tagging for absolute quantification provides a powerful extra dimension to protein analysis, allowing the detailed characterization of endogenous proteins