Structural insights into marine carbohydrate degradation by family GH16 κ-carrageenases.

Carrageenans are sulfated α-1,3-β-1,4-galactans found in the cell wall of some red algae that are practically valuable for their gelation and biomimetic properties but also serve as a potential carbon source for marine bacteria. Carbohydrate degradation has been studied extensively for terrestrial plant/bacterial systems, but sulfation is not present in these cases, meaning the marine enzymes used to degrade carrageenans must possess unique features to recognize these modifications. To gain insights into these features, we have focused on κ-carrageenases from two distant bacterial phyla, which belong to glycoside hydrolase family 16 and cleave the β-1,4 linkage of κ-carrageenan.

The Spin-Foam Approach to Quantum Gravity.

This article reviews the present status of the to the quantization of gravity. Special attention is payed to the pedagogical presentation of the recently-introduced new models for four-dimensional quantum gravity. The models are motivated by a suitable implementation of the path integral quantization of the Plebanski formulation of gravity on a simplicial regularization.

Characterization of insoluble calcium alginates by solid-state NMR.

Three series of 9 insoluble calcium alginate powders with different average calcium contents (1.5, 3.5 and 8%, w/w) are investigated by means of C solid-state NMR spectroscopy.

An evaluation of UiO-66 for gas-based applications.

In addition to its high thermal stability, repetitive hydration/dehydration tests have revealed that the porous zirconium terephthalate UiO-66 switches reversibly between its dehydroxylated and hydroxylated versions. The structure of its dehydroxylated form has thus been elucidated by coupling molecular simulations and X-ray powder diffraction data. Infrared measurements have shown that relatively weak acid sites are available while microcalorimetry combined with Monte Carlo simulations emphasize moderate interactions between the UiO-66 surface and a wide range of guest molecules including CH(4), CO, and CO(2).

Isomeric distinction of small oligosaccharides: a bottom-up approach using the kinetic method.

Isomeric distinction of di- and tri-saccharides could be efficiently achieved by using data previously obtained while performing experiments aimed at discriminating monosaccharides using trimeric ion dissociation with data analysis by the kinetic method. This study shows that effects observed for lower homologues when one of the partners is changed in the metal/reference system (typically a transition metal divalent cation associated to amino acids) can be extrapolated to upper homologues, at least for the tested analyte series. Systems allowing galactose, glucose, and fructose distinction were used as starting conditions to resolve cellobiose, lactose, maltose, and saccharose disaccharides.

Enzymatic activity and protein interactions in alpha/beta hydrolase fold proteins: moonlighting versus promiscuity.

Genes coding for members of the alpha/beta hydrolase fold superfamily of proteins are present in all known genomes. Although there is no common and essential function performed by these proteins shared in all living organisms, this fold has been used for a number of diverse functions. The ancestry of both enzymatic and protein-protein interaction capability of this structural scaffold made it an important tinkering tool kit for protein function evolution.

A common evolutionary origin for tailed-bacteriophage functional modules and bacterial machineries.

Bacteriophages belonging to the order Caudovirales possess a tail acting as a molecular nanomachine used during infection to recognize the host cell wall, attach to it, pierce it, and ensure the high-efficiency delivery of the genomic DNA to the host cytoplasm. In this review, we provide a comprehensive analysis of the various proteins constituting tailed bacteriophages from a structural viewpoint. To this end, we had in mind to pinpoint the resemblances within and between functional modules such as capsid/tail connectors, the tails themselves, or the tail distal host recognition devices, termed baseplates.

Acyclic nucleoside thiophosphonates as potent inhibitors of HIV and HBV replication.

9-[2-(Thiophosphonomethoxy)ethyl]adenine 3 and (R)-9-[2-(Thiophosphonomethoxy)propyl]adenine 4 were synthesized as the first thiophosphonate nucleosides bearing a sulfur atom at the α-position of the acyclic nucleoside phosphonates PMEA and PMPA. Thiophosphonates S-PMEA 3 and S-PMPA 4 were evaluated for in vitro activity against HIV-1 (subtypes A to G), HIV-2 and HBV-infected cells, and found to exhibit potent antiretroviral activity. We showed that their diphosphate forms S-PMEApp 5 and S-PMPApp 6 are readily incorporated by wild-type (WT) HIV-1 RT into DNA and act as DNA chain terminators.

Chemical characterization of the biomass of an edible medicinal mushroom, Agaricus subrufescens, via solid-state 13C NMR.

The biomass of 18 strains of Agaricus subrufescens and of 13 strains of Agaricus bisporus was chemically analyzed using solid-state (13)C NMR. The study focused on polysaccharides because they can play a major role as antitumor molecules. The study also examined whether biomass chemical properties varied between the vegetative mycelium and the fruiting bodies of A.

Oxygen reduction in the strict anaerobe Desulfovibrio vulgaris Hildenborough: characterization of two membrane-bound oxygen reductases.

Although Desulfovibrio vulgaris Hildenborough (DvH) is a strictly anaerobic bacterium, it is able to consume oxygen in different cellular compartments, including extensive periplasmic O₂ reduction with hydrogen as electron donor. The genome of DvH revealed the presence of cydAB and cox genes, encoding a quinol oxidase bd and a cytochrome c oxidase, respectively. In the membranes of DvH, we detected both quinol oxygen reductase [inhibited by heptyl-hydroxyquinoline-N-oxide (HQNO)] and cytochrome c oxidase activities.

Tandem mass spectrometry of trimethylsilyl-terminated poly(dimethylsiloxane) ammonium adducts generated by electrospray ionization.

Ammonium adducts of trimethylsilyl-terminated poly(dimethylsiloxane) (CH(3)-PDMS) produced by electrospray ionization were submitted to collision induced dissociation and revealed a particular MS/MS behavior: the same three main product ions at m/z 221, 295, and 369 were always generated in very similar relative abundances regardless of the size of the precursor ion. Combining accurate mass measurements and ab initio calculation allowed very stable cyclic geometries to be obtained for these ionic species. Dissociation mechanisms were proposed to account for the three targeted ions to be readily generated in a two-step or a three-step reaction from any CH(3)-PDMS ammonium adducts.

Highly selective cobalt-mediated [6 + 2] cycloaddition of cycloheptatriene and allenes.

[6 + 2] Cycloadditions between cycloheptatrienes with allenes have been investigated. Cobalt salts were found to promote this transformation efficiently. Moreover, this reaction was found to be highly selective since only one regioisomer was obtained with an excellent E/Z-selectivity.

Quantifying the contribution of foods with unfavourable nutrient profiles to nutritionally adequate diets.

That 'all foods can fit' into a healthy diet is a long-standing principle of dietetic practice. The present study quantified the relative contributions of foods to encourage and foods to limit, using new techniques of individual diet optimisation and nutrient profiling. Individual foods from every food group were assigned to four nutrient profile classes based on the French SAIN,LIM system.

Structural characterisation of degradation products formed upon di-n-butyl phthalate radiolysis by high-performance liquid chromatography electrospray tandem mass spectrometry.

Structural characterisation of 15 degradation products, formed upon di-n-butyl phthalate (DBP) radiolysis, has been achieved using a high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) coupling. The dissociation behaviour of protonated DBP was first established to be further used to characterise structural deviation in the degradation products. Based on accurate mass measurements, compounds shown by HPLC-MS analysis were all found to be DBP oxidation products, amongst which various sets of isomers could be distinguished.

Structural disorder within Henipavirus nucleoprotein and phosphoprotein: from predictions to experimental assessment.

Henipaviruses are newly emerged viruses within the Paramyxoviridae family. Their negative-strand RNA genome is packaged by the nucleoprotein (N) within alpha-helical nucleocapsid that recruits the polymerase complex made of the L protein and the phosphoprotein (P). To date structural data on Henipaviruses are scarce, and their N and P proteins have never been characterized so far.

Structural characterization of poly(amino)ester dendrimers and related impurities by electrospray tandem mass spectrometry.

An acid-terminated poly(amino)ester dendrimer was studied by electrospray ionization tandem mass spectrometry to establish its fragmentation pathways, with the aim of using them to investigate the structure of any defective molecules generated during the dendrimer synthesis. This poly(amino)ester dendrimer could be ionized in both polarities but the most structurally relevant dissociation pathways were found from the deprotonated molecule in negative ion mode. The dissociation pattern of this dendrimer is fully described and supported by accurate mass measurements.

Explanation of the adsorption of polar vapors in the highly flexible metal organic framework MIL-53(Cr).

A comparison of the adsorption of water, methanol, and ethanol polar vapors by the flexible porous chromium(III) terephthalate MIL-53(Cr) was investigated by complementary techniques including adsorption gravimetry, ex situ X-ray powder diffraction, microcalorimetry, thermal analysis, IR spectroscopy, and molecular modeling. The breathing steps observed during adsorption strongly depend on the nature of the vapor. With water, a significant contraction of the framework is observed.

Distinct oligomeric forms of the Pseudomonas aeruginosa RetS sensor domain modulate accessibility to the ligand binding site.

Bacterial two-component regulatory systems (TCSs) sense environmental stimuli to adapt the lifestyle of microbial populations. For many TCSs the stimulus is a ligand of unknown chemical nature. Pseudomonas aeruginosa utilizes the closely related RetS and LadS sensor kinases to switch between acute and chronic infections.

Methylation of acidic moieties in poly(methyl methacrylate-co-methacrylic acid) copolymers for end-group characterization by tandem mass spectrometry.

The complete structural characterization of a copolymer composed of methacrylic acid (MAA) and methyl methacrylate (MMA) units was achieved using tandem mass spectrometry. In a first step, collision-induced dissociation (CID) of sodiated MAA-MMA co-oligomers allowed us to determine the co-monomeric composition, the random nature of the copolymer and the sum of the end-group masses. However, dissociation reactions of MAA-based molecules mainly involve the acidic pendant groups, precluding individual characterization of the end groups.

The VIZIER project: overview; expectations; and achievements.

VIZIER is an acronym for a research project entitled "Comparative Structural Genomics of Viral Enzymes Involved in Replication" funded by the European Commission between November 1st, 2004 and April 30th, 2009. It involved 25 partners from 12 countries. In this paper, we describe the organization of the project and the culture created by its multidisciplinary essence.

Conformational disorder.

In recent years it was shown that a large number of proteins are either fully or partially disordered. Intrinsically disordered proteins are ubiquitary proteins that fulfill essential biological functions while lacking a stable 3D structure. Despite the large abundance of disorder, disordered regions are still poorly detected.

Analytical strategy for the molecular weight determination of random copolymers of poly(methyl methacrylate) and poly(methacrylic acid).

Molecular weight characterization of random amphiphilic copolymers currently represents an analytical challenge. In particular, molecules composed of methacrylic acid (MAA) and methyl methacrylate (MMA) as the repeat units raise issues in commonly used techniques. The present study shows that when random copolymers cannot be properly ionized by MALDI, and hence detected and measured in MS, one possible analytical strategy is to transform them into homopolymers, which are more amenable to this ionization technique.

Solution and electron microscopy characterization of lactococcal phage baseplates expressed in Escherichia coli.

We report here the characterization of several large structural protein complexes forming the baseplates (or part of them) of Siphoviridae phages infecting Lactococcus lactis: TP901-1, Tuc2009 and p2. We revisited a "block cloning" expression strategy and extended this approach to genomic fragments encoding proteins whose interacting partners have not yet been clearly identified. Biophysical characterization of some of these complexes using circular dichroism and size exclusion chromatography, coupled with on-line light scattering and refractometry, demonstrated that the over-produced recombinant proteins interact with each other to form large (up to 1.

Structure-function relationships of the alpha/beta-hydrolase fold domain of neuroligin: a comparison with acetylcholinesterase.

The neuroligins are postsynaptic cell adhesion proteins whose extracellular domain belongs to the alpha/beta-hydrolase fold family of proteins, a family characterized through the enzyme acetylcholinesterase (AChE) and other enzymes with various substrate specificities. Neuroligin associations with the pre-synaptic neurexins participate in synapse maturation and maintenance. Alternative splicing of the neuroligin and neurexin genes results in multiple isoforms and presumably regulation of activity, while mutations appear to be associated with autism spectrum disorders.

Synthesis and antiviral activity of boranophosphonate isosteres of AZT and d4T monophosphates.

We report synthesis, in vitro antiviral activity, and stability studies in biological media of original boranophosphonate isosteres of AZT and d4T monophophates. A convenient route for the synthesis of 3'-Azido-3'-deoxythymidine-5'-boranophosphonate 8 and 2',3'-Didehydro-3'-dideoxythymidine-5'-boranophosphonate 12 is described. H-phosphinates 7 and 11, and alpha-boranophosphonates 8 and 12 exhibited no significant in vitro activity against HIV-infected cells, neither against a broad panel of viruses, up to 200 microM.