Plasmon channels in the electronic relaxation of diamond under high-order harmonics femtosecond irradiation

We used high order harmonics of a femtosecond titanium-doped sapphire system (pulse duration 25 fs) to realise Ultraviolet Photoelectron Spectroscopy (UPS) measurements on diamond. The UPS spectra were measured for harmonics in the range 13 to 27. We also made ab initio calculations of the electronic lifetime of conduction electrons in the energy range produced in the UPS experiment. Such calculations show that the lifetime suddenly diminishes when the conduction electron energy reaches the plasmon energy, whereas the UPS spectra show evidence in this range of a strong relaxation mechanism with an increased production of low energy secondary electrons. We propose that in this case the electronic relaxation proceeds in two steps : excitation of a plasmon by the high energy electron, the latter decaying into individual electron-hole pairs, as in the case of metals. This process is observed for the first time in an insulator and, on account of its high efficiency, should be introduced in the models of laser breakdown under high intensity

Three-dimensional Structure of L-2-Haloacid Dehalogenase from Xanthobacter autotrophicus GJ10 Complexed with the Substrate-analogue Formate

The L-2-haloacid dehalogenase from the 1,2-dichloroethane degrading bacterium Xanthobacter autotrophicus GJ10 catalyzes the hydrolytic dehalogenation of small L-2-haloalkanoic acids to yield the corresponding D-2-hydroxyalkanoic acids. Its crystal structure was solved by the method of multiple isomorphous replacement with incorporation of anomalous scattering information and solvent flattening, and was refined at 1.95-Å resolution to an R factor of 21.3%. The three-dimensional structure is similar to that of the homologous L-2-haloacid dehalogenase from Pseudomonas sp. YL (1), but the X. autotrophicus enzyme has an extra dimerization domain, an active site cavity that is completely shielded from the solvent, and a different orientation of several catalytically important amino acid residues. Moreover, under the conditions used, a formate ion is bound in the active site. The position of this substrate-analogue provides valuable information on the reaction mechanism and explains the limited substrate specificity of the Xanthobacter L-2-haloacid dehalogenase.

Crystal Structure of the C-type Lectin-like Domain from the Human Hematopoietic Cell Receptor CD69

CD69, one of the earliest specific antigens acquired during lymphoid activation, acts as a signal-transducing receptor involved in cellular activation events, including proliferation and induction of specific genes. CD69 belongs to a family of receptors that modulate the immune response and whose genes are clustered in the natural killer (NK) gene complex. The extracellular portion of these receptors represent a subfamily of C-type lectin-like domains (CTLDs), which are divergent from true C-type lectins and are referred to as NK-cell domains (NKDs). We have determined the three-dimensional structure of human CD69 NKD in two different crystal forms. CD69 NKD adopts the canonical CTLD fold but lacks the features involved in Ca(2+) and carbohydrate binding by C-type lectins. CD69 NKD dimerizes noncovalently, both in solution and in crystalline state. The dimer interface consists of a hydrophobic, loosely packed core, surrounded by polar interactions, including an interdomain beta sheet. The intersubunit core shows certain structural plasticity that may facilitate conformational rearrangements for binding to ligands. The surface equivalent to the binding site of other members of the CTLD superfamily reveals a hydrophobic patch surrounded by conserved charged residues that probably constitutes the CD69 ligand-binding site.Fil: Llera, Andrea Sabina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Viedma, Fernando. Universidad Autónoma de Madrid; EspañaFil: Sánchez Madrid, Francisco. Universidad Autónoma de Madrid; EspañaFil: Tormo, José. Universidad Autónoma de Madrid; Españ

Use of the point defect model to interpret the iron oxidation kinetics under proton irradiation

This article concerns the study of iron corrosion in wet air under mega-electron-volt proton irradiation for different fluxes at room temperature and with a relative humidity fixed to 45%. Oxidized iron sample surfaces are characterized by ion beam analysis (Rutherford backscattering spectrometry and elastic recoil detection analysis), for the elemental analysis. The structural and physicochemical characterization is performed using the x-ray photoelectron spectroscopy and transmission electron microscopy techniques. We have also measured the iron oxidation kinetics. Radiation enhanced diffusion and transport processes have been evidenced. The modeling of the experimental data shows that the apparent oxygen diffusion coefficient increases whereas the oxygen transport velocity decreases as function of flux. Finally, the point defect model has been used to determine the electric field value in the samples. Results have shown that the transport process can be attributed to the presence of an electrical potential gradient

Substrate Binding Mode and Its Implication on Drug Design for Botulinum Neurotoxin A

The seven antigenically distinct serotypes of Clostridium botulinum neurotoxins, the causative agents of botulism, block the neurotransmitter release by specifically cleaving one of the three SNARE proteins and induce flaccid paralysis. The Centers for Disease Control and Prevention (CDC) has declared them as Category A biowarfare agents. The most potent among them, botulinum neurotoxin type A (BoNT/A), cleaves its substrate synaptosome-associated protein of 25 kDa (SNAP-25). An efficient drug for botulism can be developed only with the knowledge of interactions between the substrate and enzyme at the active site. Here, we report the crystal structures of the catalytic domain of BoNT/A with its uncleavable SNAP-25 peptide 197QRATKM202 and its variant 197RRATKM202 to 1.5 Å and 1.6 Å, respectively. This is the first time the structure of an uncleavable substrate bound to an active botulinum neurotoxin is reported and it has helped in unequivocally defining S1 to S5′ sites. These substrate peptides make interactions with the enzyme predominantly by the residues from 160, 200, 250 and 370 loops. Most notably, the amino nitrogen and carbonyl oxygen of P1 residue (Gln197) chelate the zinc ion and replace the nucleophilic water. The P1′-Arg198, occupies the S1′ site formed by Arg363, Thr220, Asp370, Thr215, Ile161, Phe163 and Phe194. The S2′ subsite is formed by Arg363, Asn368 and Asp370, while S3′ subsite is formed by Tyr251, Leu256, Val258, Tyr366, Phe369 and Asn388. P4′-Lys201 makes hydrogen bond with Gln162. P5′-Met202 binds in the hydrophobic pocket formed by the residues from the 250 and 200 loop. Knowledge of interactions between the enzyme and substrate peptide from these complex structures should form the basis for design of potent inhibitors for this neurotoxin

Benefits of Automated Crystallization Plate Tracking, Imaging, and Analysis

SummaryWe describe the design of a database and software for managing and organizing protein crystallization data. We also outline the considerations behind the design of a fast web interface linking protein production data, crystallization images, and automated image analysis. The database and associated interfaces underpin the Oxford Protein Production Facility (OPPF) crystallization laboratory, collecting, in a routine and automatic manner, up to 100,000 images per day. Over 17 million separate images are currently held in this database. We discuss the substantial scientific benefits automated tracking, imaging, and analysis of crystallizations offers to the structural biologist: analysis of the time course of the trial and easy analysis of trials with related crystallization conditions. Features of this system address requirements common to many crystallographic laboratories that are currently setting up (semi-)automated crystallization imaging systems

Formation of interfacial molybdenum carbide for DLC lubricated by MoDTC: Origin of wear mechanism

A large amount of research has been devoted to the effect of molybdenum dithiocarbamate (MoDTC) additives on the lubricating performances of carbon-based coatings, showing that a high wear rate is produced when the MoDTC is blended with the base oil. However, the mechanisms leading to the coating removal are not fully understood yet. In this work, the friction and wear performances of an amorphous hydrogenated DLC coating doped with silicon and oxygen have been analysed when lubricated by MoDTC-containing oils. Tribological experiments have been conducted with DLC/steel and DLC/DLC contacts under boundary lubrication conditions using a ball-on-flat tribometer. To understand the wear mechanism, the chemical composition of the tribofilm formed on the steel ball counterpart was investigated by X-ray Photoelectron Spectroscopy (XPS). Transmission Electron Microscopy (TEM) coupled with Energy Dispersive X-Ray Spectroscopy (EDX). A new DLC wear model has been proposed and validated

Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility

Escherichia coli endonuclease VIII (Nei) excises oxidized pyrimidines from DNA. It shares significant sequence homology and similar mechanism with Fpg, a bacterial 8-oxoguanine glycosylase. The structure of a covalent Nei–DNA complex has been recently determined, revealing critical amino acid residues which are important for DNA binding and catalysis. Several Fpg structures have also been reported; however, analysis of structural dynamics of Fpg/Nei family proteins has been hindered by the lack of structures of uncomplexed and DNA-bound enzymes from the same source. We report a 2.8 Å resolution structure of free wild-type Nei and two structures of its inactive mutants, Nei-E2A (2.3 Å) and Nei-R252A (2.05 Å). All three structures are virtually identical, demonstrating that the mutations did not affect the overall conformation of the protein in its free state. The structures show a significant conformational change compared with the Nei structure in its complex with DNA, reflecting a ∼50° rotation of the two main domains of the enzyme. Such interdomain flexibility has not been reported previously for any DNA glycosylase and may present the first evidence for a global DNA-induced conformational change in this class of enzymes. Several local but functionally relevant structural changes are also evident in other parts of the enzyme