UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions

UROX is software designed for the interactive fitting of atomic models into electron-microscopy reconstructions. The main features of the software are presented, along with a few examples

AMoRe: classical and modern

An account is given of the latest developments of the AMoRe package

Absolute peptide/protein quantification using elemental mass spectrometry (ICPMS)

Comunicaciones a congreso

Crystal structure and infrared and Raman spectra of K3[Cr(CN)5NO].2H2O, a member of an iconic family of complexes in coordination chemistry

Potassium pentacyanonitrosylchromate(I) dihydrate salt, K3[Cr(CN)5NO].2H2O, forms spontaneously from aqueous solution below about 15 °C while the anhydrous salt is obtained above 20 °C. The molecular structure of the dihydrate has been determined by X-ray diffraction, taking full advantage of modern data collection, advanced space group and structure solution and refinement. It crystallizes in the monoclinic space group Cc, is isomorphic to the Mn(I) analog, and shows the pseudo-symmetry of space super-group C2/c. The [Cr(CN)5NO]3− ion has an umbrella-like conformation with the equatorial Cr-CN bonds slightly bent away from the Cr-NO link. The crystallographic study fills a gap left in the literature on accurate structural data for alkaline and alkaline-earth salts of [M(CN)5NO]n- (M = V, Cr, Mn, Fe) series of coordination compounds. We also report here the solid-state vibration structure of the new compound, as probed by IR and Raman spectroscopy. Water mode assignments were assisted through deuterium enrichment. The thermal dehydration behavior complements structural and spectroscopic information on water molecules.Fil: Piro, Oscar Enrique. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física La Plata; ArgentinaFil: Echeverría, Gustavo Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física La Plata; Argentina. Universidad de la Cuenca del Plata. Facultad de Ingeniería. Departamento de Ciencias Basicas; ArgentinaFil: Navaza, Alda. Universite de Paris 13-Nord; FranciaFil: Guida, Jorge Alberto. Universidad de la Cuenca del Plata. Facultad de Ingeniería. Departamento de Ciencias Basicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Química Inorgánica "Dr. Pedro J. Aymonino". Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Química Inorgánica "Dr. Pedro J. Aymonino"; Argentina. Universidad Nacional de Luján; Argentin

High resolution dynamic studies of peptide phosphorylation using element mass spectrometry

Comunicaciones a congreso

Structure of the Triatoma virus capsid

The members of the Dicistroviridae family are non-enveloped positive-sense single-stranded RNA (+ssRNA) viruses pathogenic to beneficial arthropods as well as insect pests of medical importance. Triatoma virus (TrV), a member of this family, infects several species of triatomine insects (popularly named kissing bugs), which are vectors for human trypanosomiasis, more commonly known as Chagas disease. The potential use of dicistroviruses as biological control agents has drawn considerable attention in the past decade, and several viruses of this family have been identified, with their targets covering honey bees, aphids and field crickets, among others. Here, the crystal structure of the TrV capsid at 2.5 14;Å resolution is reported, showing that as expected it is very similar to that of Cricket paralysis virus (CrPV). Nevertheless, a number of distinguishing structural features support the introduction of a new genus (Triatovirus; type species TrV) under the Dicistroviridae family. The most striking differences are the absence of icosahedrally ordered VP4 within the infectious particle and the presence of prominent projections that surround the fivefold axis. Furthermore, the structure identifies a second putative autoproteolytic DDF motif in protein VP3, in addition to the conserved one in VP1 which is believed to be responsible for VP0 cleavage during capsid maturation. The potential meaning of these new findings is discussed.Centro de Estudios Parasitológicos y de Vectore

Structure of the Triatoma virus capsid

The members of the Dicistroviridae family are non-enveloped positive-sense single-stranded RNA (+ssRNA) viruses pathogenic to beneficial arthropods as well as insect pests of medical importance. Triatoma virus (TrV), a member of this family, infects several species of triatomine insects (popularly named kissing bugs), which are vectors for human trypanosomiasis, more commonly known as Chagas disease. The potential use of dicistroviruses as biological control agents has drawn considerable attention in the past decade, and several viruses of this family have been identified, with their targets covering honey bees, aphids and field crickets, among others. Here, the crystal structure of the TrV capsid at 2.5 14;Å resolution is reported, showing that as expected it is very similar to that of Cricket paralysis virus (CrPV). Nevertheless, a number of distinguishing structural features support the introduction of a new genus (Triatovirus; type species TrV) under the Dicistroviridae family. The most striking differences are the absence of icosahedrally ordered VP4 within the infectious particle and the presence of prominent projections that surround the fivefold axis. Furthermore, the structure identifies a second putative autoproteolytic DDF motif in protein VP3, in addition to the conserved one in VP1 which is believed to be responsible for VP0 cleavage during capsid maturation. The potential meaning of these new findings is discussed.Centro de Estudios Parasitológicos y de Vectore

On the three-dimensional reconstruction of icosahedral particles

Issue Title : Analytical Methods and Software Tools for Macromolecular MicroscopyInternational audienceThe problem of reconstructing an isolated particle from its projections, using spherical harmonics to represent the scattering density, is reformulated. A technique that makes explicit and efficient use of the symmetry to describe the angular part of the scattering density is developed in full detail for the particular case of icosahedral symmetry. It provides a very concise method, where the effort is concentrated in the determination of the radial part of the Fourier transform of the particle scattering density. The method allows individual-image model-independent view determination. An illustrative numerical example is given

On the explicit use of experimental images in high resolution cryo-EM refinement

International audienceSingle particle cryogenic electron microscopy (cryo-EM) is transforming structural biology by enabling the analysis of difficult macromolecular specimens, such as membrane proteins or large complexes with flexible elements, at near atomic resolution with an accuracy close to that of X-ray crystallography. As the technique continues to improve, it is important to assess and exploit its full potential to produce the most possible reliable atomic models. Here we propose to use the experimental images as the data for refinement and validation, instead of the reconstructed maps as currently used. This procedure, which is in spirit quite similar to that used in X-ray crystallography where the data include experimental phases, should contribute to improve the quality of the models