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The zinc protease AmpDh2 is a virulence determinant of Pseudomonas aeruginosa, a problematic human pathogen. The mechanism of how the protease manifests virulence is not known, but it is known that it turns over the bacterial cell wall. A research conducted by the Instituto de Química-Física Rocasolano and the University of Notre Dame (Indiana, USA) provided insights into the mechanism of action of AmpDh2. The reaction of AmpDh2 with the cell wall was investigated and nine distinct turnover products were characterized by LC/MS/MS. The enzyme turns over both the crosslinked and non-crosslinked cell wall. Three high-resolution X-ray structures, of the apo enzyme and of two complexes with turnover products, were solved. The X-ray structures show how the dimeric protein interacts with the inner leaflet of the bacterial outer membrane and that the two monomers provide a more expansive surface for recognition of the cell wall. This binding surface can accommodate the three-dimensional solution structure of the crosslinked cell wall. We have disclosed in this report the nature of the reactions of AmpDh2 with the bacterial sacculus and have determined the structure of the protein, which reveals the importance of the dimeric nature in accommodating larger segments of the cell wall. The present study reveals at atomic detail the structural attributes of this important virulence factor of P. areruginosa in the reactions that it performs, which are at the roots of the manifestation of the virulence.

 Reference:

Siseth Martínez-Caballero, Mijoon Lee, Cecilia Artola-Recolons, César Carrasco-López, Dusan Hesek, Edward Spink, Elena Lastochkin, Weilie Zhang, Lance M. Hellman, Bill Boggess, Shahriar Mobashery* and Juan A. Hermoso*

Reaction products and the X-ray structure of AmpDh2, a virulence determinant of Pseudomonas aeruginosa.

Journal of the American Chemical Society (2013) 135, - (in press)  (doi:10.1021/ja405464b)

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Oxide surfaces are usually considered to be static, even when they are catalyzing chemical reactions. But researchers at Instituto de Química-Física “Rocasolano” and the Sandia National Labs showed that this view is incorrect for magnetite (Fe3O4), an important industrial catalyst. Real-time microscopy reveals that magnetite’s surface steps advance continuously during oxygen exposure. The iron needed for this growth of new magnetite comes from the material’s interior. The first step of oxidation, dissociative oxygen adsorption, occurs uniformly over magnetite’s terraces. The common assumption in heterogeneous catalysis, in contrast, is that redox reactions occur at surface steps. Furthermore, this research establishes that catalytic redox cycles on magnetite do not involve creating and destroying oxygen vacancies, as usually assumed. Instead, catalytic cycles grow and etch the crystal through a different defect, iron vacancies.

(a-d) Low-energy electron microscopy images from Fe3O4(100) exposed to O2. Surface steps are at the boundaries between the bright/dark bands. The red lines show one step advancing. Field of view = 20 m. (e) Spiral step topography. (f) Model of Fe3O4 growth at the surface. e un escalón. Campo de visión = 20 µm. (e) Topografía de escalón espiral. (f) Modelo de crecimiento de Fe3O4 (100) en la superficie.

 (e)

Shu Nie,1 Elena Starodub,1 Matteo Monti,2 David Siegel,1 Lucía Vergara,2 Farid El Gabaly,1 Norman Bartelt,1 Juan de la Figuera,2 and Kevin McCarty1, Insight into magnetite’s redox catalysis from observing surface morphology during oxidation, J. Am. Chem. Soc., in press (2013). 1 = SNL, 2 = IQFR

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Scientists from IQFR have revealed the inhibition mechanism of UDG, a key enzyme for DNA repair. The work has been developed in collaboration with scientists from CBMSO (CSIC-UAM).

UDG is the first enzyme acting in a specific DNA repair pathway, called BER, where it detects uracil in DNA. Once detected, uracil is removed and subsequent enzymes within the BER pathway continue the process. Several proteins have been identified capable to inhibit UDG, among them p56 encoded by different phages probably as a defence mechanism.

p56 is a DNA mimic protein that blocks the UDG active site. The structure of the complex showed a specific recognition pattern between UDG and p56 that explains the lack of cross-reactivity among p566 and other DNA binding proteins. Therefore, our results shed light onto the UDG-blocking mechanism used by some viruses to proliferate into the host cell. Moreover, they pave the way to the potential use of p56 as antiviral agent against some infectious caused by herpes and poxvirus.

Publication:
José Ignacio Baños-Sanz, Laura Mojardín, Julia Sanz-Aparicio, José M. Lázaro, Laurentino Villar, Gemma Serrano-Heras, Beatriz González*, and Margarita Salas*.
Crystal structure and functional insights into uracil-DNA glycosylase inhibition by phage ϕ29 DNA mimic protein p56
Nucl. Acids Res. 2013 doi:10.1093/nar/gkt395

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 Researchers from IQFR (J. Dávalos, A. Guerrero, J. Gonzalez, A. Chana) in collaboration of Prof. T. Baer (University of North Carolina-USA) have determined the acidity GA -in the gas phase- of the hydroxyl and carboxyl local groups of the hydroxycinnamic acids, applying the kinetic method (EKM) in a mass spectrometer with electrospray (ESI)-source. Hydroxycinnamic acids are natural compounds found in several biological sources mostly in the plant kingdom either as esters of organic acids or glycosides, bound to proteins or as free acids.

The most important contribution of this work has been to show that is possible to determine gas-phase acidities (GAs) or basicities (GBs) of different deprotonation or protonation sites of a same molecule, only by a careful control of the ESI-experimental conditions; since the measurement of GA or GB of monofunctional molecules not offer a new scientific challenge.

This work opens the implementation of new experimental methodologies (e.g. using ESI-MS) to extract and quantify reliable thermodynamic properties, such as GA or GB, of different local groups within a multifunctional molecule.

Reference: Gas phase acidity measurement of local acidic groups in multifunctional species: Controlling the binding sites in hydroxycinnamic acids, A. Guerrero, T. Baer, A. Chana, F.J. González, and J.Z. Dávalos, J. Amer. Chem. Soc. (2013) DOI:10.1021/ja400571r