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iqfr enThe Institute of Physical Chemistry "Rocasolano" (IQFR) is located at the seat of the former National Institute of Physics and Chemistry, that in the period 1932-1936 spearheaded Spanish science. These days, the research interests of the IQFR range from fundamental aspects of physical chemistry to nanoscience and atmospheric chemistry or the application of physical-chemical techniques to problems of biological interest. Our research priorities include a variety of subjects, such as structural biology, functional biophysics, chemical kinetics and reactivity, computational chemistry and physics, laser design and applications, or surface structure and chemistry, together with other topics connected to interdisciplinary research in the field materials science and nanotechnology and the molecular basis of biological processes.

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Europhysics Letters Presentation Award to Dr. Luis Cerdán

cerdanDr. Luis Cerdán, postdoctoral researcher at IQFR, has been distinguished with the “EPL Presentation Award 2017” in recognition of the best oral presentation at the IX Jornadas de Jóvenes Investigadores en Física Atómica y Molecular (J2IFAM 2017) for his work entitled “Enhanced and exotic laser performance in novel BODIPY dyes”. The prize, sponsored by the Europhysics Letters (EPL) journal, consists of a certificate and an economic reward.
The J2IFAM conferences, sponsored by the Grupo Especializado de Física Atómica y Molecular (GEFAM) of the RSEF and RSEQ, started nearly a decade ago and have run nine editions throughout the national territory. They are characteristically organized by and for young doctoral or postdoctoral researchers and intend to promote the dissemination of their research work and foster the establishment of collaborations between them.

 

 

Alejandro Manjavacas, granted with the Young Investigator 2016 Prize

manjavacasAlejandro Manjavacas Arévalo, a former PhD student at the IQFR, has been distinguished with the Young Investigator 2016 prize, granted jointly by the Spanish Physical Royal Society and the BBVA Foundation.
Dr Manjavaca, now at the New Mexico University (USA) as Associated Investigator, carried out his PhD research on “Light-matter interactions at nano-level” at this Institute, under the supervision of Prof. J. García Abajo. His doctoral dissertation, together with that of Dr. Luis Cerdán also from the IQFR, was distinguished with the “Premio Extraordinario 2012-2013” by the Complutense University of Madrid.

 

Highlights

photoregulationLiving organisms sense and respond to light, a crucial environmental factor, using photoreceptors, which rely on bound chromophores such as retinal, flavins, or linear tetrapyrroles for light sensing. The discovery of photoreceptors that sense light using 5'-deoxyadenosylcobalamin, a form of vitamin B12 that is best known as an enzyme cofactor, expanded the number of known photoreceptor families and unveiled a new biological role of this vitamin. The prototype of these B12-dependent photoreceptors, the transcriptional repressor CarH, is widespread in bacteria and mediates light-dependent gene regulation in a photoprotective cellular response. CarH activity as a transcription factor relies on the modulation of its oligomeric state by 5'-deoxyadenosylcobalamin and light. This article surveys current knowledge of this new family of B12-dependent photoreceptors, their discovery, distribution and mode of action, and the structural and photochemical basis of how they orchestrate signal transduction and control gene expression. The main focus of the review is largely based on results stemming from the collaborative work by members of IQFR and the Dpto. de Genética-Universidad de Murcia (Unidad Asociada al IQFR), and more recently with groups in MIT (USA), and the Univ. Manchester (UK) that have been published in, among others, PNAS, Nature Communications and Nature. This article is an invited review by Prof. Roger Kornberg (Nobel Prize in Chemistry, 2006) on behalf of the Editorial Committee of Annu Rev Biochem.

S. Padmanabhan, Marco Jost, Catherine L. Drennan, and Montserrat Elías-Arnanz. “A New Facet of Vitamin B12: Gene Regulation by Cobalamin-Based Photoreceptors”. Annu Rev Biochem 86, 485–514 (2017).
DOI: 10.1146/annurev-biochem-061516-044500

 

NagZThe N-acetylglucosaminidase NagZ of Pseudomonas aeruginosa catalyzes the first cytoplasmic step in recycling of muropeptides, cell-wall-derived natural products. This reaction regulates gene expression for the β-lactam resistance enzyme, β-lactamase. The structural and functional aspects of catalysis by NagZ were investigated by a total of seven X-ray structures, three computational models based on the X-ray structures, molecular-dynamics simulations and mutagenesis. The structural insights came from the unbound state and complexes of NagZ with the substrate, products and a mimetic of the transient oxocarbenium species. The catalytic mechanism involves a histidine as an acid/base catalyst, which is unique in glycosidases and is inhibited by zinc ion. This analysis provides a seamless continuum for the catalytic cycle, incorporating the large motions by loops that surround the active site. This is part of a collaborative effort between the IQFR and the Univ. of Notre Dame (Indiana, USA).

Acebrón, I.; Mahasenan, K.; De Benedetti, S.; Lee, M.; Artola-Recolons, C.; Hesek, D.; Wang, H.; Hermoso*, J.A.; Mobashery*, S. “Catalytic Cycle of the N-Acetylglucosaminidase NagZ from Pseudomonas aeruginosa”. J. Am. Chem. Soc. (2017).
DOI:10.1021/jacs.7b01626

 

LombaCoincident with the anniversary of the demise of our colleague Noé García Almarza, Soft Matter has published one of his last research studies that has also been highlighted in the Inside Front Cover of the aforementioned journal. In this work the self-assembly of spherical particles with three attractive sites distributed symmetrically along the particle equator was investigated under planar confinement. The study of this type of colloidal systems is interesting both from a practical point of view, for the design of new materials with properties 'a la carte', and from a fundamental one, as they often exhibit unusual physical behavior. Indeed, in this article, it is shown that, under certain conditions, these trivalent particles assemble into a rather exotic hybrid solid-gas phase formed by a honey-comb lattice and a gas of particles located at the lattice voids. The concentration of particles at the interstices of the honey-comb lattice varies continuously with pressure without undergoing a true thermodynamic transition, so that at low pressure all the voids are empty, whereas at high pressure all are occupied forming a triangular lattice. The Mechanical Statistics and Condensed Matter group dedicates this work to the memory of our dear friend Noé.

Eva G. Noya, Noé G. Almarza & Enrique Lomba. “Assembly of trivalent particles under confinement: from an exotic solid phase to a liquid phase at low temperature”. Soft Matter 13, 3221 (2017).
DOI:10.1039/C7SM00217C

 

 

oxidantesOzone (O3) and hydroxyl (OH) and nitrate (NO3) radicals are the main atmospheric components that oxidize organic and inorganic pollutants, therefore affecting air quality, environmental health and climate. Measurements from the air quality monitoring network in Madrid show an increase in ozone levels of 30-40% from 2007 to 2014, while nitrogen dioxide (NO2) has dropped by 20-40%. Based on these measurements and a high spatial resolution air quality model, we estimate an average increase of 10% and 32% in OH and NO3, respectively, in Madrid, with increases of up to 70% and 90%, respectively, downtown. Our results also show a reduction of 11% in nitric acid (HNO3), which implies a considerable denoxification of the urban atmosphere and decrease of the minus 2.5 micrometre particle (PM2.5) levels. These results suggest that current NOx (NO + NO2) emission reduction policies lead to significant changes in the chemistry and the oxidative capacity of the atmosphere in and around large cities. The image shows the modelled change in OH levels between 2007 and 2014. These results have been published in Scientific Reports.

A. Saiz-Lopez, R. Borge, A. Notario, J. A. Adame, D. de la Paz, X. Querol, B. Artíñano, F. J. Gómez-Moreno & C. A. Cuevas. “Unexpected increase in the oxidation capacity of the urban atmosphere of Madrid, Spain”. Sci. Rep. (2017) 7, 45956.
DOI: 10.1038/srep45956

 

sulfatidos enMyelin, the substance that forms the sheaths surrounding the axon of neurons, is an electrical insulator, and therefore is essential for the correct transmission of electrical impulses in the nervous system. The myelin sheath is particularly rich in cholesterol, galactosylceramides and sulfatides. The latter are sulfoglycolipids that can present different unsaturation and hydroxylation degrees. It is known that the nature and ratio of the different sulfatide molecular species change with age. They have also been associated with the pathogenesis of various diseases of the human Central Nervous System, including multiple sclerosis, Parkinson’s disease, leukodystrophy and Alzheimer’s disease. Consequently, these molecules could potentially be used as biomarkers of neurological diseases. However, the identification and quantification of sulfatides is a very difficult task due to their low concentrations and the high number of different molecular species. This is the reason why most of the studies only analyse the main sulfatides.
The use of liquid chromatography coupled to high-resolution tandem mass spectrometry with electrospray ionisation (LC-ESI(+)-MS/MS) has allowed us to develop an analytical method capable of carrying out a reliable identification and quantification of 37 sulfatides, many of them not detected so far. These results can be very useful in bioanalysis, due to the capability of correctly identifying these potential markers, even at concentrations of nanograms per millilitre.
This work has been possible thanks to the collaboration of researchers from IQFR, IQOG, ICTP and Cajal Institute, all of CSIC.

M. Pintado-Sierra, I. García-Álvarez, A. Bribián, E.M. Medina-Rodríguez, R. Lebrón-Aguilar, L. Garrido, F. de Castro, A. Fernández-Mayoralas, J.E. Quintanilla-López. “A comprehensive profiling of sulfatides in myelin from mouse brain using liquid chromatography coupled to high-resolution accurate tandem mass spectrometry” Anal. Chim. Acta, (2017) 951, 89-98.
DOI: 10.1016/j.aca.2016.11.054

 

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