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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).


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


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).



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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