Coincident 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.

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

 

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.

 

 

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

 

historia contaminacionWe have reconstructed the mercury and lead atmospheric deposition in NE Spain during the last 700 years using the concentration of these pollutants in lake sediments from the Pyrenees (Lake Montcortès). The main source of atmospheric mercury deposited in the lake is related to the mercury production in Almadén (the world´s largest mercury mine). Lead pollution is related to local mining activities in the Pyrenees and the use of leaded gasoline during the second half of the 20th century. This study highlights the sensitiveness of lake sediments to atmospheric pollution from a historical perspective.
The attached figure (linked to a bigger one) shows the Mercury (Hg) and lead (Pb) deposition rates since the 14th century, and their relationship to i) mercury production in Almadén, ii) local galena mining in the Pyrenees, and iii) the period using leaded gasoline in Europe (between 1950 and 1990).
Corella, J.P., Valero-Garcés, B.L., Wang, F., Martínez-Cortizas, A., Cuevas, C.A., Saiz-Lopez, A. “700 years reconstruction of mercury and lead atmospheric deposition in the Pyrenees (NE Spain)”. Atmospheric Environment (2017) 155, 97-107. (doi: 10.1016/j.atmosenv.2017.02.018)

 

 

pbp2a complexThe mechanism of the β-lactam antibacterials is the functionally irreversible acylation of the enzymes that catalyze the cross-linking steps in the biosynthesis of their peptidoglycan cell wall. The Gram-positive pathogen Staphylococcus aureus uses one primary resistance mechanism based on an enzyme, called penicillin-binding protein 2a (PBP2a), which is involved in this biosynthetic pathway being able to discriminate effectively against the β-lactam antibiotics as potential inhibitors, and in favor of the peptidoglycan substrate. The basis for this discrimination is an allosteric site, distal from the active site, that when properly occupied concomitantly opens the gatekeeper residues within the active site and realigns the conformation of key residues to permit catalysis. Throughout a combination of different techniques (X-ray crystallography and computational analysis by molecular dynamics and quantum mechanics), our results provide critical information about the regulation mechanism of PBP2a, a key protein in the primary resistance mechanism against antibiotics, giving us detailed information about the structural basis of communication between the allosteric and catalytic sites. Furthermore, this study reveals how β-lactam antibiotics mimicry the peptidoglycan substrates, as foundational to the mechanistic understanding of emerging PBP2a resistance mutations. This is part of a collaborative effort between the IQFR and the Univ. of Notre Dame (Indiana, USA).

Mahasenan, K.; Molina, R.; Bouley, R.; Batuecas, M.; Fisher, J.; Hermoso, J.A.; Chang, M. and Mobashery*, S. “Conformational dynamics in penicillin-binding protein 2a of methicillin-resistant Staphylococcus aureus, allosteric communication network and enablement of catalysis”. J. Am. Chem. Soc. (2017).
DOI: 10.1021/jacs.6b12565

 

NPThe oriented attachment of molecules in general and proteins in particular at the interface of nanoparticles is currently a challenge in (bio)nanotechnology. In this work carried out by research groups of the Institute of Physical Chemistry Rocasolano, Institute of Material Science of Madrid and Institute of Catalysis and Petroleochemistry, agarose-coated magnetic nanoparticles have been prepared and characterized. They have shown that these nanoparticles constitute an excellent experimental platform for the oriented attachment of recombinant proteins tagged with the β-trefoil lectin LSL150. Optimization of the preparation of the agarose-coated magnetic nanoparticles as followed by a survey of techniques such as dynamic light scattering (DLS), Fourier transform infrared spectroscopy (FTIR) and thermogravimetric studies, required the decoupling of particle formation from agarose coating. LSL150 interacted with these agarose-coated nanoparticles exclusively through the recognition of the sugars of the polymer, forming highly stable complexes. The marked topological polarity of this small lectin makes it an excellent molecular adaptor for the oriented attachment of proteins at the nanoparticle interface since they always face the bulk solvent. This fact opens up new possibilities for the design of novel and more efficient (bio)sensors.

Iván Acebrón, Amalia G. Ruiz-Estrada, Yurena Luengo, María del Puerto Morales, José Manuel Guisán, and José Miguel Mancheño. “Oriented Attachment of Recombinant Proteins to Agarose-Coated Magnetic Nanoparticles by Means of a β‑Trefoil Lectin Domain”. Bioconjugate Chemistry (2016) 27, 2734−2743.
(doi:10.1021/acs.bioconjchem.6b00504)

 

apoptinaApoptin is a small protein from the chicken anemia virus‎ which selectively induces apoptosis (programmed cell suicide) in over 80 different cancer cell lines, yet does not harm healthy cells. Apoptin is a promising cancer lead and is progressing through clinical trials. Nevertheless, Apoptin's strong tendency to oligomerize limits its ability to enter cells and thwarts studies of its structure. Therefore, we have prepared and characterized a monomeric Apoptin variant that retains most of the wild type protein's selective anti-cancer activity. Using NMR spectroscopy, this variant was shown to be intrinsically disordered and dynamic on ps-ms time scales. The conformational ensemble is not significantly affected by specific phosphorylation, addition of Mg++, pH changes or red/ox conditions. These findings support a model for Apoptin's mechanism of action in which cancer specific kinases phosphorylate Apoptin, leading to its accumulation in the nucleus and activation of p53-independent apoptosis.

Referencias:

1. "Insights into the mechanism of Apoptin's exquisitely selective anti-tumor action from atomic level characterization of its conformation and dynamics." Ruiz-Martínez S, Pantoja-Uceda D, Castro J, Vilanova M, Ribó M, Bruix M, Benito A, Laurents DV. Arch Biochem Biophys. (2017) 614:53-64.
doi:10.1016/j.abb.2016.12.010

2. "A truncated Apoptin protein variant selectively kills cancer cells." Ruiz-Martínez S, Castro J, Vilanova M, Bruix M, Laurents DV, Ribó M, Benito A. Invest New Drugs (2017).
doi:10.1007/s10637-017-0431-6

 

NCS1 Ric8aThe protein complex formed by the Ca2+ sensor NCS-1 and the guanine exchange factor Ric8a co-regulates in a antagonistic manner synapse number and probability of neurotransmitter release, emerging as a potential therapeutic target for diseases affecting synapses such as Fragile X syndrome (FXS), the most common heritable autism disorder. By combining crystallographic and chemoinformatic methodologies, a new and small phenothiazine derivative has been found to inhibit this protein complex, whose contact surface is big and complex. The administration of the compound reduces the aberrant excess of synapse number to normal levels and improves associative learning in a Drosophila FXS model. Finally, the structure-function studies have demonstrated the mechanism of action of this new molecule. This work opens the path to the generation of new drugs to treat neuronal diseases affecting synapse function, such as Autism or Alzheimer.

This work has been carried out by researchers from three CSIC Institutes (Instituto de Química-Física “Rocasolano”, Instituto Cajal and Centro de Investigaciones Biológicas) and the BSRC “Alexander Fleming” in Greece.

Alicia Mansilla, Antonio Chaves-Sanjuan, Nuria E. Campillo, Ourania Semelidou, Loreto Martínez-González, Lourdes Infantes, Juana María González-Rubio, Carmen Gil, Santiago Conde, Efthimio M. C. Skoulaki, Alberto Ferrús, Ana Martínez, María José Sánchez-Barrena. “Interference of the complex between NCS-1 and Ric8a with phenothiazines regulates synaptic function and is an approach for fragile X syndrome”. Proc. Nat. Acad. Sci., PNAS (2017).
doi:10.1073/pnas.1611089114
EFE press release
CSIC press release

 

amprA complex link exists between cell-wall recycling/repair and the manifestation of resistance to β-lactam antibiotics in many Enterobacteriaceae and Pseudomonas aeruginosa. This process is mediated by specific cell-wall-derived muropeptide products. These muropeptides are internalized into the cytoplasm and bind to the transcriptional regulator AmpR, which controls the cytoplasmic events that lead to expression of β-lactamase, an antibiotic-resistance determinant. By a combination of X-ray crystallography, mass spectrometry and molecular dynamics techniques we have characterized the effector-binding domain (EBD) of AmpR. Our results provide insights on the muropeptides triggering antibiotics resistance and revises the dogma in the field.
This is part of a collaborative effort between the IQFR and the Univ. of Notre Dame (Indiana, USA).

Dik, D.A.; Domínguez-Gil, T.; Lee, M.; Hesek, D.; Byun, B.; Fishovitz, J.; Boggess, B.; Hellman, L.M.; Fisher, J. F.; Hermoso, J.A.; Mobashery, S. “Muropeptide Binding and the X-Ray Structure of the Effector Domain of the Transcriptional Regulator AmpR of Pseudomonas aeruginosa”. J. Am. Chem. Soc. (2017).
doi:10.1021/jacs.6b12819

 

zenonWe study thermochemical [1] and electronic properties [2] of halogen-containing species with relevance to several atmospherical processes (e.g. catalytic ozone destruction and air quality).
On the one hand, we found that Gn (Gaussian-n, n = 3,4) ab initio computations are accurate theoretical methods to provide reliable heat of formation and carbon-halogen bond-energy values of a wide variety of chlorinated and brominated organic species [1]. These data will be implemented in climate models in order to evaluate the atmospheric-impact of these compounds.

On the other hand, we have shown that the CASPT2 methodology ("Complete Active Self Consistent Field Perturbation Theory”) is also an excellent method for providing reliable values of absorption optical parameters (within the UV-Vis range) of representative species such as IBr and HgBr2 which have particular connotation in photochemical atmospheric processes [2].

[1] J.Z. Dávalos, R. Notario, C.A. Cuevas, J.M. Oliva, A. Saiz-Lopez: “Thermochemistry of halogen-containing organic compounds with influence on atmospheric chemistry”. Comp. Theor. Chem. 1099 (2017) 36-44. DOI:10.1016/j.comptc.2016.11.009
[2] S.P. Sitkiewicz, J.M. Oliva, J.Z. Dávalos, R. Notario, A. Saiz-Lopez, D.R. Alcoba, O.B. Oña, D. Roca-Sanjuán; “Ab initio quantum-chemical computations of the electronic states in HgBr2 and IBr: Molecules of interest on the Earth's atmosphere”. J. Chem. Phys. 145 (2016) 244304, 1-14. DOI:10.1063/1.4971856

 

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.

 

ERC alfonso saizAlfonso Saiz-Lopez, Research Scientist at CSIC and Head of the Link to the ERC press release in this Institute, has obtained an ERC Consolidator Grant 2016 funded with 2 M euros by the European Research Council for the 5-year project “Climate dimension of natural halogens in the Earth system: Past, present, future (CLIMAHAL)”.
Through an extremely competitive selection process, the ERC Consolidator Grants will fund 314 projects (24 in Spain) out of 2300 applications. The CLIMAHAL project will use a multidisciplinary approach including spectroscopic and kinetic methods, and theoretical modelling to determine for the first time how natural halogen molecules affect the climate of our planet in past, present and future scenarios.
The ERC Consolidator Grants open every year to support research of consolidated and exceptional scientists of any nationality and age. The ERC selects pioneering and high risk projects with ground-breaking ideas within their fields of research.

Link to the ERC press release

 

imagen1

IPERION CH (http://www.iperionch.eu/) is a program with participation of 11 countries of the European Union, among them Spain through CSIC, and USA. The main objective of IPERION CH is to provide to researchers in Heritage Science a network of installations and laboratories in Europe that supports the advance of knowledge and innovation in the preservation of Cultural Heritage. This objective encompasses the offer of transnational access to first order instruments and diagnostic methods, in an integrated platform that includes large installation and mobile laboratories, and to important data archives.

Researchers of the LANAMAP Group at IQFR participate in joint research activities of IPERION CH aiming at 1) advancing new techniques and instruments, mainly based in laser methods, for non-invasive stratigraphic analysis, 2) integration of analytical techniques in portable instruments, and 3) development of diagnostic techniques for monitoring deterioration and conservation treatments.

 

 

imagen2

IPERION CH pursues the integration of European world-class facilities to create a cohesive entity playing a leading role in the global community of Heritage Science. For this reason, IPERION CH has applied for inclusion in the ESFRI (European Strategy Forum on Research Infrastructures) roadmap trough the E-RIHS PP (European Research Infrastructure for Heritage Science Preparatory Phase) proposal, approved in March of this year (http://www.e-rihs.eu/). In the near future, IPERION CH will work towards fulfilling all conditions necessary to establish a European Research Infrastructure that will give continuity to IPERION CH.

Finally, PARTHENOS (http://www.parthenos-project.eu/) is a program integrated by with 15 partners and designed to strengthening the cohesion of research in the broad sector of Humanities, Cultural Heritage, Archaeology and related fields through a thematic cluster of European research infrastructures, integrating initiatives, e-infrastructures and other world-class infrastructures. Strong links between the activity of PARTHENOS and IPERION CH are been established in the parallel running of these two projects.

More information in: http://bit.ly/2fe1D93

imagen1

IPERION CH (http://www.iperionch.eu/) es un programa en el que participan 11 países de la Unión Europea, entre ellos España a través del CSIC, y Estados Unidos. El principal objetivo de IPERION CH es proporcionar a los investigadores en Ciencia del Patrimonio una red de instalaciones y equipamientos en Europa que les permita avanzar en sus proyectos. Dicho objetivo se cumple mediante la oferta de acceso transnacional a herramientas y métodos de diagnóstico de primer orden, en una plataforma integrada que incluye grandes instalaciones y laboratorios móviles, así como importantes archivos de datos.

Investigadores del grupo LANAMAP del IQFR participan en las actividades conjuntas de investigación en IPERION CH enfocadas a: 1) al avance de nuevas técnicas e instrumentos, principalmente basadas en métodos láser, para el análisis estratigráfico no invasivo, 2) a la integración de técnicas analíticas en instrumentos portátiles, y 3) al desarrollo de técnicas de diagnóstico para la monitorización del deterioro y de los tratamientos de conservación.

 

 

 

imagen2

Con la intención de establecer una única infraestructura de investigación Europea en Ciencia del Patrimonio, en el contexto de la iniciativa ESFRI (European Strategy Forum on Research Infrastructures)se presentó la propuesta E-RIHS PP (European Research Infrastructure for Heritage Science Preparatory Phase). Tras su aprobación en marzo de este año (http://www.e-rihs.eu/), será posible dar los primeros pasos para establecer el funcionamiento de los aspectos científicos, administrativos y políticos de una infraestructura estable que dé continuidad a IPERION CH.

Finalmente PARTHENOS (http://www.parthenos-project.eu/) es un proyecto integrado por 15 socios Europeos que pretende fortalecer la cohesión de la investigación en los amplios sectores de las Humanidades, la Ciencia del Patrimonio, la Arqueología y campos relacionados mediante la agrupación temática de infraestructuras de investigación europeas, iniciativas integradoras, e infraestructuras virtuales. La importante conexión entre la actividad de PARTHENOS e IPERION CH se manifiesta en el desarrollo en paralelo de ambos proyectos.

Más información en http://bit.ly/2fe1D93

escudero2016Dr María Escribano Escudero, former PhD student of the Institute under the tutelage of Dr Angel Cuesta, has been recognized with one of the European Young Chemists Awards 2016. This prize honors and encourages younger chemists whose current research displays a high level of excellence and distinction. It seeks to recognize and reward younger chemists of exceptional ability who show promise for substantial future achievements in chemistry-related research fields. Dr Escudero Escribano presented eight polycrystalline Pt–lanthanide and Pt–alkaline-earth oxygen reduction reaction (ORR) electrocatalysts for use in polymer electrolyte membrane fuel cells.

 

escudero2016La Dra. María Escribano Escudero, ex estudiante de doctorado del Instituto bajo la tutela del Dr. Ángel Cuesta, ha sido reconocida con uno de los Premios para Jóvenes Químicos Europeos 2016 (European Young Chemists Awards 2016). Este premio honra y anima a los químicos más jóvenes cuya investigación actual muestra un alto nivel de excelencia y reconoce capacidades excepcionales de investigadores que parecen ser prometedores para futuros logros sustanciales en los campos de investigación relacionados con la química. La Dra Escudero Escribano presentó ocho compuestos policristalinos del tipo Pt-lantánido y Pt-alcalinotérreo activos en la reacción electro-catalítica para la reducción de oxígeno (ORR, oxygen reduction reaction) en pilas de combustible de membrana con electrolito polimérico.

 

RNE

In the radio program released on 10.10.2016, current aspects of computational chemistry, from quantum chemistry to modeling of biochemical systems have been discussed. Scientific issues in the chemistry of boron have also been mentioned, from new materials to biological aspects, related to this particular element. Recent activities of the "Julio Palacios" Chair, as well as the work carried out by the IQFR library on the updating of the Chair website with scientific, academic, and bibliographic documentation of Julio Palacios, were also described..

 

 

Este Año el IQFR Duplica el Número de Actividades que Va a Realizar en el Marco de la Semana de la Ciencia.

Los días jueves 10 y viernes 11 de noviembre, tendremos días de puertas abiertas con charlas demostrativas seguidas con visitas a los laboratorios. El día 10, pondremos el foco sobre la investigación con una vertiente biológica, mientras el día 11 tendrá protagonismo la investigación con láseres, química atmosférica y nanomateriales. Estas actividades están principalmente dirigidas a los estudiantes de bachillerato.

**Se busca estudiantes de doctorando o técnicos jóvenes para servir como guías para las visitas a los laboratorios.**

Además, los días miércoles 16, jueves 17 y viernes 18 de noviembre, hemos programado tres encuentros y charlas con científicos sobre la resistencia de plantas a sequías, haciendo películas con electrones y amiloides respectivamente, desde las 18 - 19 horas de la tarde. Estas actividades son para una audiencia general, ¡QUE VENGA TODO EL MUNDO!

Tras la jubilación de Luis de la Vega, para facilitar las reservas a estas actividades, hemos puesto en marcha un Gestor:

reservas_sc16@iqfr.csic.es

Las escuelas o personas interesadas en asistir a las actividades deben escribir a esta dirección, indicando el nombre de la actividad que les interese, el nombre de la escuela, el número de estudiantes que quisieran acudir, y el nombre y un número de teléfono de la persona responsable.

Por otra parte, el día 8 de noviembre de 2016, habrá un taller de limpieza con láseres (5 sesiones de 45 minutos entra las 10 y 14 horas). Las personas interesadas en este taller deben contactar con Mohamed Oujja (m.oujja@iqfr.csic.es).

Por favor, tengan en cuenta que por las normas de la CAM, no podemos aceptar o gestionar reservas antes del 24 de octubre.

GFCThe Final Conference of the GLYCOPHARM project  will take place at the Institute of Physical Chemistry  Rocasolano (IQFR, CSICa) from Wednesday 27 to Friday 29, July 2016, in Madrid.

GLYCOPHARM is a Marie Curie Initial Training Network devised to offer training to young researchers in the interdisciplinary field of glycosciences. The research programme of this project is aimed at the development of innovative therapeutic agents and strategies, new diagnostic/prognostic tests and new methodologies, e.g., for drug screening. GLYCOPHARM focuses on a family of endogenous lectins, the galectins, which play key roles in many clinically relevant processes, including cancer and the immune and inflammatory processes. 

The conference will be also open to external participants.

Detailed information is available on the program.

Contact details: bmorales@iqfr.csic.es

 

magnetiteMagnetite is the material used to track the history of the Earth magnetic field. Thus its magnetism, and especially its changes with temperature, have attracted a long-standing interest. Magnetite undergoes several phase transitions, some purely magnetic, like the spin-reorientation transition (typically at 130-140K) where the magnetization changes direction, and others, like the Verwey transition, a metal-insulator transition due to a change in the crystal structure, from cubic to monoclinic. We have recently employed novel microscopy techniques to observe the changes of magnetic domains due to these transitions: one, spin-polarized low-energy electron microscopy (SPLEEM), of which there are four instruments in the world, in collaboration with Andreas K. Schmid and coworkers from the Berkeley National Laboratory, and the other, spin-resolved photoemission electron microscopy (spin-PEEM), of which there is currently only one instrument, at the Max Planck Insitute for Microstructure Physics (Halle), in collaboration with Christian Tusche. Upper left-hand figure: SPLEEM image of the magnetic domains below the Verwey temperature, color-coded for the orientation of the magnetization as shown in the circle below (1). Right-hand figure: spin-PEEM image (2) of the magnetization above (upper image) and below (lower image) the Verwey temperature. These techniques allowed us to obtain images with nm resolution of the magnetic domains below and above the transition temperature.

(1) Laura Martín-García, Arantzazu Mascaraque, Beatriz M. Pabón, Roland Bliem, Gareth S. Parkinson, Gong Chen (陈宫), Andreas K. Schmid, and Juan de la Figuera, "Spin reorientation transition on magnetite (001)", Phys. Rev. B 93 (2016) 134419, DOI:10.1103/PhysRevB.93.134419

(2) J. de la Figuera and C. Tusche, "The Verwey transition observed by spin-resolved photoemission electron microscopy", App. Surf. Sci. (2016), DOI:10.1016/j.apsusc.2016.05.140

 

Simposio Julio Palacios

Under the auspices of the "Julio Palacios" Chair, created by the Spanish National Research Council (CSIC) in 2015, the First "Julio Palacios" International Symposium will take place between 20th and 22nd July 2016 in the city of La Coruña (Spain). The symposium, of broad interest and with a multidisciplinary character, is intended for a general public and especially for university students. The main goal is to provide a meeting point and informative debate on the frontiers of modern science. Registration is free up to the venue capacity. Among the speakers, we can highlight Ignacio Cirac, a renowned theoretical physicist, Douglas Klein, a world-wide expert in mathematical chemistry, Ángel Carracedo, an expert in genomic medicine, or Harald Helfgott, the mathematician who recently proved the ternary Goldbach conjecture, an unsolved problem dated on 1742.

Julio Palacios (1891-1970), a physicist and Professor from The Central University in Madrid (nowadays Complutense University) and researcher in the Spanish National Research Council (CSIC), can be considered among the most relevant Spanish scientists. He was member of different institutions: President of the Spanish Royal Society of Physics and Chemistry, President of the Royal Academy of Exact, Physical and Natural Sciences and member of the Spanish Royal Academy (Spanish language) and of the Royal Academy of Medicine, among others.

More information in: jpalacios.iqfr.csic.es

 

MCS2016We are pleased to announce the sixth edition of the Macromolecular Crystallography School - MCS2016, to be held at the CBE (Department of Crystallography and Structural Biology) of the Institute of Physical-Chemistry "Rocasolano", CSIC (Spanish National Research Council), in Madrid, May 2016.

The MCS2016 is directed to 25 graduate students and/or researchers with some previous expertise in crystallography which need a deeper insight into most advanced crystallographic techniques to carry out their research projects. The school program covers aspects such as sample preparation, phasing, model building, crystallographic refinement, validation, and analysis of the structural results

 

 

 

HBC revised-MMRThe discovery of stable amyloids composed solely of polar residues surprised scholars who believed that protein conformational stability is chiefly due to the hydrophobic effect. These amyloids, rich in Asn and Gln residues, form extensive hydrogen bonding networks. When aligned, hydrogen bond networks are strengthened due to cooperative effects arising from hyperpolarization. In this work, Density Functional Theory and Natural Bonding Orbital analysis were applied to study a series of polar and hydrophobic peptides in amyloid-like oligomers of different sizes and revealed that hydrogen bond networks formed by Asn and Gln side chains experience a distinct class of cooperativity that strengthens them significantly relative to main chain hydrogen bond networks. These computational results were corroborated experimentally utilizing recognition by amyloid specific molecular probes, nuclear magnetic resonance spectroscopy and experimental electric conductivity measurements on Asn/Gln-rich and hydrophobic peptides. On the basis of these findings, approaches to selectively inhibit the formation of polar versus hydrophobic amyloids can now be devised.

The figure shows a schematic representation of the delocalized electron density (blue shading) in the H-bond networks formed by Asn side chains (left) and the peptide backbone (right).

Miguel Mompeán, Aurora Nogales, Tiberio A. Ezquerra & Douglas V. Laurents ( "Complex System Assembly Underlies a Two-Tiered Model of Highly Delocalized Electrons" J. Phys. Chem. Lett. (2016) 7(10): 1859-1864.
(doi:10.1021/acs.jpclett.6b00699)

 

imanes-molecularesA scientific collaboration between the Institute of Physical Chemistry "Rocasolano" (CSIC), the University of Buenos Aires (Argentina), the National University of La Plata (Argentina) and the University of the Basque Country has been front cover of the journal Molecular Physics, as an invited article of a special volume on the Proceedings of the 55th Sanibel Symposium on theoretical and computational chemistry. These Symposia were initiated in 1961 by Per-Olov Löwdin, a former member of the Nobel Committee. Molecular magnetism manifests itself macroscopically through the magnetic moment (total spin, S) of a molecule, and is due to the presence of unpaired electrons – (poly)radicals – in the ground state of the system. The main conclusion of the article is the prediction of a system with a maximum spin Smax = 6 in its ground state (high-spin state), constructed by connecting twelve NB11H11 radical type (S = ½) icosahedra, forming a magnetic supericosahedron (first iteration). This prediction opens the door towards the design of molecular magnets based on boron molecules (boranes), since the system can be extended in three dimensions, thereby maximizing the total spin Smax in the series Smax(n) = {1/2, 6, 72, ..., 12n/2}.

Diego R. Alcoba, Ofelia B. Oña, Gustavo E. Massaccesi, Alicia Torre, Luis Lain, Rafael Notario, Josep M. Oliva
"Molecular magnetism in closo-azadodecaborane supericosahedrons", Molecular Physics (2016) 114, 3-4, 400-406.
doi:10.1080/00268976.2015.1076900

TDP-43TDP-43 is a protein which acts in part like an editor and in part like a postman; he modifies his "messages" written in RNA, before delivering them to the cytoplasm. Under certain "bad weather" conditions, part of the TDP-43 protein acts like an "umbrella" (really a hydrogel or functional amyloid) to protect the messages. But sometimes these "umbrellas" can break and become tangled together, forming a "net" (harmful amyloid aggregates) that disrupts the message editing and delivery system, and putatively leads to cell death. In fact, TDP-43 aggregates are linked to amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disease that kills 4000 Spaniards per year. The elucidation by NMR of the structure, dynamics and stability of the first quarter, or N-terminal domain, of the TDP-43 protein's structure, dynamics and stability by NMR methods provides the keys to better understand the function and malfunction of this important protein.

Mompeán M, Romano V, Pantoja-Uceda D, Stuani C, Baralle FE, Buratti E and Laurents DV "The TDP-43 N-Terminal Domain Structure at High Resolution." FEBS J. Jan 12th, 2016
doi: 10.1111/febs.13651

 

Monday, February 29th 2016, Madrid

Abstract book

Schedule

foto III simposio jovenes 201610:20 - 10:30 WELCOME

10:30 - 12:30 SHORT TALKS

  1. Alejandra Angela Carriles Linares · IQFR. "Structural Biology: From Protein Crystallization to Drug Design"
  2. Elsa Franco Echevarría · IQFR. "Estudios cristalográficos de una IPK de mamífero". 3rd prize.
  3. Fernando Serranía · IQFR. "Espectroscopía LP-DOAS: una técnica para la detección de especies atmosféricas en concentración sub partes por millón". 1st prize.
  4. Maria Muñiz Unamunzaga · IQFR. "Impacto de la química de halógenos en la calidad del aire de ciudades costeras"
  5. Erney Ramírez Aportela · IQFR. “FRODOCK 2.0: Fast Protein-Protein docking server”
  6. María Sebastián · U. de Zaragoza. “Comparing Two Bacterial FAD Synthetases: Little Variations yet Big Differences”
  7. Héctor Zamora Carreras · IQFR. “Investigating the Mechanism of Action of the Membrane-Active Peptide BP11 by Alanine Scan and 2H ssNMR”. 2nd prize.
  8. Sandra Ruiz Gómez · U. Complutense de Madrid. “Desarrollo de supercondensadores de grafeno funcionalizados con óxidos metálicos para aplicaciones en energía”
  9. Aránzazu Gallego García · U. de Murcia. “Función de la proteína CdnL en las bacterias Myxococcus xanthus y Caulobacter crescentus”

12:30 - 13:30 POSTER SESSION

Additional participation of: 

  1. Manuel Alberto Iglesias Bexiga · IQFR. “Nueva familia de inhibidores de LytA, la principal autolisina de Streptococcus pneumoniae”
  2. Noemí Bustamante · IQFR. “Insights of a Novel Kind of Cell Wall Binding Domain that Cleaves the Peptidoglycan Muropeptide: The CW_7 Motif”

13:40 AWARDS AND CLOSING

 

Orrego-et-alA new method for connecting the dynamics and function of proteins immobilized on agarose beads is demonstrated. The mobility of proteins was quantified in any location of agarose beads, at different depths (0-100 microns; 500-600 nm spatial resolution), from fluorescence anisotropy optical sections of the beads. Protein fluorescence anisotropy informs about restriction of the global rotation of the immobilized proteins onto a solid surface. A general protein mobility scale was defined, which is independent of instrumental settings and fluorescent probes. Protein mobility is very sensitive to the chemistry of immobilization, as well as to the hydrogel porous microstructure resulting from the immobilization reactions. In this way better immobilization processes may be designed, leading to more stable heterogeneous biocatalysts with interest for the biodiesel and food industries.

Orrego AH, García C, Mancheño JM, Guisán JM, Lillo MP, López-Gallego F
"Two-Photon Fluorescence Anisotropy Imaging to Elucidate the Dynamics and the Stability of Immobilized Proteins" J Phys Chem B (2016) 120, 485-491.
DOI: 10.1021/acs.jpcb.5b12385

 

web-enCrystallography tells us about the nature of crystals and how they show us the shape and dimensions of molecules, hormones, nucleic acids, enzymes, proteins..., what their properties are and how they work in a chemical reaction, in a test tube, or inside of a living being. The Department of Crystallography and Structural Biology offers an internationally recognized website for learning Crystallography: http://www.xtal.iqfr.csic.es/Cristalografia/.
Written in two languages (Spanish and English), this website was announced by the International Union of Crystallography (http://bit.ly/dHj0Q0) and selected by this institution as one of the most interesting sites for learning crystallography (http://bit.ly/1zCsBOX). It was also offered as such in the commemorative web for 2014 International Year of Crystallography (http://bit.ly/1BYMGyd), and suggested as the educational website to learn about crystals, diffraction and crystal structure determination in the brochure (http://bit.ly/1DXoqxP) prepared for the Crystal-Growing competition for UNESCO Associated Schools. It is also offered as one of the best learning online tools by several US universities (see for example: http://bit.ly/guMQax, http://bit.ly/gCLbYk). As it can be seen through any of its independent visitor counters it collects over 1,500 different visitors a day, distributed by all countries, but especially US, Europe, India and Latin America.

 

Last December 2015 died in Madrid Prof. R. Moreno, a leading specialist on historic scientific instruments, who carefully classified the documentation and restored many historic instruments exposed in our Institute and other CSIC's centers.

 

ozono tropicalTropospheric ozone is an important greenhouse gas. Ozone has exerted an increase in the global radiative forcing of climate almost equal to that of methane over the period between 1750 and 2011. The largest contribution to the climatic influence of ozone is due to its increase in the tropical troposphere. A recent international study, with participation of scientists from the Dept. of Atmospheric Chemistry and Climate of this Institute, shows that ozone concentration in the mid-troposphere (8-10 km) over the western Pacific is three times larger than in the tropics. From the analysis of satellite data, aircraft observations and climate modeling reported here it was concluded that fires in tropical Africa and Southeast Asia are the dominant source of high ozone over the western Pacific. High ozone and low water structures in the tropical western Pacific are commonly attributed to transport from the stratosphere or mid-latitudes. However, these observations suggest a larger role for biomass burning in the radiative forcing of climate in the remote tropical western Pacific than is commonly appreciated.

D. C. Anderson, J. M. Nicely, R. J. Salawitch, T. P. Canty, R. R. Dickerson, T. F. Hanisco, G. M. Wolfe, E. C. Apel, E. Atlas, T. Bannan, S. Bauguitte, N. J. Blake, J. F. Bresch, T. L. Campos, L. J. Carpenter, M. D. Cohen, M. Evans, R. P. Fernandez, B. H. Kahn, D. E. Kinnison, S. R. Hall, N. R. Harris, R. S. Hornbrook, J.-F. Lamarque, M. Le Breton, J. D. Lee, C. Percival, L. Pfister, R. R. Pierce, D. D. Riemer, A. Saiz-Lopez, B. J. Stunder, A. M. Thompson, K. Ullmann, A. Vaughan and A. J. Weinheimer. A pervasive role for biomass burning in tropical high ozone/low water structures. Nature Communications (2015).

DOI:10.1038/ncomms10267.

 

figura-nota-PNASDrought and salinity are the major threats to crop productivity at a worldwide scale. A fundamental portion of the plant response to these environmental stresses occurs at the cell membrane, where the molecular machinery to preserve cell turgor and the appropriate balance of intracellular ions is found. The C2-domain ABA-related (CAR) family of proteins contributes to these processes by delivering the regulatory proteins controlling this machinery from other cell compartments to the cell membrane. Our analysis provides an explanation on how CAR proteins specifically reach a particular membrane place to develop their function and trigger the plant defense mechanism against stress.

Maira Diaz, Maria Jose Sanchez-Barrena, Juana Maria Gonzalez-Rubio, Lesia Rodriguez, Daniel Fernandez, Regina Antoni, Cristina Yunta, Borja Belda-Palazon, Miguel Gonzalez-Guzman, Marta Peirats-Llobet, Margarita Menendez, Jasminka Boskovic, Jose A. Marquez, Pedro L. Rodriguez and Armando Albert. "Calcium-dependent oligomerization of CAR proteins at cell membrane modulates ABA signaling", PNAS (2015).
DOI: 10.1073/pnas.1512779113.

 

foto-becaria

Angélica Partida Hanon, PhD student from the department of Biological Physical Chemistry has been awarded with one of the two Universia Foundation scholarships intended for the completion of the PhD thesis.

Universia Foundation (www.fundacionuniversia.net) is a private entity of Santander group which promotes the access to higher education and qualified employment for people with disabilities in Spain. 2015’s call included two scholarships intended to carry doctoral studies, which are allocated based on the merits of the applicant and the host research group. One of them have been granted to Angelica Partida Hanon, graduated in Biological Sciences from the Complutense University of Madrid, who joined the group of Structure, Dynamics and Protein Interactions by NMR in September of 2014, for her doctoral studies on the applications of NMR to determine the structural basis of the antigen-antibody recognition in two model systems: immunogenic peptides derived from the gp41 glycoprotein of HIV-1 virus and the allergenic protein “Ani s 1” of Anisakis simplex

 

imagen-lytb

Streptococcus pneumoniae (the pneumococus), a superbug bacteria, is a leading cause of bacterial sepsis and the most frequent ethiologic-agent in the community adquired pneumoniae and non-epidemic bacterial meningitis. LytB, a member of the family of pneumococcal choline-binding protein, is responsible for the physical separation of daugther cells after division and participates in nasopharinx colonization and invasion, biofilm formation and evasion from the host immunity. Because of this, LytB is considered a putative vaccine/drug target. Here, IQFR and CIB investigators, in collaboration with scientists from the Universities of Newcastle (Newcastle upon Tyne, UK) and Notre Dame (Indiana, USA), have shown that LytB is a glucosaminidase and the basis for its high substrate specificity are unveiled. The catalytic mechanism and model of binding to the bacterial peptidoglycan together with determinants of its polar localization on pneumococcal cells is also advanced. Reported data provide a better understanding of the complex physiological role played by LytB in the bacterium and the host-pathogen interaction.

 

Rico-Lastres P, Díez-Martínez R, Iglesias-Bexiga M, Bustamante N, Aldridge C, Hesek D, Lee M, Mobashery S, Gray J, Vollmer W, García P, Menéndez M. 2015. “Substrate recognition and catalysis by LytB, a pneumococcal peptidoglycan hydrolase involved in virulence”. Sci Rep. 5:16198. doi: 10.1038/srep16198.

 

Within the "Julio Palacios Project", Professor Francisco González de Posada will give a colloquium on "The problem of time: Newton's and Einstein's concepts", next Monday, November 23rd, at 12:00h at the Institute of Physical Chemistry "Rocasolano" (CSIC). The colloquium is directed to public in general, students, professors, academicians and researchers.

"Mecanismos patogénicos y rescate terapéutico del polimorfismo P187S en la enzima NQO1 asociado a cáncer"

Ángel Luis Pey

Universidad de Granada

Viernes 20 de noviembre

12:00, Sala 300

USTS

The first edition of the Ultrafast Science and Technology Spain meeting (USTS2015) will take place in the Main Campus of the Spanish National Research Council (CSIC) in Madrid, in November 24th and 25th, 2015. Oral Sessions will be celebrated in the Instituto de Quimica Fisica Rocasolano. The Meeting has been promoted by the Grupo Especializado de Láseres Ultrarrápidos (GELUR) of the RSEF.

The scope of this Meeting is broad and will cover topics including ultrafast laser development, extreme light, materials processing, femtosecond laser spectroscopy and dynamics, nonlinear optical phenomena, ultrafast processes in biology, femtosecond microscopy or attosecond physics.

With nearly 70 contributions and over 90 registered attendees, we expect to enjoy a successful and exciting meeting. Details can be found in http://www.ultrafast.es/USTS2015.

 

IPERIONCH-PARTHENOSThrough IQFR and CENIM researchers, CSIC participates in two H2020 European projects, IPERION CH and PARTHENOS.
IPERION CH (Integrated Platform for the European Research Infrastructure ON Cultural Heritage), with 23 partners, offers trans‐national access to world‐class diagnostic tools and methods in one integrated platform, including large scale installations and mobile laboratories with a wide range of portable scientific instruments, and to unique and important archives of scientific data for advancing knowledge and innovation in Cultural Heritage. Further information at http://www.iperionch.eu/


PARTHENOS (Pooling Activities, Resources and Tools for Heritage E-research Networking, Optimization and Synergies), with 15 partners, is aimed to strengthening the cohesion of research in the broad sector of Linguistic Studies, Humanities, Cultural Heritage, History, Archaeology and related fields through a thematic cluster of European Research Infrastructures, integrating initiatives, e-infrastructures and other world-class infrastructures. Strong links between the activity of PARTHENOS and IPERION CH are envisaged in the parallel running of these two projects. Further information at http://www.parthenos-project.eu/

 

"anti-B18H22, UN BORANO QUE BRILLA DE NUEVO"
Luis Cerdán Pedraza
 
jueves 12 de noviembre 2015
Salón de Actos, 12:00

foto-NASA-en

Bromine is an effective ozone destruction catalyst in the stratosphere, the region of the atmosphere that contains the ozone layer. Most bromine reaching the stratosphere comes from anthropogenic sources, which are controlled by the Montreal Protocol (an international treaty designed to protect the ozone layer of the Earth). In addition, an uncertain amount of natural organic bromine compounds, emitted from the oceans as a result of the marine biological activity, can reach the stratosphere where it contributes to the destruction of the ozone layer. In this work, these ocean-emitted organic bromine compounds have been measured for the first time both over the East and West Pacific Ocean in profiles from the ocean surface up to the gateway of the stratosphere, at 18 km. The measurements were made aboard the NASA´s non-tripulated Global Hawk aircraft as part of the NASA´s Airborne Tropical Tropopause Experiment (ATTREX) campaigns. This study also uses a climate model to quantify the impact of the injected natural bromine on the destruction of the ozone layer. 

Maria A. Navarro, Elliot L. Atlas, Alfonso Saiz-Lopez, Xavier Rodriguez-Lloveras, Douglas E. Kinnison, Jean-Francois Lamarque, Simone Tilmes, Michal Filus, Neil R. P. Harris, Elena Meneguz, Matthew J. Ashfold, Alistair J. Manning, Carlos A. Cuevas, Sue M. Schauffler, and Valeria Donets. Airborne measurements of organic bromine compounds in the Pacific tropical tropopause layer. PNAS.
DOI: 10.1073/pnas.1511463112

 

"Molecular Scissors for Gene Therapy"

Rafael Molina Monterrubio

Viernes 6 de noviembre

Salón de actos, 12:00

"Estudio termoquímico de derivados de imidazol"
Gastón Perdomo León
Facultad de Ciencias Químicas
Benemérita Universidad Autónoma de Puebla
Puebla, México

Miércoles, 28 de Octubre de 2015
Hora: 12:00 Salón de Actos

Resumen

nature-2015-def

 

 

 

 

 

 

 

 

 

 

 

Light is crucial for many essential biological processes such as photosynthesis, vision, circadian rhythms, etc., but can also cause photooxidative cellular damage. Living organisms sense and respond to light using photoreceptors, proteins associated with a light-sensing chromophoric cofactor such as retinal in the photoreceptors of the eye. In 2011, the research teams of Dr. S. Padmanabhan (NMR group, IQFR) and Prof. Montserrat Elías-Arnanz (Universidad of Murcia/Associated Unit to IQFR) discovered a novel photoreceptor family that uses vitamin B12 as the light-sensing molecule and revealed its mode of action in light-dependent gene regulation. These two teams, in collaboration with that of Prof. Catherine L. Drennan (Massachusetts Institute of Technology, USA), now report the crystal structures of the B12-dependent photoreceptor in all three relevant states: in the dark (both free and bound to DNA), and after light exposure; that is, three high-resolution snapshots that reveal the light-dependent conformational changes behind its mechanism of action. These findings expand the biological role assigned to vitamin B12, and enable a framework for the development of a new class of optogenetic tools for controlled gene expression.

Marco Jost, Jésus Fernández-Zapata, María Carmen Polanco, Juan Manuel Ortiz-Guerrero, Percival Yang-Ting Chen, Gyunghoon Kang, S. Padmanabhan, Montserrat Elías-Arnanz, and Catherine L. Drennan. “Structural basis for gene regulation by a B12-dependent photoreceptor” Nature 526, 536–541 (22 October 2015) DOI: 10.1038/nature14950 (Published online September 28, 2015).

 

cover-art

Vitamin B12 is an essential enzyme cofactor in humans and other animals. Lack of B12 causes pernicious anemia, neural dysfunction and other disorders. A new molecular function for this vitamin was discovered a few years ago (PNAS, Vol. 108, p 7565-7570, 2011) in a collaboration between Dr. S. Padmanabhan of the NMR group (IQFR) and the Molecular Genetics group of Prof. Montserrat Elías-Arnanz (Universidad of Murcia and Associated Unit to IQFR). It was shown that B12 displays a new role as a light-sensing molecule and that it is involved in light-dependent gene regulation. Now, these researchers in collaboration with others at the University of Manchester (UK), have published a detailed photochemical mechanism for this new class of photoreceptors. The work provides a mechanistic foundation for the emerging field of B12 photobiology and a basis for the development of this class of photoreceptors as optogenetic tools for controlled gene expression in cells and organisms.

Roger J. Kutta, Roger J. Kutta, Samantha J. O. Hardman, Linus O. Johannissen, Bruno Bellina, Hanan L. Messiha, Juan Manuel Ortiz-Guerrero, Montserrat Elías-Arnanz, S. Padmanabhan, Perdita Barran, Nigel S. Scrutton, Alex R. Jones. The photochemical mechanism of a B12-dependent photoreceptor protein. Nature Communications, 6,
Article number 7907, August 12, 2015. doi: 10.1038/ncomms8907.

 

RMN-como-herramientaWe all know someone who has undergone a Nuclear Magnetic Resonance (NMR) scan. But only very few know that NMR is a powerful tool for the determination of the three-dimensional structure of molecules. This has been explained by Dr. Marta Bruix, from the Protein Structure, Dynamics and Interactions by NMR Group, on April 20th in the RTVE program “On Giant's Shoulders” (http://bit.ly/1LbRKEk).

 

 

book Boron Fifth Element-def

A collaboration between the Institute of Physical-Chemistry “Rocasolano” (CSIC) and the Institute of Molecular Sciences from the University of Valencia has led to a chapter in the book “Boron: The fifth element” (Springer Verlag), within the series “Challenges and Advances in Computational Chemistry and Physics”. Since the disclosure of borane compounds - polyhedral BxHy structures - as rocket fuel in the 1950’s, the research in this field, particularly on the synthesis of boranes and their derivatives, has grown exponentially. This multi-author book reviews the recent developments in boron chemistry, with a particular emphasis on the contribution of computational chemistry.
Josep M. Oliva, Antonio Francés-Monerris, and Daniel Roca-Sanjuán, “Quantum Chemistry of Excited States in Polyhedral Boranes”. Capítulo 4 en “Boron: The Fifth Element”, volumen 20 de la serie “Challenges and Advances in Computational Chemistry and Physics”, Editorial Springer (2016) ISBN 978-3-319-22282-0.

ParaBioF-small

Only 2% of the genome codes for proteins. What does the rest do? What is its structure? One of the most intriguing and unknown regions in the eukaryotic genome is the centromere. IQFR and CMBSO researchers have recently shown that centromeric sequences of organisms as distant in the evolutionary tree as fruit flies and humans are able to fold in vitro forming the same type of secondary structure, known as the “i-motif”. The presence of these structures in such distant organisms suggests that they may be involved in the structural organization of the centromere. If this were the case, the centromeric DNA could have been selected during evolution not for its primary sequence, but for its capability to form this non-canonical structure, the “i-motif”. 
 
This work is the result of a collaboration with our colleague and friend Alfredo Villasante, to whose memory it is dedicated.
 
M. Garavís, N. Escaja, V. Gabelica,  A. Villasante and C. González. Centromeric alpha-satellite DNA adopts dimeric i-motif structures capped by AT Hoogsteen base pairs. Chemistry-A Eur. J., 21, 9816-9824, 2015. doi: 10.1002/chem.201500448 (artículo del mes SBE, junio 2015)
 
M. Garavís, M. Méndez-Lago, V. Gabelica, S. L. Whitehead  G. González, and A. Villasante. The structure of an endogenous Drosophila centromere reveals the prevalence of tandemly repeated sequences able to form i-motifs. Sci. Rep., 5, 13307, 2015. doi: 10.1038/srep13307
 
 

nanoestructuras-ferrita

Ultrathin islands of up to 100 μm2 with atomically flat surfaces and free from antiphase boundaries are developed. The extremely low defect concentration leads to a robust magnetic order, even for thicknesses below 1 nm, and exceptionally large magnetic domains. This approach allows the evaluation of the influence of specific extrinsic effects on domain wall pinning. The work has been performed by researchers of the Instituto de Quimica-Física "Rocasolano" and other CSIC institutes (ICV, ICMM) in collaboration with Alba synchrotron scientists.

 

L. Martín-García, A. Quesada, C. Munuera, J.F. Fernández, M. García-Hernández, M. Foerster, L. Aballe, J. de la Figuera. Atomically flat ultrathin cobalt ferrite islands.Advanced Materials. DOI: 10.1002/adma.201502799

 

 

GPDH

Galactitol-1-phosphate 5-dehydrogenase (GPDH) is a polyol dehydrogenase that catalyses the Zn2+ and NAD+-dependent stereoselective dehydrogenation of L-galactitol-1-phosphate to D-tagatose-6-phosphate. J.M. Mancheño (Dept. of Crystallography) in collaboration with Gert W. Kohring, Federico Gago and Rosario Muñoz, have reported three crystal structures of GPDH from Escherichia coli: the open state with Zn2+ in the catalytic site and also those of the closed state in complex with the polyols Tris and glycerol, respectively, but with no cofactor bound, which contrast with the behaviour of the prototypical mammalian liver alcohol dehydrogenase. Unexpectedly, a large internal cavity was found at the main contacting interface between GPDH subunits (GPDH is a dimer) that probably facilitates their relative movement. The binding mode of the substrate analogue glycerol reveals, for the first time in the polyol dehydrogenases, a penta-coordinated zinc ion in complex with a polyol and also a strong hydrogen bond with the conserved Glu144, an interaction originally proposed more than thirty years ago that supports a catalytic role for this acidic residue.

 

Rocío Benavente, María Esteban-Torres, Gert-Wieland Kohring, Álvaro Cortés-Cabrera, Pedro A. Sánchez-Murcia, Federico Gago, Iván Acebrón, Blanca De Las Rivas, Rosario Muñoz, José M. Mancheño. “Enantioselective oxidation of galactitol-1-phosphate by galactitol-1-phosphate 5-dehydrogenase from Escherichia coli”. Acta Crystallographica (2015) D71, 1540-1554. 
(doi: 10.1107/S1399004715009281)

 

web page figure

Amyotrophic Lateral Sclerosis (ALS) is a mortal neuromuscular disease that affects 2800 persons in Spain, with two new cases being diagnosed each day. Abnormal aggregates of the protein “TDP-43” (transactive response DNA binding protein 43 kDa) are found in >95% of dying motor neurons, and have been linked to other neurodegenerative disease, including Alzheimer’s disease and Frontotemporal Lobar Degeneration. Aggregation of TDP-43 was traced to a small, Asn- and Gln-rich region of the protein spanning residues 341-357, but the conformation of this segment and how it oligomerizes into harmful aggregates was unknown. Here, on the basis of multiple biochemical assays and biophysical experiments, IQFR investigators in collaboration with scientists from Columbia University (New York), the Cajal Institute (CSIC), IMDEA Nanoscience (CAM), and the International Centre for Genetic Engineering and Biotechnology (Trieste, IT) show that this segment’s beta hairpin motifs assemble into an amyloid-like structure with an unusual fibril morphology. Using computational methods, they have advanced an amyloid-like structural model for the aggregate in which TDP-43 (341-357) beta hairpins dock in a novel, parallel topology. This structural model will likely aid our understanding of TDP-43’s role in neurodegenerative diseases and may help guide the search for treatments.

M. Mompeán, R. Hervás, Y. Xu, T.H. Tran, C. Guarnaccia, E. Buratti, F. Baralle, L. Tong, M. Carrión-Vázquez, A.E. McDermott, D.V. Laurents 
J. Phys. Chem. Letters, June 2015, doi: 10.1021/acs.jpclett.5b00918

 

Fig2IQFRweb 24June2015

Autolysin LytA is a protein involved in the virulence of pneumococcus, a pathogenic microorganism in humans. Its C-terminal domain (CLytA) consists of six choline-binding repeats (CBR), arranged in the β-solenoid structure characteristic of choline-binding modules. In the NMR group of the Institute of Physical-Chemistry ‘Rocasolano’ (CSIC) we have structurally characterised a 14-residue peptide encompassing the sequence of the core β-hairpin from the third CBR repeat of CLytA. It has been found that this peptide conserves its native β-hairpin fold in aqueous solution, but forms a stable, amphipathic α-helix (i.e. with two faces, one hydrophobic and the other polar) in detergent micelles (with a hydrophilic surface and a hydrophobic core). These β-hairpin and α-helix structures differ greatly in the distribution of polar hydrophobic side chains. As far as we know, this "chameleonic" behaviour of a micelle-induced structural transition between two ordered peptide structures has not been reported before, and shows the dramatic effect of hydrophobic-hydrophilic interactions. These results could not only be of relevance in the field of peptide design and biosensors, but may also help to understand the molecular basis for the peculiar mechanism of LytA translocation from the cytoplasm to the bacterial surface.
Reference:

 

Hector Zamora-Carreras, Beatriz Maestro, Erik Strandberg, Anne S. Ulrich, Jesús M. Sanz, y M. Angeles Jiménez. “Micelle-triggered β-hairpin to α-helix transition in a 14-residue peptide derived from the pneumococcal choline-binding protein LytA”. Chemistry-Eur J. 21, 8076-8089 (2015). doi:10.1002/chem.201500447
Enlace a artículos destacados en mayo 2015 por la SBE (http://biofisica.info/zamora-carreras-jimenez-chemistry-21-8076/

 

"A Strategy to Accelerate Diabetic Wound Healing"
Mayland Chang
Department of Chemistry and Biochemistry
University of Notre Dame, Indiana, USA

Martes, 30 de Junio de 2015
Hora: 12:00 Salón de Actos

Contacto: Juan A. Hermoso

Julia-Sanz-figura2

Plant cell walls are highly complex structures of interlocking polysaccharides that are recalcitrant to biological degradation. Within the complex molecular machinery involved in its deconstruction, one of the greatest challenges is to decipher the mechanism that display enzymes with multiple copies of ancillary non-catalytic domains. Most of these domains are Carbohydrate Binding Modules (CBMs). Homogeneous multimodularity has been related to multivalency and avidity effects, while heterogeneous pattern is supposed to provide distinct substrate-binding specificities. However, recent work suggests that this panorama may be more complex. Researchers at IQFR have performed structural and functional studies on a large xylanase (Xyn10c) showing a distinctive modular structure that contains an N-terminal tandem of two CBM22s and a duplicated CMB9 at its C-terminus. We have discovered novel features that attribute a different functionality to each CBM22 module and suggest a deliver strategy of Xyn10C mediated by its CBM22 tandem. Our work will contribute to unravel the mechanisms ruling modularity, which is essential to understand the biomass recycling and to produce efficient biocatalysts. This will result in more environmentally sustainable industries.

The Journal of Biological Chemistry (2015)
First published in May 22
(doi:10.1074/jbc.M115.659300)

 

CoverJBC Def small2

Glycoproteins gp120 and gp41 are part of the AIDS HIV virus envelope. These proteins are involved in both, virus / host cell membrane fusion, a step essential for viral infection, and in the immune response to the virus. The knowledge of the structure of these proteins is crucial to understand these mechanisms at molecular level.
Scientists from the NMR group at the Institute of Physical-Chemistry ‘Rocasolano’ (CSIC), in collaboration with Dr. J. L. Nieva (University of the Basque Country) and Dr. J.M.M. Caaveiro (University of Tokyo) have determined the structure of several peptides reproducing sequences of the MPER (membrane-proximal external region) and TM (trans-membrane) sub-domains of the HIV gp41 protein. This work shows that the structure of the trans-membrane region, which has not been solved previously, presents two helices connected by a flexible segment. In addition, it has been found that the final MPER region and the initial TM region form a unique uninterrupted helix, in contrast to bioinformatics prediction. A model for the mechanism of virus / host cell membrane fusion has been proposed on the basis of these structural data. More interestingly, these data also explain the observed differences in antibody affinity, as well as the immune response of MPER-derived peptides. Accordingly, this information would be of great interest for a rational design of novel vaccines and inhibitors, useful as alternative therapies against AIDS.
The work has been selected as “Paper of the Week” by the editors of J. Biol. Chem.
Virion and envelope glycoprotein contour images were kindly provided by Dr. S. Subramaniam.
Reference:
B. Apellaniz, E. Rojas, S. Serrano, K. Morante, K. Tsumoto, J.M.M. Caaveiro, M.A. Jiménez, & J.L. Nieva. “The atomic structure of the HIV-1 gp41 MPER-TMD region reveals a continuously helical inter-domain connection flanked by two metastable hinge segments. Implications for MPER immunogenicity”. J. Biol. Chem. (2015). doi:10.1074/jbc.M115.644351.
Link to CSIC news

 

Reunión del Claustro Científico

Viernes 29 de mayo de 2015

10:00, salón de actos

"Glicomica funcional: hacia la aplicación biomédica"

Ioanna Kalograiaki

Miércoles 3 de junio

12:00, salón de actos

Conferencia: ATOMS AT PLAY AND THE CHALLENGE OF COMPUTATIONAL MATERIALS SCIENCE: FROM NANO- TO GEO-
Conferenciante: Profesor Neil L. Allan (Universidad de Bristol, Reino Unido)
Fecha: Viernes, 29 de Mayo de 2015
Hora: 12:00 horas
Lugar: Salón de Actos del IQFR (CSIC). C/Serrano, 119. Madrid

catedrajuliopalacios.iqfr.csic.es

"Current state of Fluorescence Micro-Spectroscopy Methods at the IQFR: Living cells and in vitro applications"

María Pilar Lillo

Miércoles 20 de mayo

Salón de actos, 12:00

"Amyloids: Friends or Foes"

Douglas Laurents

Miércoles 13 de mayo

Salón de Actos, 11:00 (Atención al cambio de hora)

"Exploring the structural basis of DNA repair and RNA degradation by using 3D-electron microscopy"

Dr. Oscar Llorca
Centro de Investigaciones Biológicas de Madrid CSIC Jueves 23 de Abril a las 12.00, Sala 300

Bacteria microarrays for exploring pathogen-host interactions

Miércoles 8 de abril

Salón de actos, 12:00

Inauguración Cátedra Julio Palacios

Martes 14 de abril de 2015

Salón de Actos del CSIC, 17:00 horas

Programa:

-Profesor Ignacio Cirac, Premio Wolf de Física 2013 y Director del Instituto Max Planck de Óptica Cuántica (Alemania)

-Profesor Albino Arenas,Catedrático de la Universida Politécnica de Madrid

-Profesor Francisco González de Posada, Catedrático de la Universidad Politécnica de Madrid

Inscripción:secretaria2@iqfr.csic.es

INAUGURACIÓN "CÁTEDRA JULIO PALACIOS" (programa-cartel)
 
El próximo 14 de Abril de 2015 a las 17:00 horas, en el Salón de Actos del CSIC (C/Serrano, 117. Madrid) tendrá lugar el acto de inauguración de la "Cátedra Julio Palacios". Julio Palacios (1891-1970) fué un insigne científico y académico español, pionero de la investigación en física en nuestro país. La conferencia inaugural será a cargo del Profesor Ignacio Cirac, Premio Wolf de Física 2013 y Director del Instituto Max Planck de Óptica Cuántica (Alemania). A continuación se impartirán sendas conferencias sobre la vida y obra científica de Julio Palacios por parte de los Catedráticos de la UPM, Profesor Albino Arenas y Profesor Francisco González de Posada. Al finalizar el acto se servirá un catering.
 
Para inscribirse al acto, enviar un correo electrónico a "secretaria2@iqfr.csic.es" con el nombre, apellidos, institución y correo electrónico.
 

“Micelle-triggered chameleonic behaviour in peptides derived from pneumococcal LytA autolysin”

Héctor Zamora Carreras

Miércoles 11 de marzo

Salón de actos, 12:00

Norbert M. Nemes
Departamento de Fisica Aplicada III
Universidad Complutense de Madrid

"Signatures of a Two-Dimensional Ferromagnetic Electron Gas at the La0.7Sr0.3MnO3/SrTiO3Interface Arising From Orbital Reconstruction"

Viernes 6 de marzo, 10:30, sala 300

TerremotoUn terremoto de magnitud 5.2 en la escala Richter  ha sacudido la  tarde del 23 de Febrero de 2015 a las 17:16 horas la zona centro de la península, según ha confirmado el Instituto Geográfico Nacional. El epicentro del movimiento sísmico se ha situado a 17 Km de profundidad de la localidad albaceteña de  Ossa de Montiel.

 

En el Instituto de Química Física Rocasolano (IQFR) de Madrid, que dista aproximadamente 180 Km de dicha localidad, se ha sentido el terremoto, y ha quedado registrado en el experimento que se estaba realizando en el Laboratorio de RMN Manuel Rico.

 

En la figura se observa como la señal del experimento de RMN aparece perturbada por dicho terremoto a la hora indicada.

 

 

"Manipulación de las propiedades físicas de virus basada en la estructura"

 Dr. Mauricio G. Mateu (Centro de Biología Molecular)

Viernes 27 febrero

Sala 300, 12:00

II Simposio de Jóvenes Investigadores del IQFR
 
 * Sesión de Charlas Cortas     10 - 12 horas
 * Sesión de Carteles           12 - 13
 * Asamblea del Instituto       13 - 13:30
 
Jueves 26 de febrero en el Salón de Actos

¿Para qué sirve...? ¿...un seminario? ¿...una zeolita? ¿...un experimento? ¿...una simulación?

Vicente Sánchez Gil

Miércoles 25 de febrero

Salón de actos, 12:00

imagen-shadows1 small

The ability to resist the effect of a wide range of antibiotics makes methicillin-resistant Staphylococcus aureus (MRSA) a leading global human pathogen. A key determinant of resistance to -lactam antibiotics in this organism is penicillin-binding protein 2a (PBP2a), an enzyme that catalyzes the crosslinking reaction between two adjacent peptide stems during the peptidoglycan biosynthesis. In the face of the clinical challenge posed by resistant bacteria, the present needs for novel classes of antibiotics are genuine. In silico docking and screening, followed by chemical synthesis of a library of quinazolinones, led to the discovery of (E)-3-(3-carboxyphenyl)-2- (4-cyanostyryl)quinazolin-4(3H)-one as an antibiotic effective in vivo against methicillin-resistant Staphylococcus aureus (MRSA). This antibiotic impairs cell-wall biosynthesis as documented by functional and structural assays showing binding of new antibiotic to PBP2a. We document that the antibiotic also inhibits PBP1 of S. aureus, indicating a broad targeting of structurally similar PBPs by this antibiotic. This class of antibiotics holds promise in fighting MRSA infections.

Reference:
Bouley, R.; Kumarasiri, M.; Peng, Z.; Otero, L.; Song, W.; Suckow, M.; Schroeder, V.; Wolter, W.; Lastochkin, E.; Antunes, N.; Pi, H.; Vakulenko, S.; Hermoso, J.; Chang, M.; Mobashery, S. Discovery of Antibiotic (E)-3-(3-Carboxyphenyl)-2-(4-cyanostyryl)quinazolin-4(3H)-one, J. Am. Chem. Soc. 2015, 137, 1738-1741.

 

leem and peemMagnetite is the oldest magnetic material known to mankind. With applications in catalysis and magnetic storage of information, it has been proposed for use in spintronics. However, its surface magnetic properties are still under discussion. A basic property is the magnetic moment which on the surface may differ from its volumen value. However, the magnetic moment at surfaces and interfaces is crucial for its use in devices that manipulate the spin such as spin valves.

The first research work performed uniquely by means of the only low-energy electron and photoelectron microscope in Spain, located at the Alba synchrotron Alba, ​​has just been published. The study, a collaboration between researchers from the Instituto de Química Física "Rocasolano" and the Alba synchrotron, has used the high surface sensitivity and multi-technique capabilities of the microscope to characterize the magnetic moment at the magnetite surface, finding that it is crucially affected by the local atomic structure.

Laura Martín-García, Raquel Gargallo-Caballero, Matteo Monti, Michael Foerster, José F. Marco, Lucía Aballe, and Juan de la Figuera, "Spin and orbital magnetic moment of reconstructed √2x√2R45º magnetite(001)", Phys. Rev. B (Rapid Comm) 91 (2015) 020408(R).

CSIC link.

 

"A Novel Structure of a Cross-Beta Spine Implicated in Amyotrophic Lateral Sclerosis"

Miguel Mompeán

Miércoles 11 de febrero

Salón de actos, 12:00

"Bioquímica de Sistemas de la division bacteriana"

Germán Rivas

Centro de Investigaciones Biológicas de Madrid

Jueves 29 de enero

Sala 300, 12:00

"Control de un proceso de fotodisociación molecular con campos láser intensos"

Rebeca de Nalda

Miércoles 28 de enero

Salón de actos, 12:00

jpeg1

Researchers at IQFR, in close collaboration with researchers from the Institute of Inorganic Chemistry of the Academy of Sciences of the Czech Republic, have demonstrated the existence of a new inorganic compound that emits laser light and that belongs to a kind of materials never considered before for such application; the boron hydrides or boranes. Specifically, the researchers have concentrated in their work on solutions of anti-B18H22, a polyhedral inorganic molecule containing 18 boron and 22 hydrogen atoms, with architecture resembling that of a split soccer ball joint at opposite edges.
With a quantum yield of fluorescence of 97%, this compound emits laser light at a wavelength of 400 nm, with an efficiency and photostability that is superior or similar to many of the commercially available state-of-the-art organic dyes in this spectral region. Such properties will enable, in a future to come, the reduction in the number of times the laser medium has to be replaced in the devices based in the use of solutions, helping to solve issues with costs, occupational hazards, and environmental impact due to handling of solvents, which are toxic, flammable, and even carcinogenic.

The scientific relevance of this discovery, which has been published in the journal Nature Communications, represents a milestone in the history of lasers, since there are not many occasions in which a new family of laser materials is unveiled.

L. Cerdán, J. Braborec, I. García-Moreno, A. Costela, M. G. S. Londesborough. A borane laser. Nature Communications (2015), DOI: 10.1038/ncomms6958

CSIC press note link

 

MRICOProfesor de Investigación del CSIC
Premio Nacional de Investigación, Enrique Moles (2003)
Medalla de Oro de la Real Sociedad española de Química (2002)

El 1 de diciembre de 2014 falleció Manuel Rico Sarompas. Licenciado y Doctor en Ciencias Químicas en la Universidad Complutense, realizó su postdoc en el Imperial College (Londres) especializándose en la técnica de Resonancia Magnética Nuclear (RMN). A su regreso se instaló en el Instituto Rocasolano del CSIC el primer espectrómetro de RMN de nuestro país, del que se hizo cargo. Sus primeras investigaciones en este campo se encuadraron en la obtención de parámetros magnéticos precisos y en el análisis conformacional de moléculas de "mediana complejidad", a la vez que hizo una amplia labor de difusión de la técnica y colaboró con diversos investigadores en la resolución de problemas de química orgánica y en la identificación de productos naturales. Pronto evolucionó a las aplicaciones biológicas de la RMN, en la que conseguiría valiosos resultados. A comienzos de los años 80 del siglo pasado demostró la presencia en solución acuosa de poblaciones significativas de hélice alfa en péptidos lineales. Estos estudios sobre el plegamiento autónomo de péptidos los completó con el análisis de otros elementos de estructura secundaria, horquillas y láminas beta, tanto con fragmentos de proteína como con péptidos de diseño.
Más tarde, en la década de los 90, determinó la primera estructura tridimensional de una proteína por RMN en nuestro país y la caracterización del plegamiento a nivel de residuo, poniendo de manifiesto la presencia de estructura residual en el estado desplegado en condiciones nativas. A estos estudios siguieron la resolución de un buen número de estructuras tridimensionales de proteínas y de ácidos nucleicos así como la caracterización biofísica de sistemas complejos utilizando fundamentalmente la técnica de RMN.


El trabajo de Manuel Rico se caracterizó por una clara visión de su campo y por el rigor y el tesón con el que abordaba sus investigaciones. Manolo tuvo mucho interés en que en su grupo se incluyeran y desarrollaran los últimos avances de la técnica de RMN y siempre peleó por conseguir la mejor instrumentación para el laboratorio de RMN del IQFR. Es de destacar su apuesta incondicional por los científicos jóvenes, aconsejándoles y animándoles a tomar riesgos y a apostar por su formación de postgrado. El resultado fue la formación de nuevos expertos y el crecimiento de los grupos de RMN en nuestro país.
Asimismo siempre se interesó por proporcionar a la comunidad científica foros de difusión y formación, participó en numerosos actos divulgativos y era miembro activo de varias sociedades científicas. Fue promotor de la Escuela de verano de RMN, de la que dirigió varias ediciones, por la que han pasado prácticamente todos los espectroscopistas de RMN del país. Fue el impulsor y creador de la Red Nacional de Estructura y Función de Proteínas que aúna a todos aquellos científicos que trabajan sobre esta temática en España, sirviendo de cauce de divulgación científica y de formación de estudiantes en el área.

 

"Frequenin/NCS-1 as a pharmacological target for synapse regulation in X-linked mental retardation and autism"

María José Sánchez Barrena

Miércoles 17 de diciembre

12:00 Salón de actos

Calendario de seminarios del curso 2014-2015 (Versión actualizada)

fig web1Plants have to endure adverse environmental conditions, among them, drought and salinity constrain agricultural productivity most dramatically. Many of the plant adaptive responses take place at cell membrane where it is required the regulation o a variety of ion channels and transporters. This adjusts the intracellular ion concentration necessary for cell live.  From a molecular point of view, the levels of abscisic acid (ABA) and calcium encode the information to orchestrate cell response to stress. We have discovered and characterized a new family of proteins, CAR for C2-domain ABA-related, that target ABA recognition machinery to the cell membrane. The joined structural and biochemical analyses has provided a working model that illustrates how CAR proteins anchor to plasma membrane and specifically bind the ABA receptors. As the activity of these proteins is dependent of calcium, they represent a central hub decoding ABA and calcium stimuli and provide a target for biotechnological work for the use of plants in our benefit.

C2-Domain Abscisic Acid-Related Proteins Mediate the Interaction of PYR/PYL/RCAR Abscisic Acid Receptors with the Plasma Membrane and Regulate Abscisic Acid Sensitivity in Arabidopsis

L. Rodriguez, M. Gonzalez-Guzmán, M. Díaz, A. Rodrigues, A.C. Izquierdo-Garcia, M. Peirats-Llobet, R. Antonia, D. Fernández, J.A. Márquez, J.M. Mulet, A. Albert and P.L. Rodríguez
The Plant Cell (2014) Advanced Online Publication (doi:10.1105/tpc.114.129973)

 

 

Charla sobre el servicio de AFM del IQFR

Esther Rebollar

Vienres, 28 de Noviembre de 2014

Sala 300, 12:00

 "Deciphering the structure of human CAD"

Dr. Santiago Ramon-Maiques

Centro Nacional de Investigaciones Oncologicas  de Madrid

Jueves 27 de noviembre a las 12.00

Sala 300

Hora        Conferenciante

10 - 10:30  Marta Castillejo
10:30 - 11  Lourdes Infantes
11 - 11:30  Mª Ángeles Jiménez
11:30 - 12  Eva Noya González

 

12 - 12:30 (pausa para tomar café)
12:30 - 13:15 (claustro científico (investigadores de plantilla)

pegaso1pegaso2

El proyecto PEGASO (Plankton-derived Emissions of trace Gases and Aerosols in the Southern Ocean) nace con el objetivo general de investigar cómo el océano participa en los procesos atmosféricos y, por lo tanto, interacciona con el sistema climático global. Pretende evaluar la importancia relativa de estos fenómenos en un escenario de cambio climático global. El proyecto PEGASO aprovechará el tránsito desde Cartagena hasta Punta Arenas, previo a la campaña en la Antártida, a bordo del Buque de Investigación Oceanográfica (BIO) Hespérides.

El Grupo de Química Atmosférica y Clima (AC2), liderado por Alfonso Saiz-López, es uno de los dos grupos españoles (junto al ICM-CSIC) que participa en esta expedición, aportando un dispositivo MAX-DOAS (multi-axis differential optical absorption spectroscopy) desarrollado en el IQFR y un monitor de ozono, con los que se pretende recoger una extensa base de datos de alta resolución que nos permitirá inferir la distribución espacio-temporal de gases traza, emitidos desde los océanos y que son climáticamente activos, como IO, BrO, HCHO y (CHO)2 a lo largo de las distintas etapas de la expedición. Con ello, podremos mejorar nuestro conocimiento sobre la interacción océano-atmósfera, así como su relación con el clima.

Telescopio situado a babor de la cubierta superior del BIO-Hespérides

 

AMALCP2Alejando Manjavacas Arévalo

Tesis: "Light-Matter Interaction at the Nanoscale"
Director: Prof. Javier García de Abajo
Grupo: Nanophotonics Theory Group
Posición actual: J. Evans Attwell-Welch Postdoctoral Fellow en el grupo "Norlander Nanophotonics Group" de la Rice University

Luis Cerdán Pedraza

Tesis: "Solid State Dye Lasers: Scattering feedback and integrated devices"
Directores: Prof. Ángel Costela y Prof. Inmaculada García-Moreno
Grupo: Grupo de Materiales Láser e Interacciones Láser-Materiales
Posición actual: Ayudante Postdoctoral en el mismo grupo.

 

 

Bases estructurales de la homeostasis del potasio en plantas: Regulación del transportador AKT1 y de la quinasa CIPK23

Viernes 24 octubre a las 12:00

Salón de Actos

MBruix13102014

In collaboration with a group led by the CNIO and the CRG, the IQFR has participated in a study to understand the interactions that regulate the dynamic properties of microtubules and their organization during mitosis. The work has focused on the characterization of the molecular interaction between TACC3 and chTOG. These proteins are key in forming the internal cellular framework that enables and sustains cell division. The work was carried out by a multiexperimental approximation using a variety of biophysical (SAXS, NMR, CD), biochemical and cellular techniques. It has been possible to define the minimum active domain of TACC3 and derive a 3D model by SAXS. By NMR we have identified key residues for molecular interaction. From these data, designed mutants have allowed us to see, in cells, how preventing this association the mitotic spindle assembly is not produced.

The results may help to optimise current oncological therapies specifically designed to fight against this framework, named by the scientific community as microtubules

This study was funded by the CONSOLIDER programme of the Ministry of Economy and Competitiveness, the Ramón Areces Foundation, and the Community of Madrid.

XTACC3-XMAP215 association reveals an asymmetric interaction promoting microtubule elongation.

Mortuza GBCavazza TGarcia-Mayoral MFHermida DPeset IPedrero JGMerino NBlanco FJLyngsø JBruix MPedersen JSVernos IMontoya GNat Commun. 2014 Sep 29;5:5072. doi: 10.1038/ncomms6072.

 

FIgura web smallerThe transport of ions through the plant cell membrane establishes the key physicochemical parameters for cell function. Stress situations such as those created by soil salinity or low potassium conditions alter the ion transport across the membrane producing dramatic changes in the cell turgor, the membrane potential, and the intracellular pH and concentrations of toxic cations such as sodium and lithium. As a consequence, fundamental metabolic routes are inhibited.

 

The CIPK family of twenty-six protein kinases regulates the function of several ion transporters at the cell membrane to restore ion homeostasis under stress situations. Our analyses provide an explanation on how the CIPKs are differentially activated to coordinate the adequate cell response to a particular stress.

  

Proceedings of the National Academy of Sciences, PNAS (2014), (doi:10.1073/pnas.1407610111)

http://www.pnas.org/content/early/2014/10/02/1407610111

 

MBB Premio2014

La Profesora Marta Bruix, ha recibido el Premio Bruker del GERMN (Grupo Especializado de RMN de la RSEQ) durante la Reunión Bienal que ha tenido lugar recientemente en Alcalá de Henares, en reconocimiento a su trayectoria científica y en particular a sus trabajos en la RMN de proteínas.

 

Este galardón, patrocinado por Bruker Española S.A., fue instituido por el GERMN para premiar a investigadores españoles que hayan tenido una contribución significativa en el campo de la espectroscopía de RMN y una labor de diseminación de la técnica a la comunidad científica española.

 

Los investigadores galardonados en ediciones anteriores son:

 

▪ Dr. Manuel Rico, Instituto de Química Física “Rocasolano” – CSIC, en ocasión de su 65 aniversario y en conmemoración de los 40 años de la espectroscopía de RMN en España (Madrid, 2002).
▪ Dr. Ernest Giralt, Institut de Recerca Biomèdica and Universitat de Barcelona, en la I Reunión Bienal del GERMN (Calella de Mar, 2002)
▪ Dr. Jorge Santoro, Instituto de Química Física “Rocasolano” – CSIC, en la II Reunión Bienal GERMN (Santiago de Compostela, 2004)
▪ Dr. Francesc Sánchez Ferrando, Universitat Autònoma de Barcelona, en la III Reunión Bienal GERMN (Alicante, 2006)
▪ Dr. Jesús Jiménez Barbero, Centro de Investigaciones Biológicas – CSIC, en la IV Reunión Bienal GERMN (Sevilla, 2008)
▪ Dr. Miquel Pons, Institut de Recerca Biomèdica and Universitat de Barcelona, en la V Reunión Bienal GERMN (Bilbao, 2010)
▪ Dr. Teodor Parella, Universitat Autònoma de Barcelona, en la VI Reunión Bienal GERMN (Aveiro, 2012)

 

 

El próximo lunes 6 de octubre tenemos a Ivan Plaza-Menacho que impartirá un seminario en la sala 300 a las 12:00:
 
Molecular mechanisms of RET tyrosine kinase cis-regulation and oncogenic deregulation in trans: implications for targeted therapy
 
Ivan Plaza-Menacho, Structural Biology Laboratory, London Research Institute, Cancer Research UK

 

The IQFR will participate in one of the next Mars rover instruments, the Mars Environmental Dynamics Analyzer (MEDA), a set of sensors that will provide measurements of temperature, wind speed and direction, pressure, relative humidity and dust size and shape. The principal investigator is Jose' Antonio Rodriguez-Manfredi, Centro de Astrobiologia, Instituto Nacional de Tecnica Aeroespacial, Spain, and the team of Alfonso Sáiz of the IQFR will participate in the ozone sensor.

 

The evolution of nitrogen dioxide (NO2) over Spain from 1996 to 2012 has been analyzed by a group of scientists led by the Atmospheric Chemistry and Climate Group (AC2) at IQFR (CSIC), with the participation of the University of Bremen, the University of Castilla-La Mancha (UCLM) and the National Institute for Aerospace Technology (INTA).

The study is focused ondensely populated cities of Barcelona, Bilbao, Madrid, Sevilla and Valencia, employing 17 years of NO2 measurements, from 1996 to 2012. This data series combines observations from in-situ air quality monitoring networks and the satellite-based instruments GOME and SCIAMACHY. The results in these five cities show a smooth decrease in the NO2 concentrations of 2% per year in the period 1996-2008, due to the implementation of emissions control environmental legislation, and a more abrupt descend of ~7% per year from 2008 to 2012 as a consequence of the economic recession. In the whole Spanish territory the NO2 levels have decreased by ~22% from 1996 to 2012. In some cities, e.g. Madrid, the decrease in NO2 concentrations surpasses 40%. Statistical analysis of several economic indicators is used to investigate the different factors driving the NO2 concentration trends over Spain during the last two decades.

The work has been published in Scientific Reports

C.A. Cuevas, A. Notario, J.A. Adame, A. Hilboll, A. Richter, J.P. Burrows and A. Saiz-Lopez. Sci. Rep 4, 5887; DOI:10.1038/srep05887 (2014).

no2 spain

 

Averaged tropospheric NO2 vertical column density for 1996 (left) and 2011 (right)

rnalda

Many dynamical processes in molecules occur in extraordinarily short timescales, of the order of femtoseconds (1 fs = 10-15 s). In order to follow these processes in real time it is necessary to use the fastest stopwatches available, which are made of ultrashort laser light pulses. In the Center for Ultrashort Lasers (CLUR), in the Complutense University, Madrid, a research team with the participation of Rebeca de Nalda, from IQFR (CSIC), has been taking snapshots of some of these ultrafast processes in molecular systems, while trying to understand the details of the underlying light-matter interaction phenomena.

The new ingredient that has been recently added to these studies is an additional laser pulse that goes beyond the observation of the reaction, and is capable of modifying its course. This pulse is sufficiently intense to alter the molecular potentials, and thus, it causes changes in the products of the reaction and the speeds they acquire in reactions where bonds are broken. This work has been published in Nature Chemistry, and it is a demonstration that the fine control of the properties of this "control" laser pulse turns it into a true "photonic scalpel" capable of manipulating chemical reactions, as well as shedding new light into the dynamics of complex molecular dynamical processes.

M. E. Corrales, J. González-Vázquez, G. Balerdi, I. R. Solá, R. de Nalda, L. Bañares, Control of ultrafast molecular photodissociation by laser field induced potentials, Nature Chemistry (2014), doi:10.1038/nchem.2006

 

Matteo Monti
Instituto de Química Física "Rocasolano"
calle Serrano 119, Madrid
viernes 11 de julio, 11:30, Salón de actos
Supervisors: J.F. Marco, J. de la Figuera
 

Iron oxides are common compounds which are widespread in nature and constitute an important class of materials. Thinking about the importance of iron oxides for the humankind, magnetite, one of the most abundant magnetic minerals in earth's crust, comes to mind as a clear example. For many years, magnetite found a wide technological application range from navigation (compasses) to modern high density magnetic recording media. Moreover, iron oxides prepared in several nanostructure forms are also involved in environmental science, catalysis, biology, electronics, and other fields.


This dissertation studies several aspects of iron oxide grown on Ru(0001) and the modification of their properties when one dimension is reduced at the nanoscale limit. Since the preparation of iron oxides with defined structure and stoichiometry turned out to be not trivial, the basic understanding about the chemical and physical properties of ultrathin films becomes fundamental in order to tailor desired applications.
 
PDF of the PhD thesis: 
 

Matteo Monti
Instituto de Química Física "Rocasolano"
calle Serrano 119, Madrid
viernes 11 de julio, 11:30, Salón de actos
Supervisors: J.F. Marco, J. de la Figuera

Atomic-ensemble effects and non-covalent interactions at the electrode-electrolyte interface

Jueves 10 de julio a las 10:30 en el Salón de actos.

"Explorando Patrones de Glicosilación de Bacterias Patógenas y Vesículas Extracelulares como Marcadores para Receptores Endógenos"

Miércoles 11 de junio

Salón de actos, 12:00

Estructura de vacantes de oxígeno en el óxido de cerio reducible y función catalíticauna perspectiva teórica del papel de la localización del exceso de carga



Viernes 6 de junio

Aula 300, 10:30

"Mecanismos de Reconocimiento de Proteínas +TIPS (Tip Interacting Proteins)"

Viernes 6 de junio

Aula 300, 12:00

"Búsqueda de nuevas léctinas fúngicas con estructura trébol beta: desarrollo de nuevas aplicaciones biotecnológicas"

Jueves 22 de Mayo

Salón de Actos 12:00

Universidad Texas A&M

“Entropy vs. Mixing: What Determines Complexity”

Martes 27 de Mayo

Salón de actos, 12:00

xtal libroM. Martínez-Ripoll, J.A. Hermoso & Armando Albert (coord.), CSIC-Catarata (2014), 196 pp., ISBN: 978-84-00-09800-1.

Un libro de divulgación científica en el contexto del Año Internacional de la Cristalografía 2014.

Se puede encontrar un ejemplar en la biblioteca del IQFR.

A book for scientific dissemination in the context of the International Year of Crystallography 2014 (IYCr2014).

You may find a copy at the IQFR library.

cover-1

    Separation of daughter cells during bacterial cell division requires that the septal cross wall be split by peptidoglycan hydrolases. In Streptococcus pneumoniae an essential protein termed PcsB is predicted to perform this critical operation. Recent evidence shows that the activity of PcsB is regulated by the transmembrane FtsEX complex. In this work the muralytic activity of PcsB is demonstrated for the first time. Furthermore, we report the crystal structure of full-length PcsB showing an unprecedented dimeric structure in which the unique V-shaped coiled-coil domain of each monomer acts as a molecular tweezers locking down the catalytic domain of its dimeric partner in an inactive configuration. This finding strongly suggests that the release of the catalytic domains requires an ATP-driven conformational change in the FtsEX complex, which is most likely conveyed towards the catalytic domains through a set of coordinated movements of the α-helices forming the coiled-coil domain of PcsB.

 

Sergio G. Bartual, Daniel Straume, Gro Anita Stamsås, Inés G. Muñoz, Carlos Alfonso, Martín Martínez-Ripoll, Leiv Sigve Håvarstein* & Juan A. Hermoso *

Structural basis of PcsB-mediated cell separation in Streptococcus pneumoniae

Nature Communications (2014). DOI: 10.1038/ncomms4842

 

 

 

Detener el tiempo: pulsos de luz para observar cambios ultrarrápidos

Thursday, May 8th

Assembly hall 12:00

Prof. Gautam R. Desiraju, President of the IUCr, will give a talk entitled

"Crystal engineering. From molecule to crystal".

May 9th, 2014.

Assembly hall, 12:00 

CW_7 cell wall-binding motifs of the Cpl-7 endolysin target the peptidoglycan muropeptide

Miércoles 30 de abril

Salón de actos, 12:00

"Focal Adhesion Kinase: A Molecular Signalling Switch controlling Growth and Adhesion Signals"

Jueves 24 de Abril

Aula 215, 12:00

"Laboratory studies on the photochemistry of metallic layer reservoirs and nucleation of mesospheric smoke particles"

Viernes 25 de Abril

Aula 215, 12:00

"La RMN como herramienta en el estudio de interacciones proteína-membrana en modelos simplificados"

Miércoles 2 de abril

Salón de Actos, 12:00

Structural insights into the the TRiC/CCT complex function and mechanism

Martes 25 de marzo

Aula 300, 12:00

Understanding the structure of hydrogen-bonded liquids by combining diffraction experiments and computer simulations
Jueves 27 de marzo
Aula 300, 12:00

Caracterización estructural y funcional de la glucosaminidasa LytB de Streptococcus pneumoniae

Miércoles 26 de marzo

Salón de Actos 12:00

"The role of protein structure in controlling the reactions of pterin-dependent non-heme hydroxylases"

Martes 18 de marzo

Salón de actos a las 12:00

Coarse-grained modelling of DNA: biophysics and nanotechnology

Jueves 20 de marzo a las 12:00

Aula 300

Evolution of NO2 levels in Spain from 1996 to 2012 and UVAS retrieval algorithms

Miércoles 12 de marzo a las 12:00

Salón de actos

JCCcover

"Pablo García-Risueño started his work on this subject when doing his PhD at the institute."

 

The problem of the electrostatic potential is almost ubiquituous in chemical and atomic/molecular simulations. In this paper just published at the Journal of Computational Chemistry (and appearing at its front cover), Pablo García-Risueno et al. present an analysis of different methods to calculate the classical electrostatic Hartree potential created by charge distributions. This work may enable more accurate and efficient simulations, helping scientists to tackle many new systems.

 

 

webMetabolic resistance to insecticides is the biggest threat to the continued effectiveness of malaria vector control. In the frame of a transnational research program, we have demonstrated that a single amino acid change in the glutathione-s-transferase confers high levels of DDT resistance in the African mosquito Anopheles funestus.  Interestingly, this metabolic resistance marker perfectly correlates with patterns of DDT resistance across Africa. The x-ray structures of two polymorphic GSTe2 corresponding to those populations presenting an intensified resistance or sensitiveness phenotypes show that the mutation confers resistance by enlarging the GSTe2 DDT-binding cavity leading to increased DDT access and metabolism. This knowledge constitutes a valuable tool for future operational monitoring of insecticide resistance in Africa and allows us to design novel molecules with enhanced insecticide properties.

Reference:

A single mutation in the GSTe2 gene allows tracking of metabolically based insecticide resistance in a major malaria vector

Riveron JM, Yunta C, Ibrahim SS, Djouaka R, Irving H, Menze BD, Ismail HM, Hemingway J, H. Ranson, A. Albert  and C.S. Wondji
Genome Biology 2014, 15:R27 (25 February 2014)

Highlighted at:

Insecticide resistance comes of age (ffrench-Constant RH Genome Biology 2014, 15:106 (25 February 2014))

 

ULTRASOFT, CLUSTER-FORMING SYSTEMS UNDER COMPRESSION
Martes 4 de marzo a las 12:00 en el aula 300

"Dynamics and phase transitions of complex fluids on porous glasses"

Miércoles 9 de abril

Salón de actos, 12:00

On Monday 17 we will have Carlos Villar, from Bruker, to give us an introduction to the use of the FTIR spectrometer Tensor-27. It will take about 3 hours, and he will bring a liquid cell and an ATR setup.

 

The Tensor-27 spectrometer is part of the biophysics lab of use for the IQFR members, located at room 324.

brukerFTIR

 

We will have a get-together to give our farewell to Isabel Cabo as manager of the Institute. It will take place at the hall in front of room 300 at 13:00-13:30. 

Jueves 20 de febrero

10:00-12:00 Charlas en el salón de actos

12:00-14:00 Exposición de pósters en el hall del Instituto

Miércoles 19 de febrero a las 12:00 en el salón de actos

“The Oldest Metal-Insulator Transition in Condensed Matter: the Verwey Transition of Magnetite, from the Bulk to the Surface”

Miércoles 12 de febrero

Salón de actos, 12:00

"Química de heteroboranos poliédricos"

Miércoles 5 de febrero, 12:00

Salón de Actos

“How do pneumococci and other bacteria subvert the function of human proteins”

Friday 29th, 12:00

Room 300

Magnetic Properties Across Metal to Insulator Transitions

Room 300, Friday 10th January, 10:30

streptococcus pneumoniaeThe respiratory pathogen Streptococcus pneumoniae has evolved efficient mechanisms to resist oxidative stress conditions and to displace other bacteria in the nasopharynx. Here we characterize at physiological, functional and structural levels two novel surface-exposed thioredoxin-family lipoproteins, Etrx1 and Etrx2. The impact of both Etrx proteins and their redox partner methionine sulfoxide reductase SpMsrAB2 on pneumococcal pathogenesis was assessed in mouse virulence studies and phagocytosis assays. The results demonstrate that loss of function of either both Etrx proteins or SpMsrAB2 dramatically attenuated pneumococcal virulence in the acute mouse pneumonia model and that Etrx proteins compensate each other. The deficiency of Etrx proteins or SpMsrAB2 further enhanced bacterial uptake by macrophages, and accelerated pneumococcal killing by H2O2 or free methionine sulfoxides (MetSO). Moreover, the absence of both Etrx redox pathways provokes an accumulation of oxidized SpMsrAB2 in vivo. Taken together our results reveal insights into the role of two extracellular electron pathways required for reduction of SpMsrAB2 and surface-exposed MetSO. Identification of this system and its target proteins paves the way for the design of novel antimicrobials.

Reference:
Malek Saleh, Sergio G. Bartual, Mohammed R. Abdullah, Inga Jensch, Tauseef M. Asmat, Lothar Petruschka, Thomas Pribyl, Juan A. Hermoso* and Sven Hammerschmidt*
Molecular architecture of Streptococcus pneumoniae surface thioredoxin-fold lipoproteins crucial for extracellular oxidative stress resistance and maintenance of virulence
EMBO Molecular Medicine (2013) 5, 1852-1870  (doi:10.1002/emmm.201202435)

Referencia:

Malek Saleh, Sergio G. Bartual, Mohammed R. Abdullah, Inga Jensch, Tauseef M. Asmat, Lothar Petruschka, Thomas Pribyl, Juan A. Hermoso* and Sven Hammerschmidt*

Molecular architecture of Streptococcus pneumoniae surface thioredoxin-fold lipoproteins crucial for extracellular oxidative stress resistance and maintenance of virulence

EMBO Molecular Medicine (2013) 5, 1852-1870  (doi:10.1002/emmm.201202435)

We will have the traditional yearly meeting to briefly review 2013 at the main conference rooma t 13:00 and an informal lunch afterwards.

Cest-2923 figure-2

The alpha/beta hydrolase fold is one of the most versatile structures in the protein realm according to the diversity of sequences adopting such a three dimensional architecture. We found that the versatility of a canonical alpha/beta-hydrolase fold, particularly that of the carboxylesterase Cest-2923 from the lactic acid bacterium Lactobacillus plantarum WCFS1, also extends to its oligomeric behavior in solution. Thus, we discovered that Cest-2923 exhibits a pH-dependent pleomorphic behaviour in solution involving monomers, canonical dimers and tetramers. Whereas at neutral pH the system is mainly shifted to dimeric species, at acidic conditions tetrameric species predominate. Interestingly, despite that these tetramers result from the association of canonical dimers, as commonly found in many other carboxylesterases from the hormone-sensitive lipase family, they can be defined as “non canonical” since they represent a different association mode. The observed associative behaviour is consistent with different crystallographic results of Cest-2923 from structural genomics consortia. Finally, we benefit from the presence of sulphate or acetate molecules (depending on the crystal form analysed) in the close vicinity of the nucleophile Ser116, to identify interactions with the putative oxyanion hole and also to deduce the existence of hydrolytic activity within Cest-2923 crystals.

 

 

Reference:
Benavente R, Esteban-Torres M, Acebrón I, de Las Rivas B, Muñoz R, Alvarez Y, Mancheño JM. “Structure, biochemical characterization and analysis of the pleomorphism of carboxylesterase Cest-2923 from Lactobacillus plantarum WCFS1”. FEBS J. 2013 Oct 16. doi: 10.1111/febs.12569.

 

summary figure
Magnetite is a magnetic material known since more than two thousand years ago. It presents a phase transition known as the Verwey transition (at ~ 120K), in which the crystal structure changes from cubic to monoclinic, and at the same time the conductivity is reduced by two orders of magnitude. This transition strongly promoted research on metal-insulator transitions. For the first time, a team of researchers from the IQFR, Berkeley National Laboratory and the Vienna Technical University have observed this transition with surface-sensitive microscopies for the (100) orientation of magnetite. It has been found that the surface "rumbles" forming a roof-like surface at a micrometer scale, whereas the actual surface reconstruction has the same structure through the transition. This indicates that although the surface reconstruction is conceptually similar to the bulk structure below the transition, they are two distinct phenomena.
 
J. de la Figuera, Z. Novotny, M. Setvin, T. Liu, Z. Mao, G. Chen, A. T. N'Diaye, M. Schmid, U. Diebold, A. K. Schmid, G. S. Parkinson,  "Real Space Imaging of the Verwey Transition at the (100) Surface of Magnetite", Phys. Rev. B 88 (2013) 161410(R), DOI:10.1103/PhysRevB.88.161410,  arxiv 1310.1373
 
The figure shows at the top, low-energy electron microscope images (8.6 um wide) above (left) and below (right) the Verwey transition. In the middle, scanning tunneling microscopy images with atomic resolution are shown also above and below the transition. At the bottom, a profile showns the "roof" surface below the transition.
 
 
 

Exocytosis and Endocytosis; from membranes and molecules to mechanisms

Date: 28th Nov 2013, 15:30. Room 300

Activities for Week of Science

Date: Thursday 14th November, 10:30 - 14:00 horas
10:30 - 12:00 Talks at the Hall Conference Room
12:00 - 14:00 Visits to laboratories

"The role of Gbp2p, Nab2p and Pub1p along the mRNA cycle: structural and molecular recognition studies by NMR and other biophysical techniques"

Date: Friday 15th November, 12:00
Place: Salón de Actos

surface-cov-1-green-01

The expression of penicillin binding protein 2a (PBP2a) is the basis for the broad clinical resistance to the β-lactam antibiotics by methicillin-resistant Staphylococcus aureus (MRSA). The highmolecular mass penicillin binding proteins of bacteria catalyze in separate domains the transglycosylase and transpeptidase activities required for the biosynthesis of the peptidoglycan polymer that comprises the bacterial cell wall. In bacteria susceptible to β-lactam antibiotics, the transpeptidase activity of their penicillin binding proteins (PBPs) is lost as a result of irreversible acylation of an active site serine by the β-lactam antibiotics. In contrast, the PBP2a of MRSA is resistant to β-lactamacylation and successfully catalyzes the DD-transpeptidation reaction necessary to complete the cell wall. The inability to contain MRSA infection with β-lactam antibiotics is a continuing public health concern. We report herein the identification of an allosteric binding domain—a remarkable 60 Å distant from the DD-transpeptidase active site—discovered by crystallographic analysis of a soluble construct of PBP2a. When this allosteric site is occupied, a multiresidue conformational change culminates in the opening of the active site to permit substrate entry. This same crystallographic analysis also reveals the identity of three allosteric ligands: muramic acid (a saccharide component of the peptidoglycan), the cell Wall peptidoglycan, and ceftaroline, a recently approved anti-MRSA β-lactam antibiotic. The ability of an anti-MRSA β-lactam antibiotic to stimulate allosteric opening of the active site, thus predisposing PBP2a to inactivation by a second β-lactam molecule, opens an unprecedented realm for β-lactam antibiotic structure-based design.

Reference:

Lisandro H. Oteroa, Alzoray Rojas-Altuvea, Leticia I. Llarrull, Cesar Carrasco-López, Malika Kumarasiri, Elena Lastochkin, Jennifer Fishovitz, Matthew Dawley, Dusan Hesek, Mijoon Lee, Jarrod W. Johnson, Jed F. Fisher, Mayland Chang, Shahriar Mobashery, Juan A. Hermoso. How allosteric control of Staphylococcus aureus penicillin binding protein 2a enables methicillin resistance and physiological function. PNAS. DOI: 10.1073/pnas.1300118110

 

dosuno

Modified nucleic acids are very interesting molecules because of their application in Biomedicine, as therapeutic agents, and in Nanoscience, as potential components of nano-devices. Of particular relevance is the substitution of a hydrogen atom at the 2’ position of the DNA deoxyribose by fluorine. Fluorine is the most electronegative element and alters the electronic distribution in its surroundings, provoking interactions that are not present, or are much weaker, in natural nucleic acids.

In two recent papers researchers of the IQFR, in collaboration with colleagues of McGill University in Canada and in the IRB in Barcelona, have described these effects at structural level and analysed their physico-chemical basis in double helical and guanine quadruplex structures.

 

Reference:

N. Martín-Pintado, M. Yahyaee-Anzahaee, G. F. Deleavey, G. Portella, M. Orozco, M.J. Damha, and C. González.Dramatic effect of furanose C2´-substitution on structure and stability:  Directing the folding of the human telomeric quadruplex with a single fluorine atom.J. Am. Chem. Soc., 135, 5344-5347, 2013.doi: 10.1021/ja401954t

N. Martín-Pintado, G. F. Deleavey, G. Portella, R. Campos-Olivas, M. Orozco, M.J. Damha, and C. González.Backbone FC-H...O hydrogen bonds in 2´F-substituted nucleic acids.Angewandte Chemie Int Ed, en prensa, 2013.doi:10.1002/anie.201305710

 

arriba

abajo

Scientists from the Department of Biophysical Chemistry discovered novel water-soluble oxocines and azocines that produce blue fluorescence with 100% quantum yield. These molecules are the main product of a new fluorogenic reaction that converts non-emitting biocompounds as L-DOPA, dopamine, hydroxytyrosol, etc. into useful photostable fluorophores. The new molecular structures contain the rare four-ring chromophore which originated the first written account of fluorescence emission in 1565 (Acuña et al. Org. Lett. 2009, 11, 3020). At that time, the medical doctor N. Monardes from Sevilla reported the unusual blue “color” (fluorescence) of the infusion of a medicinal wood widely used in preHispanic Aztec culture.

 

Reference:

Synthesis and photophysics of novel biocompatible fluorescent oxocines and azocines in aqueous solution.

A.Ulises Acuña, Mónica Älvarez-Pérez, Marta Liras, Pedro B. Coto and Francisco Amat-Guerri.

Phys. Chem. Chem. Phys. Sept. 2013 (DOI: 10:1039/c3cp52228h)

 

nap2pNab2p is an essential protein involved in mRNP (messenger ribonucleoprotein particles) formation and export in Saccharomyces cerevisiae. Its specific poly(A) RNA recognition ability resides on a region containing 7 CCCH-type zinc finger domains, of which, the last three zinc finger structure was previously known. In our group, we have solved the NMR structure of the first 4 zinc fingers that show novel elements in their fold. The first two zinc fingers (Zf1 and Zf2) form a compact tandem stabilized by a new -helix contacting both. Zf3 and Zf4 form a second tandem in which the metallic centres associate in a singular symmetric way with mutual recognition of the Zn2+ coordinating histidines. NMR, fluorescence anisotropy and mutagenesis studies identify the -helix in the first tandem and the exposed surface of Zf3 as the RNA binding interface. Our results allow us to propose a recognition model where Nab2p Zf1-4 cooperates with Nab2p Zf5-7 to reconstitute the poly(A) binding profile of the full-length protein.

 

Reference

Two Singular Types of CCCH Tandem Zinc Finger in Nab2p Contribute to Polyadenosine RNA Recognition.

Martínez-Lumbreras S1,3, Santiveri CM2,3, Mirassou Y1, Zorrilla S1,2, Pérez-Cañadillas JM1*.

Structure. 2013 Aug 28. doi: 10.1016/j.str.2013.07.019.

1 IQFR-CSIC; 2 CIB-CSIC; 3 equal contribution;*corresponding author

 

Figure-4A small

Bacterial cell wall is a polymer of considerable complexity that is in constant equilibrium between synthesis and recycling. AmpDh3 is a periplasmic zinc protease of Pseudomonas aeruginosa, which is intimately involved in cell-wall remodeling. In this report we document the reactions that this enzyme performs on the cell wall, which hydrolyze the peptide stems from the peptidoglycan, the major constituent of the cell wall. We document that the majority of the reactions of this enzyme takes place on the polymeric insoluble portion of the cell wall, as opposed to the fraction that is released from it. We show that AmpDh3 is tetrameric both in crystals and in solution. Based on the X-ray structures of the enzyme in complex with two synthetic cell-wall-based ligands, we present for the first time a model for a multivalent anchoring of AmpDh3 onto the cell wall, which lends itself to its processive remodeling.

 

 

      Reference:

Lee, M.; Artola-Recolons, C.; Carrasco-López, C.; Martínez-Caballero, S.; Hesek, D.; Spink, E.; Lastochkin, E.; Zhang, W.; Hellman, L.; Boggess, B.; Hermoso*, J.; Mobashery*, S.

      Cell-Wall Remodeling by the Zinc-Protease AmpDh3 from Pseudomonas aeruginosa

      J. Am. Chem. Soc. 2013; 12605-12607.

 

ampdh2-verybigThe 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)

Generación, caracterización y control de plasmas de ablación láser

Wednesday, July 3rd 2013

12:00 Salón de Actos

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.

1(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.

2

 (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

 

Las galectinas: tan parecidas, tan diferentes

Thursday June 27th 2013

12:00 Salón de Actos

"Actividades de investigación en el Grupo de Química Atmosférica y Clima"

Thursday 20th June 2013

12:00 Salón de Actos de IQFR

"Estudios mediante RMN de la estructura y estabilidad de ácidos nucleicos con furanosas modificada"

Tuesday 18th June  2013

12:00 Salón de Actos del IQRF

"From Bayes (to electrons to proteins) to therapies"

Wednesday 19th, 2013

12:00 Salón de Actos

Modelado y simulación de procesos de adsorción en arcillas con pilares intercalados

12:00 Salón de Actos

Wednesday, June 12th 2013

Water: A Fluid Complex
16:00 Aula 300

Miércoles 12 Junio 2013

figura webScientists 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

 

Wednesday June 12th 2013

"Nonlocal effects in plasmonic devices: Exploring the quantum regime with the classical hydrodynamic approach"

June 5th 2013

2013 JACS Davalos 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 

 

“The multiple faces of RNA binding proteins”

May 29th 2013

May 22th, 10:00h. General meeting of the institute for the presentación of Dr. Juan de la Figuera as candidate for director.

Imagen Tesis ReduThe Thesis entitled Electrocatalysis and surface nanostructuring: atomic ensemble effects and non-covalent interactions, whose author is Dr. María Escudero Escribano, and which was developed at the Institute of Physical Chemistry "Rocasolano" under the supervision of Dr. Angel Cuesta Ciscar, has received the Prize to the Best PhD Thesis in the Region of Madrid in the course 2011-2012, awarded by the Madrid Chapter of the Spanish Royal Society of Chemistry (RSEQ). The research was focused on the study of the role of geometric atomic ensembles in electrocatalysis, and on the fabrication of surface nanostructures guided by a self-ordered molecular pattern, namely cyanide-modified Pt(111). The Thesis can be downloaded from Digital CSIC (http://hdl.handle.net/10261/42378).

 

Suc2 octa webScientists from IQFR have revealed the structure of the Saccharomyces invertase, a highly interesting enzyme for Biotechnology and a classical model used in early biochemical studies. In the study have participated scientists from IATA (CSIC).
Invertases catalyze the hydrolysis of the disaccharide sucrose into glucose and fructose, being key enzymes in the metabolism of plants and microorganisms. Besides its historic relevance, Saccharomyces invertase is one of the most widely used enzymes in food industry, and in the fermentation of cane molasses into ethanol. A new emerging application is the synthesis of prebiotics (FOS) for use in functional foods and pharmaceuticals.

 

Reference: Journal of Biological Chemistry (2013) 288, 9755- 9766 (doi:10.1074/jbc.M112.446435)
Three-dimensional structure of Saccharomyces invertase. Role of a non-catalytic domain in oligomerization and substrate specificity. http://www.jbc.org/content/288/14/9755#fn-9
MA Sainz-Polo. M Ramírez, A Lafraya, B González, J Marín-Navarro, J Polaina, J Sanz-Aparicio.


Its structural analysis has shown a sophisticated molecular architecture with a peculiar monomer assembly, unique to this enzyme within its family, which regulates its specificity. This assemblage is similar to the interactions that form b-amiloids, and is mediated by the non-catalytic domain. Therefore, our results highlight the role of the non-catalytic domains in fine-tuning substrate specificity and supplement our knowledge into the structural features that rule modularity, a central feature within carbohydrate-active enzymes.

Press note.

 

Streptococcus pneumoniae surface-exposed thioredoxin-like proteins that are involved in defence against oxidative stress

May 22th 2013

16th May of 2013

Figura1Investigation from the Spanish national Research Council (CSIC) has revealed new binding mechanisms of carbohydrates with quadruplex DNA. These results raise the possibility of developing carbohydrates as anticancer drugs.
DNA quadruplex structures are usually located at the telomeres (the end of chromosomes), thought they have been recently observed in oncogene promoters. In contrast with the well-known double helix, in these regions DNA adopts structures of quadruplex helix consisting of a square arrangement of guanines called tetrads.
  
Reference: Irene Gómez-Pinto, Empar Vengut-Climent, Ricardo Lucas, Anna Aviñó, Ramón Eritja, Carlos González, Juan Carlos Morales. Carbohydrate–DNA Interactions at G-Quadruplexes: Folding and Stability Changes by Attaching Sugars at the 5’-End. Chem. Eur. DOI: 10.1002/chem.201203902
http://onlinelibrary.wiley.com/doi/10.1002/chem.201203902/full

MJSanchezDue to their sessile nature, plants have to endure adverse environmental conditions, and in this context, soil salinity is a severe and increasing constraint on the productivity of agricultural crops.
The Arabidopsis thaliana Na+/H+ plasma membrane antiporter SOS1 is essential to maintain low intracellular levels of the toxic Na+ under salt stress, and it is considered a very interesting biotechnological target for crop improvement. Researchers from IQFR, Armando Albert and María José Sánchez-Barrena, in collaboration with groups from IEM and IRNAS (CSIC) have carried out in vivo, biochemical and electron microscopy studies to understand the three- dimensional structure of this critical protein for salt tolerance.

Reference: Structural insights on the plant Salt-Overly-Sensitive 1 (SOS1) Na+/H+ antiporter
Núñez-Ramírez R, Sánchez-Barrena MJ, Villalta I, Juan F. Vega, Pardo JM, Quintero FJ,  Martínez-Salazar J, Albert A. 
Journal of Molecular Biology (2012) 424, 283-294  (doi:10.1016/j.jmb.2012.09.015)

FRETThe use of commercial long-wavelength (>650 nm) laser dyes in many biophotonic applications has several important limitations, including low absorption at the standard pump wavelength (532 nm) and poor photostability. A research group headed by L. Cerdán from IQFR, in collaboration with researchers from Universidad Complutense de Madrid and Universidad del Pais Vasco, have demostrated that the use of Förster type (FRET) energy transfer can overcome these problems to enable efficient, stable near-IR lasing in a colloidal suspension of latex nanoparticles containing a mixture of Rhodamine 6G and Nile Blue dyes.


Reference: “FRET-assisted laser emission in colloidal suspensions of dye-doped latex nanoparticles,“ L. Cerdán,* E. Enciso, V. Martín, J. Bañuelos, I. Lopez Arbeloa, A. Costela and I. García-Moreno;  Nature Photonics 2012 DOI: 10.1038/ NPHOTON.2012.201
http://www.nature.com/nphoton/journal/vaop/ncurrent/full/nphoton.2012.201.html

 

FAFLife on Earth is based on nucleic acids that contain ribose (RNA) or deoxyribose (DNA) sugar moieties. However these are not the only polymers able to contain and transmit genetic information. It has been observed recently that, with the appropriated polymerases, nucleic acids based on other kind of sugars (such as arabinoses) can replicate.
So, why does nature use riboses? We do not know.
To help solve this problem, scientists from IQFR and McGill University in Montreal, funded by a CSIC I-link Project, have determined the structure of the “arabino nucleic acid” that it turned out to be very similar to our DNA.
Similar, but not identical. And the differences may be important, since they affect the stability of the double helix and other alternative structures. In addition, arabino-oligonucleotides and their fluoro-derivatives have very promising applications in biomedicine. In particular, they could prove very useful as they are resistant to ribonucleases, the enzymes which normally cleave and recycle nucleic acids, which in Earth have evolved to cleave nucleic acids based on ribose, but not in arabinose.
Referencia: The solution structure of double helical arabino nucleic acids (ANA and 2'F-ANA): effect of arabinoses in duplex-hairpin interconversion
Nerea Martin-Pintado et al., Nucleic Acids Res, 2012; doi: 10.1093/nar/gks672

evolucion imanacionA cobalt film two atoms thick has a magnetization direction perpendicular to the film plane when grown on ruthenium. Spin-polarized low-energy electron microscopy allows to observe its local magnetization, and follow in real time and real space changes in the magnetic domains of the film. When exposed to minute amounts of hydrogen, the out-of-plane magnetic domains in the film first break into smaller domains and eventually the magnetization direction switches on an in-plane orientation. The effect is understood with theoretical calculations that show that the origin is the change in the electronic structure of the topmost cobalt atoms bonded to hydrogen. This effect might be used to make gas sensors based on magnetic detection. The hydrogen pressure required for the effect is just one billionth of the atmospheric pressure, for a few minutes. Given the prevalence of hydrogen in ultra-high-vacuum experimental instruments, this effect also points to the risk hydrogen effects can pose for magnetization studies.
Reference: B. Santos, S. Gallego, A. Mascaraque, K.F. McCarty, A. Quesada, A.T. N’Diaye, A.K. Schmid, and J. de la Figuera. "Hydrogen-induced reversible spin-reorientation transition and magnetic stripe domain phase in bilayer Co on Ru(0001)",  Phys. Rev. B 85 (2012) 134409, DOI: 10.1103/PhysRevB.85.134409 (arxiv 1203.3945)

 

 

Graphene peq

A team at the Institute of Physical Chemistry "Rocasolano" in Madrid predicts that graphene – a layer of carbon just one atom thick – could be used to create a perfect absorber of light if it is doped and patterned into a periodic array. The work could lead to improved light-detection devices, particularly in the infrared part of the electromagnetic spectrum, where current technologies struggle to function.


Reference:Complete Optical Absorption in Periodically Patterned Graphene

http://physics.aps.org/articles/v5/12
http://nanotechweb.org/cws/article/tech/48463
http://physicsworld.com/cws/article/news/48464