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In its 85-year story, the mission of our institute has been to carry out excellence research in fundamental and applied physical chemistry, contributing to the scientific training of several generations of researchers at the highest level. Our vision is to be an international reference in multidisciplinary research focused on the resolution of the present challenges of our society in the fields of health, biotechnology, new materials, and environment.

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June 2018
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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)

 

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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/

 

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

 

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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.

 

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