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The 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)

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Category: Research

A 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

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TDP-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

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Monday, February 29th 2016, Madrid

Abstract book

Schedule

10:20 - 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

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A 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

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Crystallography 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.

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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.

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Category: Research

Tropospheric 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.