Protein oligomers studied by solid-state NMR the case of the full-length nucleoid-associated protein histone-like nucleoid structuring protein

Members of the histone-like nucleoid structuring protein (H-NS) family play roles both as architectural proteins and as modulators of gene expression in Gram-negative bacteria. The H-NS protein participates in modulatory processes that respond to environmental changes in osmolarity, pH, or temperature. H-NS oligomerization is essential for its activity. Structural models of different truncated forms are available. However, high-resolution structural details of full-length H-NS and its DNA-bound state have largely remained elusive. We report on progress in characterizing the biologically active H-NS oligomers with solid-state NMR. We compared uniformly ((13)C,(15)N)-labeled ssNMR preparations of the isolated N-terminal region (H-NS 1-47) and full-length H-NS (H-NS 1-137). In both cases, we obtained ssNMR spectra of good quality and characteristic of well-folded proteins. Analysis of the results of 2D and 3D (13)C-(13)C and (15)N-(13)C correlation experiments conducted at high magnetic field led to assignments of residues located in different topological regions of the free full-length H-NS. These findings confirm that the structure of the N-terminal dimerization domain is conserved in the oligomeric full-length protein. Small changes in the dimerization interface suggested by localized chemical shift variations between solution and solid-state spectra may be relevant for DNA recoginition.

Solid-phase synthesis and NMR studies of modified oligonucleotides forming triplex helix and of oligonucleopeptides mimicking the topoisomerase I-DNA covalent complex

Report for the scientific sojourn carried out at the Institut de Biologia Molecular de Barcelona of the CSIC –state agency – from april until september 2007. Topoisomerase I is an essential nuclear enzyme that modulates the topological status of DNA, facilitating DNA helix unwinding during replication and transcription. We have prepared the oligonucleotide-peptide conjugate Ac-NLeu-Asn-Tyr(p-3’TTCAGAAGC5’)-LeuC-CONH-(CH2)6-OH as model compound for NMR studies of the Topoisomerase I- DNA complex. Special attention was made on the synthetic aspects for the preparation of this challenging compound especially solid supports and protecting groups. The desired peptide was obtained although we did not achieve the amount of the conjugate needed for NMR studies. Most probably the low yield is due to the intrinsic sensitive to hydrolysis of the phosphate bond between oligonucleotide and tyrosine. We have started the synthesis and the structural characterization of oligonucleotides carrying intercalating compounds. At the present state we have obtained model duplex and quadruplex sequences modified with acridine and NMR studies are underway. In addition to this project we have successfully resolved the structure of a fusion peptide derived from hepatitis C virus envelope synthesized by the group of Dr. Haro and we have synthesized and started the characterization of a modified G-quadruplex.

New Radicals and new applications of Dynamic Nuclear Polarization of biological systems

Dynamic Nuclear Polarization (DNP) is an emerging technique that could revolutionize the NMR study of small molecules at very low concentrations by the increase in sensitivity that results from transfer of polarization between electronic and nuclear spins. Although the underlying physics has been known for a long time, in the last few years there has been a lot of excitement on the chemistry and biology NMR community caused by the demonstration that the highly polarized nuclei that are prepared in solid state at very low temperatures (1-2 K) could be rapidly transferred to liquid samples at room temperature and studied in solution by conventional NMR techniques. In favorable cases several order of magnitude increases in sensitivity have been achieved. The technique is now mature enough that a commercial instrument is available. The efficiency of DNP depends on two crucial aspects: i) the efficiency of the nuclear polarization process and ii) the efficiency of the transfer from the initial solid state to the fluid state in which NMR is measured. The preferred areas of application (iii) will be dictated by situations in which the low concentration of the sample or its intrinsic low receptivity are the limiting factors .

n=1/4 domain-growth universality class: Crossover to the n=1/2 class

The kinetic domain-growth exponent is studied by Monte Carlo simulation as a function of temperature for a nonconserved order-parameter model. In the limit of zero temperature, the model belongs to the n=(1/4 slow-growth unversality class. This is indicative of a temporal pinning in the domain-boundary network of mixed-, zero-, and finite-curvature boundaries. At finite temperature the growth kinetics is found to cross over to the Allen-Cahn exponent n=(1/2. We obtain that the pinning time of the zero-curvature boundary decreases rapidly with increasing temperature.

1.84 micron emission of Tm3+ sensitized by Yb3+ ions in monoclinic KGd(WO4)2 single crystals

By exciting at 940 nm, we have characterized the 1.84 m near infrared emission of trivalent thulium ions in Yb3+, Tm3+:KGd WO4 2 single crystals as a function of the dopant concentration and temperature, from 10 K to room temperature. An overall 3H6 Stark splitting of 470 cm−1 for the Tm3+ ions in the Yb3+, Tm3+:KGd WO4 2 was obtained. We also studied the blue emission at 476 nm Tm3+ and the near infrared emissions at 1.48 m Tm3+ and 1 m Yb3+ as a function of the dopant concentration. Experimental decay times of the 1G4, 3H4, and 3F4 Tm3+ and 2F5/2 Yb3+ excited states have been measured as a function of Yb3+ and Tm3+ ion concentrations. For the 3F4 →3H6 transition of Tm3+ ions, we used the reciprocity method to calculate the maximum emission cross section of 3.07 10−20 cm2 at 1.84 m for the polarization parallel to the Nm principal optical direction.

Preparació de materials híbrids orgànico-inorgànics a partir de sals d'imidazoli

Estudi elaborat a partir d’una estada a l’ Ecole Nationale Supérieure de Chimie de Montpellier, França, durant 2006. S’han sintetitzat materials híbrids orgànico-inorgànics mitjançant el procés sol-gel i altres estratègies sintètiques. En alguns casos, s’ha intentat estructurar aquests materials, ja sigui per autoestructuració o per mitjà de tensioactius. Com a catalitzadors de les reaccions d'hidròlisi i policondensació s’han utilitzat àcids, bases i fluorurs. Els materials obtinguts s’han caracteritzat mitjançant diferents tècniques: BET (Brunauer-Emmett-Teller), TEM (microscopia electrònica de transmissió), SEM (microscòpia electrònica de rastreig), raigs X en pols , IR i RMN (ressonància magnètica nuclear) en estat sòlid. Amb aquests materials es pretén preparar catalitzadors heterogenis de Pd per reaccions d’acoblament creuat, i de Ru per reaccions de metàtesi. També s’han sintetitzat sals d'imidazoli amb cadenes hidrocarbonades llargues amb l'objectiu de preparar gels de sílice amb aquestes molècules atrapades dins la matriu inorgànica. Aquests materials s’utilitzaran com a organocatalitzadors i també es prepararan els corresponents catalitzadors de Pd per reaccions de Heck, Suzuki i Sonogashira. Les sals d’imidazoli s’han utilitzat com a tensioactius en la preparació de gels de sílice estructurats. Aquestes molècules han resultat ser cristalls líquids i s’han caracteritzar mitjançant DSC (differential scanning calorimetry), microscopia òptica i raigs X.

Semiclassical image potential at a solid surface

A surface dielectric function of a semi-infinite plane-bounded metal is defined in the spirit of the plasmon-pole dielectric function of the bulk. It is modeled in such a way that the surface-plasmon dispersion relation is recovered for small momentum transfer. This function is employed to compute the image potential at all distances outside the surface. Interaction with bulk modes is neglected for simplicity and clarity. The interaction of a massive point charge with a metal surface is also considered in the context of a boson model for surface-plasmon excitation. We present a new definition of the image potential for this case.

Strongly correlated states of ultracold rotating dipolar Fermi gases

We study strongly correlated ground and excited states of rotating quasi-2D Fermi gases constituted of a small number of dipole-dipole interacting particles with dipole moments polarized perpendicular to the plane of motion. As the number of atoms grows, the system enters an intermediate regime, where ground states are subject to a competition between distinct bulk-edge configurations. This effect obscures their description in terms of composite fermions and leads to the appearance of novel quasihole ground states. In the presence of dipolar interactions, the principal Laughlin state at filling upsilon=1/3 exhibits a substantial energy gap for neutral (total angular momentum conserving) excitations and is well-described as an incompressible Fermi liquid. Instead, at lower fillings, the ground state structure favors crystalline order.

Evidence of the anomalous charge state 57Fe4+ in the nuclear decay of 57Co3+

The first observation of the elusive Fe4+ charge state coming from the nuclear decay of 57Co3+ has been found in the Mössbauer emission spectra of 57Co:La2Li0.5Co0.5O4. A Ti-doped sample was prepared in order to show that the Fe4+ fraction can be conveniently monitored. Both results were predicted on the basis of the electronic energy-band scheme of these oxides.

Vortex state and effect of anisotropy in sub-100 nm magnetic nanodots

Magnetic properties of Fe nanodots are simulated using a scaling technique and Monte Carlo method, in good agreement with experimental results. For the 20-nm-thick dots with diameters larger than 60¿nm, the magnetization reversal via vortex state is observed. The role of magnetic interaction between dots in arrays in the reversal process is studied as a function of nanometric center-to-center distance. When this distance is more than twice the dot diameter, the interaction can be neglected and the magnetic properties of the entire array are determined by the magnetic configuration of the individual dots. The effect of crystalline anisotropy on the vortex state is investigated. For arrays of noninteracting dots, the anisotropy strongly affects the vortex nucleation field and coercivity, and only slightly affects the vortex annihilation field

Detection of millimetric deformation using a terrestrial laser scanner: experiment and application to a rockfall event

Terrestrial laser scanning (TLS) is one of the most promising surveying techniques for rockslope characterization and monitoring. Landslide and rockfall movements can be detected by means of comparison of sequential scans. One of the most pressing challenges of natural hazards is combined temporal and spatial prediction of rockfall. An outdoor experiment was performed to ascertain whether the TLS instrumental error is small enough to enable detection of precursory displacements of millimetric magnitude. This consists of a known displacement of three objects relative to a stable surface. Results show that millimetric changes cannot be detected by the analysis of the unprocessed datasets. Displacement measurement are improved considerably by applying Nearest Neighbour (NN) averaging, which reduces the error (1¿) up to a factor of 6. This technique was applied to displacements prior to the April 2007 rockfall event at Castellfollit de la Roca, Spain. The maximum precursory displacement measured was 45 mm, approximately 2.5 times the standard deviation of the model comparison, hampering the distinction between actual displacement and instrumental error using conventional methodologies. Encouragingly, the precursory displacement was clearly detected by applying the NN averaging method. These results show that millimetric displacements prior to failure can be detected using TLS.

Rockfall monitoring by Terrestrial Laser Scanning ¿ case study of the basaltic rock face at Castellfollit de la Roca (Catalonia, Spain)

This case study deals with a rock face monitoring in urban areas using a Terrestrial Laser Scanner. The pilot study area is an almost vertical, fifty meter high cliff, on top of which the village of Castellfollit de la Roca is located. Rockfall activity is currently causing a retreat of the rock face, which may endanger the houses located at its edge. TLS datasets consist of high density 3-D point clouds acquired from five stations, nine times in a time span of 22 months (from March 2006 to January 2008). The change detection, i.e. rockfalls, was performed through a sequential comparison of datasets. Two types of mass movement were detected in the monitoring period: (a) detachment of single basaltic columns, with magnitudes below 1.5 m3 and (b) detachment of groups of columns, with magnitudes of 1.5 to 150 m3. Furthermore, the historical record revealed (c) the occurrence of slab failures with magnitudes higher than 150 m3. Displacements of a likely slab failure were measured, suggesting an apparent stationary stage. Even failures are clearly episodic, our results, together with the study of the historical record, enabled us to estimate a mean detachment of material from 46 to 91.5 m3 year¿1. The application of TLS considerably improved our understanding of rockfall phenomena in the study area.

Rockfall monitoring by Terrestrial Laser Scanning ¿ case study of the basaltic rock face at Castellfollit de la Roca (Catalonia, Spain)

This case study deals with a rock face monitoring in urban areas using a Terrestrial Laser Scanner. The pilot study area is an almost vertical, fifty meter high cliff, on top of which the village of Castellfollit de la Roca is located. Rockfall activity is currently causing a retreat of the rock face, which may endanger the houses located at its edge. TLS datasets consist of high density 3-D point clouds acquired from five stations, nine times in a time span of 22 months (from March 2006 to January 2008). The change detection, i.e. rockfalls, was performed through a sequential comparison of datasets. Two types of mass movement were detected in the monitoring period: (a) detachment of single basaltic columns, with magnitudes below 1.5 m3 and (b) detachment of groups of columns, with magnitudes of 1.5 to 150 m3. Furthermore, the historical record revealed (c) the occurrence of slab failures with magnitudes higher than 150 m3. Displacements of a likely slab failure were measured, suggesting an apparent stationary stage. Even failures are clearly episodic, our results, together with the study of the historical record, enabled us to estimate a mean detachment of material from 46 to 91.5 m3 year¿1. The application of TLS considerably improved our understanding of rockfall phenomena in the study area.