High-resolution NMR structure of an RNA model system : the 14-mer cUUCGg tetraloop hairpin RNA

We present a high-resolution nuclear magnetic resonance (NMR) solution structure of a 14-mer RNA hairpin capped by cUUCGg tetraloop. This short and very stable RNA presents an important model system for the study of RNA structure and dynamics using NMR spectroscopy, molecular dynamics (MD) simulations and RNA force-field development. The extraordinary high precision of the structure (root mean square deviation of 0.3 Å) could be achieved by measuring and incorporating all currently accessible NMR parameters, including distances derived from nuclear Overhauser effect (NOE) intensities, torsion-angle dependent homonuclear and heteronuclear scalar coupling constants, projection-angle-dependent cross-correlated relaxation rates and residual dipolar couplings. The structure calculations were performed with the program CNS using the ARIA setup and protocols. The structure quality was further improved by a final refinement in explicit water using OPLS force field parameters for non-bonded interactions and charges. In addition, the 2'-hydroxyl groups have been assigned and their conformation has been analyzed based on NOE contacts. The structure currently defines a benchmark for the precision and accuracy amenable to RNA structure determination by NMR spectroscopy. Here, we discuss the impact of various NMR restraints on structure quality and discuss in detail the dynamics of this system as previously determined

Timing of default from tuberculosis treatment: a systematic review

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73281/1/j.1365-3156.2008.02042.x.pd

High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA

We present a high-resolution nuclear magnetic resonance (NMR) solution structure of a 14-mer RNA hairpin capped by cUUCGg tetraloop. This short and very stable RNA presents an important model system for the study of RNA structure and dynamics using NMR spectroscopy, molecular dynamics (MD) simulations and RNA force-field development. The extraordinary high precision of the structure (root mean square deviation of 0.3 Å) could be achieved by measuring and incorporating all currently accessible NMR parameters, including distances derived from nuclear Overhauser effect (NOE) intensities, torsion-angle dependent homonuclear and heteronuclear scalar coupling constants, projection-angle-dependent cross-correlated relaxation rates and residual dipolar couplings. The structure calculations were performed with the program CNS using the ARIA setup and protocols. The structure quality was further improved by a final refinement in explicit water using OPLS force field parameters for non-bonded interactions and charges. In addition, the 2′-hydroxyl groups have been assigned and their conformation has been analyzed based on NOE contacts. The structure currently defines a benchmark for the precision and accuracy amenable to RNA structure determination by NMR spectroscopy. Here, we discuss the impact of various NMR restraints on structure quality and discuss in detail the dynamics of this system as previously determined

Interplay of ‘induced fit’ and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch

Riboswitches are highly structured elements in the 5′-untranslated regions (5′-UTRs) of messenger RNA that control gene expression by specifically binding to small metabolite molecules. They consist of an aptamer domain responsible for ligand binding and an expression platform. Ligand binding in the aptamer domain leads to conformational changes in the expression platform that result in transcription termination or abolish ribosome binding. The guanine riboswitch binds with high-specificity to guanine and hypoxanthine and is among the smallest riboswitches described so far. The X-ray-structure of its aptamer domain in complex with guanine/hypoxanthine reveals an intricate RNA-fold consisting of a three-helix junction stabilized by long-range base pairing interactions. We analyzed the conformational transitions of the aptamer domain induced by binding of hypoxanthine using high-resolution NMR-spectroscopy in solution. We found that the long-range base pairing interactions are already present in the free RNA and preorganize its global fold. The ligand binding core region is lacking hydrogen bonding interactions and therefore likely to be unstructured in the absence of ligand. Mg(2+)-ions are not essential for ligand binding and do not change the structure of the RNA-ligand complex but stabilize the structure at elevated temperatures. We identified a mutant RNA where the long-range base pairing interactions are disrupted in the free form of the RNA but form upon ligand binding in an Mg(2+)-dependent fashion. The tertiary interaction motif is stable outside the riboswitch context

Pointcatcher software:analysis of glacial time-lapse photography and integration with multi-temporal digital elevation models

Terrestrial time-lapse photography offers insight into glacial processes through high spatial and temporal resolution imagery. However, oblique camera views complicate measurement in geographic coordinates, and lead to reliance on specific imaging geometries or simplifying assumptions for calculating parameters such as ice velocity. We develop a novel approach that integrates time-lapse imagery with multi-temporal digital elevation models to derive full 3D coordinates for natural features tracked throughout a monoscopic image sequence. This enables daily independent measurement of horizontal (ice flow) and vertical (ice melt) velocities. By combining two terrestrial laser scanner surveys with a 73-day sequence from Sólheimajökull, Iceland, variations in horizontal ice velocity of ~10% were identified over timescales of ~25 days. An overall surface elevation decrease of ~3.0 m showed rate changes asynchronous with the horizontal velocity variations, demonstrating a temporal disconnect between the processes of ice surface lowering and mechanisms of glacier movement. Our software, ‘Pointcatcher’, is freely available for user-friendly interactive processing of general time-lapse sequences and includes Monte Carlo error analysis and uncertainty projection onto DEM surfaces. It is particularly suited for analysis of challenging oblique glacial imagery, and we discuss good features to track, both for correction of camera motion and for deriving ice velocities

Crystal packing arrangement, chain conformation, and physicochemical properties of gemfibrozil amine salts

Salt formation is used to optimize pharmaceutical properties for carboxylic acid drugs but selection can often be empirical. An extended series of salts of the anti-hyperlipidaemia carboxylic acid drug gemfibrozil was prepared using related series of amine counterions to gain a molecular insight into the impact of crystal packing arrangements on their physicochemical properties. With only a few exceptions, the salts had similar crystal packing motifs. Although there was no discernible relationship between melting point of the salt form and the aqueous solubility of the salt across the whole dataset, there were trends within structurally-related series of salts relating increasing melting enthalpy with increasing molecular weight of the counter ion

Interfacial effects on droplet dynamics in poiseuille flow

Many properties of emulsions arise from interfacial rheology, but a theoretical understanding of the effect of interfacial viscosities on droplet dynamics is lacking. Here we report such a theory, relating to isolated spherical drops in a Poiseuille flow. Stokes flow is assumed in the bulk phases, and a jump in hydrodynamic stress at the interface is balanced by Marangoni and surface viscous forces according to the Boussinesq–Scriven constitutive law. Our model employs a linear equation of state for the surfactant. Our analysis predicts slip, cross-stream migration and droplet-circulation velocities. These results and the corresponding interfacial parameters are separable: e.g., cross-stream migration occurs only if gradients in surfactant concentration are present; slip velocity depends on viscosity contrast and dilatational properties, but not on shear Boussinesq number. This separability allows a new and advantageous means to measure surface viscous and elastic forces directly from the drop interface