Identification and purification of tRNAs containing N6-(delta 2-isopentenyl) adenosine using antibodies specific for N6-(delta-isopentenyl) adenosine

Antibodies specific for the modified nucleoside N6-(delta 2-isopentenyl) adenosine (i6A) were employed to identify the tRNAs containing i6A from an unfractionated tRNA mixture by a nitrocellulose filter binding assay. When radioactive aminoacyl-tRNAs were incubated with i6A-specific antibodies and filtered through nitrocellulose membrane filters, the tRNAs possessing i6A (tRNAtyr and tRNAser) remained on the filters. tRNAarg and tRNAlys which do not contain i6A showed no binding. This finding will be useful as a very simple and rapid assay of such RNAs under a variety of conditions. Purification of i6A containing tRNAs from an unfractionated tRNA mixture was achieved by affinity chromatography of the tRNAs on an i6A antibody-Sepharose column. Nonspecific binding of tRNAs to the column was avoided by the use of purified antibodies.

Brillouin Scattering Investigation of Solvation Dynamics in Succinonitrile-Lithium Salt Plastic Crystalline Electrolytes

Temperature dependent Brillouin scattering studies have been performed to ascertain the influence of solvent dynamics on ion-transport in succinonitrile-lithium salt plastic crystalline electrolytes. Though very rarely employed, we observe that Brillouin spectroscopy is an invaluable tool for investigation of solvent dynamics. Analysis of various acoustic (long wavelength) phonon modes observed in the Brillouin scattering spectra reveal the influence of trans-gauche isomerism and as well as ion-association effects on ion transport. Although pristine SN and dilute SN-LiClO(4) samples show only the bulk longitudinal-acoustic (LA) mode, concentrated SN-LiClO(4) (similar to 0.3-1 M) electrolytes display both the bulk LA mode as well as salt induced brillouin modes at ambient temperature. The appearance of more than one brillouin mode is attributed to the scattering of light from regions with different compressibilities (''compactness''). Correspondingly, these modes show a large decrease in the full width at half-maximum (abbreviated as nu(f)) as the temperature decreases. Anomalous temperature dependent behavior of nu(f) with addition of salt could be attributed to the presence of disorder or strong coupling with a neighbor. The shape of the spectrum was evaluated using a Lorentzian and Fano line shape function depending on the nature and behavior of the Brillouin modes.

Docking and free energy simulations to predict conformational domains involved in hCG-LH receptor interactions using recombinant antibodies

Single chain fragment variables (ScFvs) have been extensively employed in studying the protein-protein interactions. ScFvs derived from phage display libraries have an additional advantage of being generated against a native antigen, circumventing loss of information on conformational epitopes. In the present study, an attempt has been made to elucidate human chorionic gonadotropin (hCG)-luteinizing hormone (LH) receptor interactions by using a neutral and two inhibitory ScFvs against hCG. The objective was to dock a computationally derived model of these ScFvs onto the crystal structure of hCG and understand the differential roles of the mapped epitopes in hCG-LH receptor interactions. An anti-hCG ScFv, whose epitope was mapped previously using biochemical tools, served as the positive control for assessing the quality of docking analysis. To evaluate the role of specific side chains at the hCG-ScFv interface, binding free energy as well as residue interaction energies of complexes in solution were calculated using molecular mechanics Poisson-Boltzmann/surface area method after performing the molecular dynamic simulations on the selected hCG-ScFv models and validated using biochemical and SPR analysis. The robustness of these calculations was demonstrated by comparing the theoretically determined binding energies with the experimentally obtained kinetic parameters for hCG-ScFv complexes. Superimposition of hCG-ScFv model onto a model of hCG complexed with the 51-266 residues of LH receptor revealed importance of the residues previously thought to be unimportant for hormone binding and response. This analysis provides an alternate tool for understanding the structure-function analysis of ligand-receptor interactions. Proteins 2011;79:3108-3122. (C) 2011 Wiley-Liss, Inc.

On the mechanism of plastic flow at 86°k in quenched and aged aluminum

The plastic flow of quenched aluminium at 86°K was investigated by ‘differential-stress’ creep tests in order to evaluate the rate-controlling mechanism in as-quenched and fully aged states. The experimental values of activation volume (4·3 × 10−21 cm3 for as-quenched and 5·5×l0−21cm3 for fully aged) and the total energy for thermal activation process (0·4 ev for both) are in accordance with the jog hardening and loop hardening mechanisms in quenched and fully aged states respectively.

Dislocation mechanisms for plastic flow of nickel in the temperature range 4.2 – 1200 K

The temperature ranges of thermal and athermal deformation behaviour of nickel are identified by employing the temperature-dependence of flow-stress and strain-rate cycling data. The results are used to present a unified view of dislocation mechanisms of glide encompassing the two thermally activated and the intermediate athermal regimes of plastic flow.In the low-temperature thermally activated region (<250 K) the strain rate is found to be controlled by the repulsive intersection of glide and forest dislocations, in accordance with current ideas. The athermal stress in this region can be attributed mainly to the presence of strong attractive junctions which are overcome by means of Orowan bowing, a small contribution also coming from the elastic interactions between dislocations. The values of activation area and activation energy obtained in the high-temperature region (> 750 K) negate the operation of a diffusion-controlled mechanism. Instead, the data support a thermal activation model involving unzipping of the attractive junctions. The internal (long-range) stress contribution here results solely from the elastic interactions between dislocations. This view concerning the high-temperature plastic flow is further supported by the observation that the Cottrell–Stokes law is obeyed over large strains in the range 750–1200 K.

Effect of temperature on the plastic zone size and the shear band density in a bulk metallic glass

High temperature bonded interface indentation experiments are carried out on a Zr based bulk metallic glass (BMG) to examine the plastic deformation characteristics in subsurface deformation zone under a Vickers indenter. The results show that the shear bands are semi-circular in shape and propagate in radial direction. At all temperatures the inter-band spacing along the indentation axis is found to increase with increasing distance from the indenter tip. The average shear band spacing monotonically increases with temperature whereas the shear band induced plastic deformation zone is invariant with temperature. These observations are able to explain the increase in pressure sensitive plastic flow of BMGs with temperature. (C) 2011 Elsevier B.V. All rights reserved.

Insights into differential modulation of receptor function by hinge region using novel agonistic lutropin receptor and inverse agonistic thyrotropin receptor antibodies

We report two antibodies, scFv 13B1 and MAb PD1.37, against the hinge regions of LHR and TSHR, respectively, which have similar epitopes but different effects on receptor function. While neither of them affected hormone binding, with marginal effects on hormone response, scFv 13B1 stimulated LHR in a dose-dependent manner, whereas MAb PD1.37 acted as an inverse agonist of TSHR. Moreover, PD1.37 could decrease the basal activity of hinge region CAMs, but had varied effects on those present in ECLs, whereas 13B1 was refractory to any CAMs in LHR. Using truncation mutants and peptide phage display, we compared the differential roles of the hinge region cysteine box-2/3 as well as the exoloops in the activation of these two homologus receptors. (C) 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.