Dimethyl sulfoxide induced structural transformations and non-monotonic concentration dependence of conformational fluctuation around active site of lysozyme

Experimental studies have observed significant changes in both structure and function of lysozyme (and other proteins) on addition of a small amount of dimethyl sulfoxide (DMSO) in aqueous solution. Our atomistic molecular dynamic simulations of lysozyme in water-DMSO reveal the following sequence of changes on increasing DMSO concentration. (i) At the initial stage (around 5% DMSO concentration) protein's conformational flexibility gets markedly suppressed. From study of radial distribution functions, we attribute this to the preferential solvation of exposed protein hydrophobic residues by the methyl groups of DMSO. (ii) In the next stage (10-15% DMSO concentration range), lysozome partially unfolds accompanied by an increase both in fluctuation and in exposed protein surface area. (iii) Between 15-20% concentration ranges, both conformational fluctuation and solvent accessible protein surface area suddenly decrease again indicating the formation of an intermediate collapse state. These results are in good agreement with near-UV circular dichroism (CD) and fluorescence studies. We explain this apparently surprising behavior in terms of a structural transformation which involves clustering among the methyl groups of DMSO. (iv) Beyond 20% concentration of DMSO, the protein starts its final sojourn towards the unfolding state with further increase in conformational fluctuation and loss in native contacts. Most importantly, analysis of contact map and fluctuation near the active site reveal that both partial unfolding and conformational fluctuations are centered mostly on the hydrophobic core of active site of lysozyme. Our results could offer a general explanation and universal picture of the anomalous behavior of protein structure-function observed in the presence of cosolvents (DMSO, ethanol, tertiary butyl alcohol, dioxane) at their low concentrations. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.3694268]

Smart polymer mediated purification and recovery of active proteins from inclusion bodies

Obtaining correctly folded proteins from inclusion bodies of recombinant proteins expressed in bacterial hosts requires solubilization with denaturants and a refolding step. Aggregation competes with the second step. Refolding of eight different proteins was carried out by precipitation with smart polymers. These proteins have different molecular weights, different number of disulfide bridges and some of these are known to be highly prone to aggregation. A high throughput refolding screen based upon fluorescence emission maximum around 340 nm (for correctly folded proteins) was developed to identify the suitable smart polymer. The proteins could be dissociated and recovered after the refolding step. The refolding could be scaled up and high refolding yields in the range of 8 mg L-1 (for CD4D12, the first two domains of human CD4) to 58 mg L-1 (for malETrx, thioredoxin fused with signal peptide of maltose binding protein) were obtained. Dynamic light scattering (DLS) showed that polymer if chosen correctly acted as a pseuclochaperonin and bound to the proteins. It also showed that the time for maximum binding was about 50 min which coincided with the time required for incubation (with the polymer) before precipitation for maximum recovery of folded proteins. The refolded proteins were characterized by fluorescence emission spectra, circular dichroism (CD) spectroscopy, melting temperature (T-m), and surface hydrophobicity measurement by ANS (8-anilinol-naphthalene sulfonic acid) fluorescence. Biological activity assay for thioredoxin and fluorescence based assay in case of maltose binding protein (MBP) were also carried out to confirm correct refolding. (C) 2012 Elsevier B.V. All rights reserved.

Enhancement of circular differential deflection of light in an optically active medium

In this letter, we investigate the circular differential deflection of a light beam refracted at the interface of an optically active medium. We show that the difference between the angles of deviation of the two circularly polarized components of the transmitted beam is enhanced manyfold near total internal reflection, which suggests a simple way of increasing the limit of detection of chiro-optical measurements. (C) 2012 Optical Society of America

Solvent effect on the fluorescence quenching of biologically active carboxamide by aniline and carbon tetrachloride in different solvents using S-V plots

The fluorescence quenching studies of carboxamide namely (E)-N-(3-Chlorophenyl)-2-(3,4,5-trimethoxybenzylideneamino)-4,5,6,7 tetrahydrobenzob]thiophene-3-carboxamide ENCTTTC] by aniline and carbon tetrachloride in six different solvents namely toluene, cyclohexane, n-hexane, n-heptane, n-decane and n-pentane have been carried out at room temperature with a view to understand the quenching mechanisms. The Stern-Volmer (S-V) plots have been found to be nonlinear with a positive deviation for all the solvents studied. In order to interpret these results we have invoked the ground state complex formation and sphere of action static quenching models. Using these models various quenching rate parameters have been determined. The magnitudes of these parameters suggest that sphere of action static quenching model agrees well with the experimental results. Hence the positive deviation is attributed to the static and dynamic quenching. Further, with the use of Finite Sink approximation model, it was possible to check these bimolecular reactions as diffusion-limited and to estimate independently distance parameter R' and mutual diffusion coefficient D. Finally an effort has been made to correlate the values of R' and D with the values of the encounter distance R and the mutual coefficient D determined using the Edward's empirical relation and Stokes Einstein relation. (C) 2011 Elsevier B.V. All rights reserved.

Cause and Effect of Feedback: Multiphase Gas in Cluster Cores Heated by AGN Jets

Multiwavelength data indicate that the X-ray-emitting plasma in the cores of galaxy clusters is not cooling catastrophically. To a large extent, cooling is offset by heating due to active galactic nuclei (AGNs) via jets. The cool-core clusters, with cooler/denser plasmas, show multiphase gas and signs of some cooling in their cores. These observations suggest that the cool core is locally thermally unstable while maintaining global thermal equilibrium. Using high-resolution, three-dimensional simulations we study the formation of multiphase gas in cluster cores heated by collimated bipolar AGN jets. Our key conclusion is that spatially extended multiphase filaments form only when the instantaneous ratio of the thermal instability and free-fall timescales (t(TI)/t(ff)) falls below a critical threshold of approximate to 10. When this happens, dense cold gas decouples from the hot intracluster medium (ICM) phase and generates inhomogeneous and spatially extended Ha filaments. These cold gas clumps and filaments ``rain'' down onto the central regions of the core, forming a cold rotating torus and in part feeding the supermassive black hole. Consequently, the self-regulated feedback enhances AGN heating and the core returns to a higher entropy level with t(TI)/t(ff) > 10. Eventually, the core reaches quasi-stable global thermal equilibrium, and cold filaments condense out of the hot ICM whenever t(TI)/t(ff) less than or similar to 10. This occurs despite the fact that the energy from AGN jets is supplied to the core in a highly anisotropic fashion. The effective spatial redistribution of heat is enabled in part by the turbulent motions in the wake of freely falling cold filaments. Increased AGN activity can locally reverse the cold gas flow, launching cold filamentary gas away from the cluster center. Our criterion for the condensation of spatially extended cold gas is in agreement with observations and previous idealized simulations.

Influence fields: a quantitative framework for representation and analysis of active dendrites

Rathour RK, Narayanan R. Influence fields: a quantitative framework for representation and analysis of active dendrites. J Neurophysiol 107: 2313-2334, 2012. First published January 18, 2012; doi:10.1152/jn.00846.2011.-Neuronal dendrites express numerous voltage-gated ion channels (VGICs), typically with spatial gradients in their densities and properties. Dendritic VGICs, their gradients, and their plasticity endow neurons with information processing capabilities that are higher than those of neurons with passive dendrites. Despite this, frameworks that incorporate dendritic VGICs and their plasticity into neurophysiological and learning theory models have been far and few. Here, we develop a generalized quantitative framework to analyze the extent of influence of a spatially localized VGIC conductance on different physiological properties along the entire stretch of a neuron. Employing this framework, we show that the extent of influence of a VGIC conductance is largely independent of the conductance magnitude but is heavily dependent on the specific physiological property and background conductances. Morphologically, our analyses demonstrate that the influences of different VGIC conductances located on an oblique dendrite are confined within that oblique dendrite, thus providing further credence to the postulate that dendritic branches act as independent computational units. Furthermore, distinguishing between active and passive propagation of signals within a neuron, we demonstrate that the influence of a VGIC conductance is spatially confined only when propagation is active. Finally, we reconstruct functional gradients from VGIC conductance gradients using influence fields and demonstrate that the cumulative contribution of VGIC conductances in adjacent compartments plays a critical role in determining physiological properties at a given location. We suggest that our framework provides a quantitative basis for unraveling the roles of dendritic VGICs and their plasticity in neural coding, learning, and homeostasis.

Potential G-quadruplex formation at breakpoint regions of chromosomal translocations in cancer may explain their fragility

Genetic alterations like point mutations, insertions, deletions, inversions and translocations are frequently found in cancers. Chromosomal translocations are one of the most common genomic aberrations associated with nearly all types of cancers especially leukemia and lymphoma. Recent studies have shown the role of non-B DNA structures in generation of translocations. In the present study, using various bioinformatic tools, we show the propensity of formation of different types of altered DNA structures near translocation breakpoint regions. In particular, we find close association between occurrence of G-quadruplex forming motifs and fragile regions in almost 70% of genes involved in rearrangements in lymphoid cancers. However, such an analysis did not provide any evidence for the occurrence of G-quadruplexes at the close vicinity of translocation breakpoint regions in nonlymphoid cancers. Overall, this study will help in the identification of novel non-B DNA targets that may be responsible for generation of chromosomal translocations in cancer. (C) 2012 Elsevier Inc. All rights reserved.

A drop of active matter

We study theoretically the hydrodynamics of a fluid drop containing oriented filaments endowed with active contractile or extensile stresses and placed on a solid surface. The active stresses alter qualitatively the wetting properties of the drop, leading to new spreading laws and novel static drop shapes. Candidate systems for testing our predictions include cytoskeletal extracts with motors and ATP, suspensions of bacteria or pulsatile cells, or fluids laden with artificial self-propelled colloids.

Comprehensive Probabilistic Seismic Hazard Analysis of the Andaman-Nicobar Regions

An updated catalog of earthquakes has been prepared for the Andaman-Nicobar and adjoining regions. The catalog was homogenized to a unified magnitude scale, and declustering of the catalog was performed to remove aftershocks and foreshocks. Eleven regional source zones were identified in the study area to account for local variability in seismicity characteristics. The seismicity parameters were estimated for each of these source zones, and the seismic hazard evaluation of the Andaman-Nicobar region has been performed using different source models and attenuation relations. Probabilistic seismic hazard analysis has been performed with currently available data and their best possible scientific interpretation using an appropriate instrument such as the logic tree to explicitly account for epistemic uncertainty by considering alternative models (source models, maximum magnitude, and attenuation relationships). The hazard maps for different periods have been produced for horizontal ground motion on the bedrock level.

Sequence and structural basis for chromosomal fragility during translocations in cancer

Chromosomal aberration is considered to be one of the major characteristic features in many cancers. Chromosomal translocation, one type of genomic abnormality, can lead to deregulation of critical genes involved in regulating important physiological functions such as cell proliferation and DNA repair. Although chromosomal translocations were thought to be random events, recent findings suggest that certain regions in the human genome are more susceptible to breakage than others. The possibility of deviation from the usual B-DNA conformation in such fragile regions has been an active area of investigation. This review summarizes the factors that contribute towards the fragility of these regions in the chromosomes, such as DNA sequences and the role of different forms of DNA structures. Proteins responsible for chromosomal fragility, and their mechanism of action are also discussed. The effect of positioning of chromosomes within the nucleus favoring chromosomal translocations and the role of repair mechanisms are also addressed.

Conformational dynamics of HIV-1 protease: a comparative molecular dynamics simulation study with multiple amber force fields

Flap dynamics of HIV-1 protease (HIV-pr) controls the entry of inhibitors and substrates to the active site. Dynamical models from previous simulations are not all consistent with each other and not all are supported by the NMR results. In the present work, the er effect of force field on the dynamics of HIV-pr is investigated by MD simulations using three AMBER force fields ff99, ff99SB, and ff03. The generalized order parameters for amide backbone are calculated from the three force fields and compared with the NMR S2 values. We found that the ff99SB and ff03 force field calculated order parameters agree reasonably well with the NMR S2 values, whereas ff99 calculated values deviate most from the NMR order parameters. Stereochemical geometry of protein models from each force field also agrees well with the remarks from NMR S2 values. However, between ff99SB and ff03, there are several differences, most notably in the loop regions. It is found that these loops are, in general, more flexible in the ff03 force field. This results in a larger active site cavity in the simulation with the ff03 force field. The effect of this difference in computer-aided drug design against flexible receptors is discussed.

Molecular probe dynamics reveals suppression of ice-like regions in strongly confined supercooled water

The structure of the hydrogen bond network is a key element for understanding water's thermodynamic and kinetic anomalies. While ambient water is strongly believed to be a uniform, continuous hydrogen-bonded liquid, there is growing consensus that supercooled water is better described in terms of distinct domains with either a low-density ice-like structure or a high-density disordered one. We evidenced two distinct rotational mobilities of probe molecules in interstitial supercooled water of polycrystalline ice Banerjee D, et al. (2009) ESR evidence for 2 coexisting liquid phases in deeply supercooled bulk water. Proc Natl Acad Sci USA 106: 11448-11453]. Here we show that, by increasing the confinement of interstitial water, the mobility of probe molecules, surprisingly, increases. We argue that loose confinement allows the presence of ice-like regions in supercooled water, whereas a tighter confinement yields the suppression of this ordered fraction and leads to higher fluidity. Compelling evidence of the presence of ice-like regions is provided by the probe orientational entropy barrier which is set, through hydrogen bonding, by the configuration of the surrounding water molecules and yields a direct measure of the configurational entropy of the same. We find that, under loose confinement of supercooled water, the entropy barrier surmounted by the slower probe fraction exceeds that of equilibrium water by the melting entropy of ice, whereas no increase of the barrier is observed under stronger confinement. The lower limit of metastability of supercooled water is discussed.

A Single-Stage Water-Gas Shift Reaction over Highly Active and Stable Si- and Al-Substituted Pt/CeO2 Catalysts

Ce0.88Si0.1Pt0.02O2-d and Ce0.88Al0.1Pt0.02O2-d catalysts were synthesized by using a low-temperature sonochemical method and characterized by using XRD, TEM, XPS, FTIR, and BET surface analyzer. The catalytic activities of these compounds were investigated for the watergas shift reaction in the temperature range of 140-440 degrees C. The substitution of Si in Ce0.98Pt0.02O2-d increased the releasing capacity of lattice oxygen, whereas the substitution of Al decreased the reducibility of Ce0.98Pt0.02O2-d, as evidenced by hydrogen temperature-programmed reduction studies. However, both the catalysts showed a considerable improvement in terms of activity and stability compared to Ce0.98Pt0.02O2-d. The combined activity measurement and characterization results suggest that the increase in the oxygen vacancy, which acts as a dissociation center for water, is the primary reason for the improvement in the activity of modified Ce0.98Pt0.02O2-d. Both the catalysts are 100?% selective toward H2 production, and approximately 99?% conversion of CO to CO2 was observed at 260 and 270 degrees C for Ce0.88Si0.1Pt0.02O2-d and Ce0.88Al0.1Pt0.02O2-d, respectively. These catalysts do not deactivate during the daily startup/shutdown operations and are sustainable even after prolonged reaction. Notably, these catalysts do not require any pretreatment or activation during startup/shutdown operations.

HIGH-RESOLUTION IMAGING OF THE ATLBS REGIONS: THE RADIO SOURCE COUNTS

The Australia Telescope Low-brightness Survey (ATLBS) regions have been mosaic imaged at a radio frequency of 1.4 GHz with 6 `' angular resolution and 72 mu Jy beam(-1) rms noise. The images (centered at R. A. 00(h)35(m)00(s), decl. -67 degrees 00'00 `' and R. A. 00(h)59(m)17(s), decl. -67.00'00 `', J2000 epoch) cover 8.42 deg(2) sky area and have no artifacts or imaging errors above the image thermal noise. Multi-resolution radio and optical r-band images (made using the 4 m CTIO Blanco telescope) were used to recognize multi-component sources and prepare a source list; the detection threshold was 0.38 mJy in a low-resolution radio image made with beam FWHM of 50 `'. Radio source counts in the flux density range 0.4-8.7 mJy are estimated, with corrections applied for noise bias, effective area correction, and resolution bias. The resolution bias is mitigated using low-resolution radio images, while effects of source confusion are removed by using high-resolution images for identifying blended sources. Below 1 mJy the ATLBS counts are systematically lower than the previous estimates. Showing no evidence for an upturn down to 0.4 mJy, they do not require any changes in the radio source population down to the limit of the survey. The work suggests that automated image analysis for counts may be dependent on the ability of the imaging to reproduce connecting emission with low surface brightness and on the ability of the algorithm to recognize sources, which may require that source finding algorithms effectively work with multi-resolution and multi-wavelength data. The work underscores the importance of using source lists-as opposed to component lists-and correcting for the noise bias in order to precisely estimate counts close to the image noise and determine the upturn at sub-mJy flux density.