Network approach for capturing ligand-induced subtle global changes in protein structures

Ligand-induced conformational changes in proteins are of immense functional relevance. It is a major challenge to elucidate the network of amino acids that are responsible for the percolation of ligand-induced conformational changes to distal regions in the protein from a global perspective. Functionally important subtle conformational changes (at the level of side-chain noncovalent interactions) upon ligand binding or as a result of environmental variations are also elusive in conventional studies such as those using root-mean-square deviations (r.m.s.d.s). In this article, the network representation of protein structures and their analyses provides an efficient tool to capture these variations (both drastic and subtle) in atomistic detail in a global milieu. A generalized graph theoretical metric, using network parameters such as cliques and/or communities, is used to determine similarities or differences between structures in a rigorous manner. The ligand-induced global rewiring in the protein structures is also quantified in terms of network parameters. Thus, a judicious use of graph theory in the context of protein structures can provide meaningful insights into global structural reorganizations upon perturbation and can also be helpful for rigorous structural comparison. Data sets for the present study include high-resolution crystal structures of serine proteases from the S1A family and are probed to quantify the ligand-induced subtle structural variations.

Probing the structural changes in the phase transitions of a Bi2MoO6 catalyst: the nature of the intermediate-temperature phase

The nature of the phase transitions of Bi2MoO6 has been investigated by the combined use of X-ray diffraction and Xray absorption spectroscopy. The distorted MoO6 octahedra in the low-temperature form are shown to undergo further distortion in the intermediate-temperature form before transforming to MoO4 tetrahedra in the high-temperature phase. (C) 1995 Academic Press, Inc.

In vitro regeneration from immature cotyledon explant and protein profile changes during organogenesis in groundnut (Arachis hypogaea L.)

Complete plants were regenerated from in vitro cultured immature cotyledon segments of groundnut (Arachis hypogaea L. cv. TMV-7) by organogenesis. Callus cultures were best Initiated from immature cotyledon segments on MS (Murashige and Skoog) salts containing B5 vitamins supplemented with indole-3-acetic acid (IAA) and alpha -naphthalene acetic acid (NAA; 4.0 mg L-1) and kinetin (KIN; 0.5 L-1). Calluses were transferred to a medium containing KIN (2.0 mg L-1) and IAA and NAA (0.5 mg L-1) for shoot Initiation. The regenerated shoots were transferred to a medium containing Indole-3-butyric acid (IBA; 2.0 mg L-1) and KIN (0.2 mg L-1) for developing roots. In vitro produced plantlets developed sucessfully, matured, and set seed. The protein profiles [sodium dodecyl sulphate - polyacrylamide gel electrophoresis (SDS-PAGE)] of callus, callus with shoot, and callus with shoot and root showed differences.

Predictive uncertainty of chaotic daily streamflow using ensemble wavelet networks approach

Perfect or even mediocre weather predictions over a long period are almost impossible because of the ultimate growth of a small initial error into a significant one. Even though the sensitivity of initial conditions limits the predictability in chaotic systems, an ensemble of prediction from different possible initial conditions and also a prediction algorithm capable of resolving the fine structure of the chaotic attractor can reduce the prediction uncertainty to some extent. All of the traditional chaotic prediction methods in hydrology are based on single optimum initial condition local models which can model the sudden divergence of the trajectories with different local functions. Conceptually, global models are ineffective in modeling the highly unstable structure of the chaotic attractor. This paper focuses on an ensemble prediction approach by reconstructing the phase space using different combinations of chaotic parameters, i.e., embedding dimension and delay time to quantify the uncertainty in initial conditions. The ensemble approach is implemented through a local learning wavelet network model with a global feed-forward neural network structure for the phase space prediction of chaotic streamflow series. Quantification of uncertainties in future predictions are done by creating an ensemble of predictions with wavelet network using a range of plausible embedding dimensions and delay times. The ensemble approach is proved to be 50% more efficient than the single prediction for both local approximation and wavelet network approaches. The wavelet network approach has proved to be 30%-50% more superior to the local approximation approach. Compared to the traditional local approximation approach with single initial condition, the total predictive uncertainty in the streamflow is reduced when modeled with ensemble wavelet networks for different lead times. Localization property of wavelets, utilizing different dilation and translation parameters, helps in capturing most of the statistical properties of the observed data. The need for taking into account all plausible initial conditions and also bringing together the characteristics of both local and global approaches to model the unstable yet ordered chaotic attractor of a hydrologic series is clearly demonstrated.

Structural changes in single-walled carbon nanotubes under non-hydrostatic pressures: x-ray and Raman studies

Using in situ x-ray diffraction and Raman scattering techniques, we have investigated the behaviour of single-walled carbon nanotubes bundles under non-hydrostatic pressures. It is seen that the diffraction line corresponding to the two-dimensional triangular lattice in the bundles is not reversible for pressures beyond 5 GPa, in sharp contrast to earlier results under hydrostatic pressure conditions. Most interestingly, radial breathing and tangential Raman modes of the pressure-cycled samples from 21 and 30 GPa match very well with those of the starting sample. Raman and x-ray results put together clearly suggest that the ordering of tubes in the bundles is only marginally regained with a very short coherence length on decompression.

Affinity-Chromatographic Procedure For The Purification Of The Enzyme From Mung-Bean (Phaseolus, Aureus) Seeds And Conformational-Changes On Its Interaction With Ortho-Phosphate

Flavokinase was purified, for the first time from a plant source [mung bean (Phaseolus aureus)] by affinity chromatography in the presence of orthophosphate and by using C-8 ATP-agarose (ATP linked through the C-8 position to beaded agarose), Cibacron Blue and riboflavin--Sepharoses. An altered substrates-saturation pattern was observed in the presence of K2HPO4. The conformational changes of the enzyme in the presence of K2HPO4 were monitored by fluorescence spectroscopy. These results highlight the regulatory nature of this enzyme.

Influence of land use changes in river basins on diversity and distribution of amphibians

Land-use changes influence local biodiversity directly, and also cumulatively, contribute to regional and global changes in natural systems and quality of life. Consequent to these, direct impacts on the natural resources that support the health and integrity of living beings are evident in recent times. The Western Ghats being one of the global biodiversity hotspots, is reeling under a tremendous pressure from human induced changes in terms of developmental projects like hydel or thermal power plants, big dams, mining activities, unplanned agricultural practices,monoculture plantations, illegal timber logging, etc. This has led to the once contiguous forest habitats to be fragmented in patches, which in turn has led to the shrinkage of original habitat for the wildlife, change in the hydrological regime of the catchment, decreased inflow in streams,human-animal conflicts, etc. Under such circumstances, a proper management practice is called for requiring suitable biological indicators to show the impact of these changes, set priority regions and in developing models for conservation planning. Amphibians are regarded as one of the best biological indicators due to their sensitivity to even the slightest changes in the environment and hence they could be used as surrogates in conservation and management practices. They are the predominating vertebrates with a high degree of endemism (78%) in Western Ghats. The present study is an attempt to bring in the impacts of various land-uses on anuran distribution in three river basins. Sampling was carried out for amphibians during all seasons of 2003-2006 in basins of Sharavathi, Aghanashini and Bedthi. There are as many as 46 species in the region, one of which is new to science and nearly 59% of them are endemic to the Western Ghats. They belong to nine families, Dicroglossidae being represented by 14 species,followed by Rhacophoridae (9 species) and Ranidae (5 species). Species richness is high in Sharavathi river basin, with 36 species, followed by Bedthi 33 and Aghanashini 27. The impact of land-use changes, was investigated in the upper catchment of Sharavathi river basin. Species diversity indices, relative abundance values, percentage endemics gave clear indication of differences in each sub-catchment. Karl Pearson’s correlation coefficient (r) was calculated between species richness, endemics, environmental descriptors, land-use classes and fragmentation metrics. Principal component analysis was performed to depict the influence of these variables. Results show that sub-catchments with lesser percentage of forest, low canopy cover, higher amount of agricultural area, low rainfall have low species richness, less endemic species and abundant non-endemic species, whereas endemism, species richness and abundance of endemic species are more in the sub-catchments with high tree density, endemic trees, canopy cover, rainfall and lower amount of agriculture fields. This analysis aided in prioritising regions in the Sharavathi river basin for further conservation measures.

Conformational changes of the chaperone SecB upon binding to a model substrate - bovine pancreatic trypsin inhibitor (BPTI)

SecB is a homotetrameric cytosolic chaperone that forms part of the protein translocation machinery in E. coli. Due to SecB, nascent polypeptides are maintained in an unfolded translocation-competent state devoid of tertiary structure and thus are guided to the translocon. In vitro SecB rapidly binds to a variety of ligands in a non-native state. We have previously investigated the bound state conformation of the model substrate bovine pancreatic trypsin inhibitor (BPTI) as well as the conformation of SecB itself by using proximity relationships based on site-directed spin labeling and pyrene fluorescence methods. It was shown that SecB undergoes a conformational change during the process of substrate binding. Here, we generated SecB mutants containing but a single cysteine per subunit or an exposed highly reactive new cysteine after removal of the nearby intrinsic cysteines. Quantitative spin labeling was achieved with the methanethiosulfonate spin label (MTS) at positions C97 or E90C, respectively. Highfield (W-band) electron paramagnetic resonance (EPR) measurements revealed that with BPTI present the spin labels are exposed to a more polar/hydrophilic environment. Nanoscale distance measurements with double electron-electron resonance (DEER) were in excellent agreement with distances obtained by molecular modeling. Binding of BPTI also led to a slight change in distances between labels at C97 but not at E90C. While the shorter distance in the tetramer increased, the larger diagonal distance decreased. These findings can be explained by a widening of the tetrameric structure upon substrate binding much like the opening of two pairs of scissors.

Climate forcing and response to idealized changes in surface latent and sensible heat

Land use and land cover changes affect the partitioning of latent and sensible heat, which impacts the broader climate system. Increased latent heat flux to the atmosphere has a local cooling influence known as `evaporative cooling', but this energy will be released back to the atmosphere wherever the water condenses. However, the extent to which local evaporative cooling provides a global cooling influence has not been well characterized. Here, we perform a highly idealized set of climate model simulations aimed at understanding the effects that changes in the balance between surface sensible and latent heating have on the global climate system. We find that globally adding a uniform 1 W m(-2) source of latent heat flux along with a uniform 1 W m(-2) sink of sensible heat leads to a decrease in global mean surface air temperature of 0.54 +/- 0.04 K. This occurs largely as a consequence of planetary albedo increases associated with an increase in low elevation cloudiness caused by increased evaporation. Thus, our model results indicate that, on average, when latent heating replaces sensible heating, global, and not merely local, surface temperatures decrease.