Theoretical study of a new molecular ion species BeN: molecular states and cross sections for electronic excitation and dissociation.

We present here a theoretical study of a new molecular ion species BeN, which has not been reported before. Using a good quality configuration interaction model, we first undertake a configuration interaction calculation of the molecular states to obtain the potential energy curves of several low lying states of BeN and the dipole and transition dipole moments of some of its states as a function of the internuclear distance. We find the ground state to be bound and of X Σ character having a shallow minimum at = 2.

Bifurcations in coupled amyloid-β aggregation-inflammation systems.

A complex interplay between various processes underlies the neuropathology of Alzheimer's disease (AD) and its progressive course. Several lines of evidence point to the coupling between Aβ aggregation and neuroinflammation and its role in maintaining brain homeostasis during the long prodromal phase of AD. Little is however known about how this protective mechanism fails and as a result, an irreversible and progressive transition to clinical AD occurs.

Assessment and mitigation of radiation hazard for individuals engaged in reconnaissance survey in uranium exploration in Jharkhand, India.

The present study attempts to obtain an a priori estimate of the absorbed dose received by an individual engaged in the reconnaissance survey in Uranium exploration using a predictive mathematical regression analysis. Other radiation safety parameters such as excess lifetime cancer risk are also calculated. Study reflects that the proper handling of naturally occurring radioactive materials accounts for an absorbed dose significantly less than the prescribed limit.

Reactive collisions between electrons and BeH above dissociation threshold.

Our previous studies of dissociative recombination and vibrational excitation/de-excitation of the BeH ion, based on the multichannel quantum defect theory, are extended to collision energies above the dissociation threshold, taking into account the vibrational continua of the BeH ion and, consequently, its dissociative excitation. We have also significantly increased the number of dissociative states of Π, Σ and Δ symmetry included in our cross section calculations, generating the most excited ones by using appropriate scaling laws. Our results are suitable for modeling the kinetics of BeH in edge fusion plasmas for collision energies up to 12 eV.

A litmus test for classifying recognition mechanisms of transiently binding proteins.

Partner recognition in protein binding is critical for all biological functions, and yet, delineating its mechanism is challenging, especially when recognition happens within microseconds. We present a theoretical and experimental framework based on straight-forward nuclear magnetic resonance relaxation dispersion measurements to investigate protein binding mechanisms on sub-millisecond timescales, which are beyond the reach of standard rapid-mixing experiments. This framework predicts that conformational selection prevails on ubiquitin's paradigmatic interaction with an SH3 (Src-homology 3) domain.

Repositioning Food and Drug Administration-Approved Drugs for Inhibiting Biliverdin IXβ Reductase B as a Novel Thrombocytopenia Therapeutic Target.

Biliverdin IXβ reductase B (BLVRB) has recently been proposed as a novel therapeutic target for thrombocytopenia through its reactive oxygen species (ROS)-associated mechanism. Thus, we aim at repurposing drugs as new inhibitors of BLVRB. Based on IC (<5 μM), we have identified 20 compounds out of 1496 compounds from the Food and Drug Administration (FDA)-approved library and have clearly mapped their binding sites to the active site.

Aromatic Interactions Drive the Coupled Folding and Binding of the Intrinsically Disordered Virus VPg Protein.

The plant virus [a (+)-ssRNA sobemovirus] VPg protein is intrinsically disordered in solution. For the virus life cycle, the VPg protein is essential for replication and for polyprotein processing that is carried out by a virus-encoded protease. The nuclear magnetic resonance (NMR)-derived tertiary structure of the protease-bound VPg shows it to have a novel tertiary structure with an α-β-β-β topology.

Dopamine promotes the neurodegenerative potential of β-synuclein.

A contribution of α-Synuclein (α-Syn) to etiology of Parkinson´s disease (PD) and Dementia with Lewy bodies (DLB) is currently undisputed, while the impact of the closely related β-Synuclein (β-Syn) on these disorders remains enigmatic. β-Syn has long been considered to be an attenuator of the neurotoxic effects of α-Syn, but in a rodent model of PD β-Syn induced robust neurodegeneration in dopaminergic neurons of the substantia nigra. Given that dopaminergic nigral neurons are selectively vulnerable to neurodegeneration in PD, we now investigated if dopamine can promote the neurodegenerative potential of β-Syn.

Conformational Dynamics and Allostery in E2:E3 Interactions Drive Ubiquitination: gp78 and Ube2g2.

Conformational dynamics plays a fundamental role in molecular recognition and activity in enzymes. The ubiquitin-conjugating enzyme (E2) Ube2g2 functions with the ubiquitin ligase (E3) gp78 to assemble poly-ubiquitin chains on target substrates. Two domains in gp78, RING and G2BR, bind to two distant regions of Ube2g2, and activate it for ubiquitin (Ub) transfer.

High-power (1)H composite pulse decoupling provides artifact free exchange-mediated saturation transfer (EST) experiments.

Exchange-mediated saturation transfer (EST) provides critical information regarding dynamics of molecules. In typical applications EST is studied by either scanning a wide range of (15)N chemical shift offsets where the applied (15)N irradiation field strength is on the order of hundreds of Hertz or, scanning a narrow range of (15)N chemical shift offsets where the applied (15)N irradiation field-strength is on the order of tens of Hertz during the EST period. The (1)H decoupling during the EST delay is critical as incomplete decoupling causes broadening of the EST profile, which could possibly result in inaccuracies of the extracted kinetic parameters and transverse relaxation rates.

Conformational Selection in a Protein-Protein Interaction Revealed by Dynamic Pathway Analysis.

Molecular recognition plays a central role in biology, and protein dynamics has been acknowledged to be important in this process. However, it is highly debated whether conformational changes happen before ligand binding to produce a binding-competent state (conformational selection) or are caused in response to ligand binding (induced fit). Proposals for both mechanisms in protein/protein recognition have been primarily based on structural arguments.

Assessment of changes in community level physiological profile and molecular diversity of bacterial communities in different stages of jute retting.

Retting of jute is essentially microbiological and biochemical in nature. Community Level Physiological Profiles (CLPP) as well as genomic diversity of bacterial communities were assessed in water samples collected during pre-retting, after 1st and 2nd charges of retting. The water samples were collected from two widely cultivated jute growing locations, Sonatikari (22 degrees 41'27"N; 88 degrees 35'44"E) and Baduria (22 degrees 44'24"N; 88 degrees 47'24"E), West Bengal, India.

A highly conserved cysteine of neuronal calcium-sensing proteins controls cooperative binding of Ca2+ to recoverin.

Recoverin, a 23-kDa Ca(2+)-binding protein of the neuronal calcium sensing (NCS) family, inhibits rhodopsin kinase, a Ser/Thr kinase responsible for termination of photoactivated rhodopsin in rod photoreceptor cells. Recoverin has two functional EF hands and a myristoylated N terminus. The myristoyl chain imparts cooperativity to the Ca(2+)-binding sites through an allosteric mechanism involving a conformational equilibrium between R and T states of the protein.

Studies on non-symbiotic diazotrophic bacterial populations of coastal arable saline soils of India.

The effect of fluctuations of salinity in three different seasons on diazotrophic populations and N(2) fixation in six mono cropped rice field soils of the coastal region of the Gangetic delta of West Bengal, India, was studied. The average pH, ECe, organic carbon and total nitrogen of the soils ranged from 4.99-7.

Low aqueous solubility of 11-cis-retinal limits the rate of pigment formation and dark adaptation in salamander rods.

We report experiments designed to test the hypothesis that the aqueous solubility of 11-cis-retinoids plays a significant role in the rate of visual pigment regeneration. Therefore, we have compared the aqueous solubility and the partition coefficients in photoreceptor membranes of native 11-cis-retinal and an analogue retinoid, 11-cis 4-OH retinal, which has a significantly higher solubility in aqueous medium. We have then correlated these parameters with the rates of pigment regeneration and sensitivity recovery that are observed when bleached intact salamander rod photoreceptors are treated with physiological solutions containing these retinoids.

Characterization and crop production efficiency of diazotrophic bacterial isolates from coastal saline soils.

Use of eco-friendly area specific salt tolerant bioinoculants is better alternatives to chemical fertilizer for sustainable agriculture in coastal saline soils. We isolated diverse groups of diazotrophic bacteria from coastal saline soils of different forest and agricultural lands in the Sundarbans, West Bengal, India, to study their effect on crop productivity in saline soils. Phenotypic, biochemical and molecular identifications of the isolates were performed.

Culture independent molecular analysis of bacterial communities in the mangrove sediment of Sundarban, India.

Background: Sundarban is the world's largest coastal sediment comprising of mangrove forest which covers about one million hectares in the south-eastern parts of India and southern parts of Bangladesh. The microbial diversity in this sediment is largely unknown till date. In the present study an attempt has been made to understand the microbial diversity in this sediment using a cultivation-independent molecular approach.

X-ray crystallographic and NMR studies of pantothenate synthetase provide insights into the mechanism of homotropic inhibition by pantoate.

The structural basis for the homotropic inhibition of pantothenate synthetase by the substrate pantoate was investigated by X-ray crystallography and high-resolution NMR spectroscopic methods. The tertiary structure of the dimeric N-terminal domain of Escherichia coli pantothenate synthetase, determined by X-ray crystallography to a resolution of 1.7 A, showed a second molecule of pantoate bound in the ATP-binding pocket.

Fractionation and bioavailability of metals and their impacts on microbial properties in sewage irrigated soil.

A study was conducted to evaluate the effect of long-term irrigation of sewage contaminated with heavy metals like Cd, Cr, Cu and Pb on microbial and biochemical parameters of soils of West Bengal, India. The microbial parameters included microbial biomass carbon (MBC), microbial metabolic quotient; the biochemical parameters included fluorescein diacetate hydrolyzing activity, beta-glucosidase, urease, phosphatase, and aryl sulphatase activities. A sequential extraction technique was used to quantify water soluble, exchangeable, carbonate bound, Fe/Mn-oxide bound, organically bound, and residual metal fractions.

Pesticide residue level in tea ecosystems of Hill and Dooars regions of West Bengal, India.

In the present study we quantified the residues of organophosphorus (e.g. ethion and chlorpyrifos), organochlorine (e.

Stability and dynamics of domain-swapped bovine-seminal ribonuclease.

The proteins of the ribonuclease-A (RNase-A) family are monomeric, with the exception of bovine-seminal ribonuclease (BS-RNase). BS-RNase is formed by swapping the N-terminal helices across the two monomeric units. A molecular-dynamics (MD) study has been performed on the protein for a simulation time of 5.

Pencycuron dissipation in soil: effect of application rate and soil conditions.

Dissipation of the fungicide pencycuron was examined under controlled laboratory conditions in clay loam soils from rice cultivated fields of alluvial soil (Typic udifluvent) and coastal saline soil (Typic endoaquept) at field rate, twice the field rate and 10 times the field rate with and without decomposed cow manure maintained at 60% of maximum water-holding capacity (WHC) and waterlogged soil condition. The half-life values depended on the initial concentrations of pencycuron. Pencycuron, in general, degraded fastest in coastal saline soil and in soil amended with decomposed cow manure at 60% of maximum WHC of soil.

High level expression of peptides and proteins using cytochrome b5 as a fusion host.

A novel fusion protein system based on the highly soluble heme-binding domain of cytochrome b5 has been designed. The ability of cytochrome b5 to increase the levels of expression and solubility of target proteins has been tested by expressing several proteins and peptides, viz., alpha hemoglobin stabilizing protein, the regulatory subunits of acetohydroxy acid synthase I (ilvM) and II (ilvN), the carboxy terminal domains of mouse neuronal kinesin and pantothenate synthatase, two peptide toxins from cone snails, and the inactivation gate from the brain voltage gated sodium channel, NaV1.