Homology modelling of the Frankia nitrogenase iron protein

The NifH protein contains an iron-sulfur cluster performing different functions during nitrogen fixation. Frankia is an actinomycete, entering into symbiotic association with a number of dicotyledonous plants and fixing nitrogen. The structure of the Frankia NifH protein was determined using homology modelling technique. Metal binding sites and functionally important regions of the protein were analyzed. Thiol ligands and active sites help in protein functioning and conformations. Structurally important nests were recognized. Clefts and cavities contain biologically important residues. Site-directed mutagenesis results reveal that mutations in functional residues hamper nitrogen fixation. The structure is rigid with an accessible surface for solvents. The structure is reliable offering insights into the 3D structural framework as well as structure-function relation of NifH protein.     

Selectable antibiotic resistance marker gene-free transgenic rice harbouring the garlic leaf lectin gene exhibits resistance to sap-sucking planthoppers

Rice, the major food crop of world is severely affected by homopteran sucking pests. We introduced coding sequence of Allium sativum leaf agglutinin, ASAL, in rice cultivar IR64 to develop sustainable resistance against sap-sucking planthoppers as well as eliminated the selectable antibiotic-resistant marker gene hygromycin phosphotransferase (hpt) exploiting cre/lox site-specific recombination system. An expression vector was constructed containing the coding sequence of ASAL, a potent controlling agent against green leafhoppers (GLH, Nephotettix virescens) and brown planthopper (BPH, Nilaparvata lugens). The selectable marker (hpt) gene cassette was cloned within two lox sites of the same vector. Alongside, another vector was developed with chimeric cre recombinase gene cassette. Reciprocal crosses were performed between three single-copy T₀ plants with ASAL- lox-hpt-lox T-DNA and three single-copy T₀ plants with cre-bar T-DNA. Marker gene excisions were detected in T₁ hybrids through hygromycin sensitivity assay. Molecular analysis of T₁ plants exhibited 27.4% recombination efficiency. T₂ progenies of L03C04(1) hybrid parent showed 25% cre negative ASAL-expressing plants. Northern blot, western blot and ELISA showed significant level of ASAL expression in five marker-free T₂ progeny plants. In planta bioassay of GLH and BPH performed on these T₂ progenies exhibited radical reduction in survivability and fecundity compared with the untransformed control plants.     

Synthesis, structure and solution chemistry of dioxidovanadium(V) complexes with a family of hydrazone ligands. Evidence of formation of centrosymmetric dimers via H-bonds in the solid state

[V^IVO(acac)₂] reacts with the methanol solution of tridentate ONO donor hydrazone ligands (H₂L^1-4, general abbreviation H₂L; are derived from the condensation of benzoyl hydrazine with 2-hydroxyacetophenone and its 5-substituted derivatives) in presence of neutral monodentate alkyl amine bases having stronger basicity than pyridine e.g., ethylamine, diethylamine, triethylamine and piperidine (general abbreviation B) to produce BH⁺[VO₂L]⁻ (1-16) complexes. Five of these sixteen complexes are structurally characterized revealing that the vanadium is present in the anionic part of the molecule, [VO₂L]⁻ in a distorted square pyramidal environment. The complexes 5, 6, 15 and 16 containing two H-atoms associated with the amine-N atom in their cationic part (e.g., diethylammonium and piperidinium ion) are involved in H-bonding with a neighboring molecule resulting in the formation of centrosymmetric dimers while the complex 12 (containing only one hydrogen atom in the cationic part) exhibits normal H-bonding. The nature of the H-bonds in each of the four centrosymmetric dimeric complexes is different. These complexes have potential catalytic activity in the aerial oxidation of l-ascorbic acid and are converted into the [VO(L)(hq)] complexes containing VO³⁺ motif on reaction with equimolar amount of 8-hydroxyquinoline (Hhq) in methanol.     

Copper-thioarylazoimidazole complexes: Structures, photochromism and redox interconversion between Cu(II) ↔ Cu(I) and correlation with DFT calculation

Reaction of Cu(ClO₄)₂·6H₂O, SRaaiNR′ (1-alkyl-2-[(o-thioalkyl)phenylazo]imidazole) and NH₄SCN (1:1:2 mol ratio) affords distorted square pyramidal, [Cu^II(SRaaiNR′)(SCN)₂] (3) compound while identical reaction with [Cu(MeCN)₄](ClO₄) yields -SCN- bridged coordination polymer, [Cu^I(SRaaiNR′)(SCN)]_n (4). These two redox states [Cu^II and Cu^I] are interconvertible; reduction of [Cu^II(SRaaiNR′)(SCN)₂] by ascorbic acid yields [Cu^I(SRaaiNR′)(SCN)]_n while the oxidation of [Cu^I(SRaaiNR′)(SCN)]_n by H₂O₂ in presence of excess NH₄SCN affords [Cu^II(SRaaiNR′)(SCN)₂]. They are structurally confirmed by single crystal X-ray diffraction study. Cyclic voltammogram of the complexes show Cu(II)/Cu(I) redox couple at ∼0.4 V and azo reductions at negative to SCE. UV light irradiation in MeCN solution of [Cu^I(SRaaiNR′)(SCN)]_n (4) show trans-to-cis isomerisation of coordinated azoimidazole. The reverse transformation, cis-to-trans, is very slow with visible light irradiation while the process is thermally accessible. Quantum yields (?_t→c) of trans-to-cis isomerisation are calculated and free ligands show higher ? than their Cu(I) complexes. The activation energy (E_a) of cis-to-trans isomerisation is calculated by controlled temperature experiment. Copper(II) complexes, 3, do not show photochromism. DFT and TDDFT calculation of representative complexes have been used to determine the composition and energy of molecular levels and results have been used to explain the solution spectra, photochromism and redox properties of the complexes.     

The affinity concept in bioseparation: evolving paradigms and expanding range of applications

The meaning of the word affinity in the context of protein separation has undergone evolutionary changes over the years. The exploitation of molecular recognition phenomenon is no longer limited to affinity chromatography modes. Affinity based separations today include precipitation, membrane based purification and two-phase/three-phase extractions. Apart from the affinity ligands, which have biological relationship (in vivo) with the target protein, a variety of other ligands are now used in the affinity based separations. These include dyes, chelated metal ions, peptides obtained by phage display technology, combinatorial synthesis, ribosome display methods and by systematic evolution of ligands by exponential enrichment (SELEX). Molecular modeling techniques have also facilitated the designing of biomimetic ligands. Fusion proteins obtained by recombinatorial methods have emerged as a powerful approach in bioseparation. Overexpression in E. coli often result in inactive and insoluble inclusion bodies. A number of interesting approaches are used for simultaneous refolding and purification in such cases. Proteomics also needs affinity chromatography to reduce the complexity of the system before analysis by electrophoresis and mass spectrometry are made. At industrial level, validation, biosafety and process hygiene are also important aspects. This overview looks at these evolving paradigms and various strategies which utilize affinity phenomenon for protein separations.     

In silico modeling and hydrogen peroxide binding study of rice catalase

Homology modeling of the catalase, CatC cloned and sequenced from rice (Oryza sativa L., cv Ratna an Indica cultivar) has been performed based on the crystal structure of the catalase CatF (PDB code 1m7s) by using the software MODELLER. With the aid of molecular mechanics and molecular dynamics methods, the final model is obtained and is further assessed by PROCHECK and VERIFY - 3D graph, which show that the final refined model is reliable. With this model, a flexible docking study with the hydrogen peroxide, the substrate for catalase, is performed and the results indicate that Arg310, Asp343 and Arg346 in catalase are three important determinant residues in binding as they have strong hydrogen bonding contacts with the substrate. These hydrogen-bonding interactions play an important role for the stability of the complex. Our results may be helpful for further experimental investigations.     

A bioconjugate of Pseudomonas cepacia lipase with alginate with enhanced catalytic efficiency

A bioconjugate of Pseudomonas cepacia lipase with alginate was prepared by simple adsorption. Atomic force microscope (AFM) images showed that this bioconjugate resulted from adsorption rather than entrapment of the enzyme as enzyme molecules were visible on the gel surface. The soluble bioconjugate exhibited increased enzyme activity in terms of high effectiveness factor (effectiveness factor was 3 for the immobilized preparation) and greater Vmax/Km value (Vmax/Km increased 25 times upon immobilization). This constitutes one of the less frequently observed instances of lipase activation by lid opening as a result of binding to a predominantly hydrophilic molecule. The bioconjugate was also more stable at 55 degrees C as compared to the free enzyme and could be reused for oil hydrolysis up to 4 cycles without any loss in activity. Fluorescence emission spectroscopy showed that the immobilized enzyme had undergone definite conformational changes.     

Effects of murine endotoxemia on lymphocyte subsets and clearance of staphylococcal pulmonary infection

In a model of staphylococcal pneumonia initiated during systemic endotoxemia in BALB/c mice, a significant reduction of the number of circulating CD4+ and CD8+ T-lymphocytes, B-lymphocytes, and NK cells, as well as lung-resident total T- and CD4+ T-lymphocytes was demonstrated. Staphylococcus aureus exposure only induced a similar decrease of lymphocyte subsets in the blood. However, the number of lung-resident total T- and CD4+ T-lymphocytes was increased. More viable bacteria were recovered from the lungs of S. aureus-infected mice than from those animals previously treated with lipopolysaccharide (LPS) followed by a staphylococcal challenge. These results indicate that LPS-induced reduction in the number of circulating lymphocyte subsets and lung-resident total T- and CD4+ T-lymphocytes do not increase susceptibility to staphylococcal respiratory infection. Moreover, LPS challenge prior to S. aureus exposure significantly improves clearance of the bacteria in the lung.     

MiRANN: a reliable approach for improved classification of precursor microRNA using Artificial Neural Network model

MicroRNA (miRNA) is a special class of short noncoding RNA that serves pivotal function of regulating gene expression. The computational prediction of new miRNA candidates involves various methods such as learning methods and methods using expression data. This article has proposed a reliable model - miRANN which is a supervised machine learning approach. MiRANN used known pre-miRNAs as positive set and a novel negative set from human CDS regions. The number of known miRNAs is now huge and diversified that could cover almost all characteristics of unknown miRNAs which increases the quality of the result (99.9% accuracy, 99.8% sensitivity, 100% specificity) and provides a more reliable prediction. MiRANN performs better than other state-of-the-art approaches and declares to be the most potential tool to predict novel miRNAs. We have also tested our result using a previous negative set. MiRANN, opens new ground using ANN for predicting pre-miRNAs with a promise of better performance.