Ab initio studies on the tri- and diphosphate fragments of adenosine triphosphate

Pyrophosphate prototypes such as methyl triphosphate and methyl diphosphate molecules in their different protonation states have been investigated at high levels of quantum chemical calculations. The optimized geometries, the thermochemistry of the hydrolysis and the molecular orbitals contributing to the high energy of these compounds have been analyzed. These investigations provide insights into the ``high energy'' character of ATP molecule. Further, the dependence of vibrational frequencies on the number of phosphate groups and the charged states has also been presented. These results can aid the interpretation of spectra obtained by experiments on complexes containing pyrophosphate prototypes. (c) 2005 Elsevier B.V. All rights reserved.

Classification of Protein Kinases on the Basis of Both Kinase and Non-Kinase Regions

Background: Protein phosphorylation is a generic way to regulate signal transduction pathways in all kingdoms of life. In many organisms, it is achieved by the large family of Ser/Thr/Tyr protein kinases which are traditionally classified into groups and subfamilies on the basis of the amino acid sequence of their catalytic domains. Many protein kinases are multidomain in nature but the diversity of the accessory domains and their organization are usually not taken into account while classifying kinases into groups or subfamilies. Methodology: Here, we present an approach which considers amino acid sequences of complete gene products, in order to suggest refinements in sets of pre-classified sequences. The strategy is based on alignment-free similarity scores and iterative Area Under the Curve (AUC) computation. Similarity scores are computed by detecting common patterns between two sequences and scoring them using a substitution matrix, with a consistent normalization scheme. This allows us to handle full-length sequences, and implicitly takes into account domain diversity and domain shuffling. We quantitatively validate our approach on a subset of 212 human protein kinases. We then employ it on the complete repertoire of human protein kinases and suggest few qualitative refinements in the subfamily assignment stored in the KinG database, which is based on catalytic domains only. Based on our new measure, we delineate 37 cases of potential hybrid kinases: sequences for which classical classification based entirely on catalytic domains is inconsistent with the full-length similarity scores computed here, which implicitly consider multi-domain nature and regions outside the catalytic kinase domain. We also provide some examples of hybrid kinases of the protozoan parasite Entamoeba histolytica. Conclusions: The implicit consideration of multi-domain architectures is a valuable inclusion to complement other classification schemes. The proposed algorithm may also be employed to classify other families of enzymes with multidomain architecture.

The effects of beta-mercaptoethanol and sodium dodecyl sulfate on the Humicola insolens beta-glucosidase

Hydrolysis of p-nitrophenyl-beta-D-glucoside by the beta-glucosidase of a thermophilic and cellulolytic fungus, Humicola insolens was stimulated by two-fold in the presence of high concentrations of beta-mercaptoethanol. This enzyme did not have any free sulfhydryl groups and high concentrations of beta-mercaptoethanol (5% v/v) reduced all of the three disulfide bonds present in the enzyme. In contrast, the hydrolysis of cellobiose and cellulose polymers was inhibited by 50% under the same conditions. Sodium dodecyl sulfate (1% w/v) even in combination with beta-mercaptoethanol did not show any significant effects on this enzyme. These unusual properties suggest that this enzyme may be of significant importance for understanding the structure of the enzyme.

An Approach Toward Homocalystegines and Silyl-homocalystegines. Acid-Mediated Migrations of Acetates in Seven-Membered Ring Systems

A short access to homocalystegine analogues silylated at C7 is described. The synthesis involves the desymmetrization of a (phenyldimethylsilyl)methylcycloheptatriene using osmium-mediated dihydroxylation, followed by the diol protection and a cycloaddition involving the remaining diene moiety and an acylnitroso reagent. Additions of the osmium and acylnitroso reagents were shown, through X-ray diffraction studies of the resulting major isomers, to occur anti and syn, respectively, relative to the SiCH2 substituent. N-O bond cleavage on the resulting cycloadduct then produces the aminopolyol having a silylmethyl substituent. Oxidation of the C-Si bond also afforded an access to unusual amino-heptitols having five contiguous stereogenic centers. In the course of this work, we finally observed a unusual rearrangement taking place on cycloheptanone 18 substituted by two acetyl groups and a neighboring Boc-protected amine. A profound reorganization of the substituents on the seven-membered ring effectively took place under acidic conditions (TFA) leading to the thermodynamically more stable homocalystegine-type compound., DFT calculations of the conformational energy of isomeric silyl homocalystegines indicated that the product observed upon the acid-mediated rearrangement was the most stable of a series of analogues with various distributions of substituents along the seven-membered ring backbone. A tentative mechanism is proposed to rationalize the acetate migrations and inversions of the stereochemistry at various stereocenters.

An unusual distribution of glucose-6-phosphate dehydrogenase deficiency of south Indian newborn population.

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is seen at a higher frequency in many national and ethnic groups in areas of current or former malaria endemicity. A screening programme undertaken to evaluate the gene frequencies for this deficiency in the highly inbred South Indian population of Karnataka revealed that of the 5140 neonates screened, 7.8% were G6PD deficient with no correlation between the reported level of inbreeding and enzyme deficiency. An interesting finding was the equal number of male (198) and female (207) individuals, with G6PD activity of less than 3 IU. The possible implications of this finding with regard to the expression of G6PD gene is discussed.

Thiol-ene Clickable Hyperscaffolds Bearing Peripheral Allyl Groups

Radical catalyzed thiol-ene reaction has become a useful alternative to the Huisgen-type click reaction as it helps to expand the variability in reaction conditions as well as the range of clickable entities. Thus, direct generation of hyper-branched polymers bearing peripheral allyl groups that could be clicked using a variety of functional thiols would be of immense value. A specifically designed AB(2) type monomer, that carries two allyl benzyl ethers groups and one alcohol functionality, was shown to undergo self-condensation under acid-catalyzed melt-transetherification to yield a hyperbranched polyether that carries numerous allyl end-groups. Importantly, it was shown that the kinetics of polymerization is not dramatically affected by the change of the ether unit from previously studied methyl benzyl ether to an allyl benzyl ether. The peripheral allyl groups were readily clicked quantitatively, using a variety of thiols, to generate an hydrocarbon-soluble octadecyl-derivative, amphiphilic systems using 2-mercaptoethanol and chiral amino acid (N-benzoyl cystine) derivatized hyperbranched structures; thus demonstrating the versatility of this novel class of clickable hyperscaffolds. (C) 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 49:1735-1744, 2011

Thermodynamic and structural consequences of changing a sulfur atom to a methylene group in the M13Nle mutation in ribonuclease-S

Two fragments of pancreatic ribonuclease A, a truncated version of S-peptide (residues 1-15) and S-protein (residues 21-124), combine to give a catalytically active complex. We have substituted the wild-type residue at position 13, methionine (Met), with norleucine (Nle), where the only covalent change is the replacement of the sulfur atom with a methylene group. The thermodynamic parameters associated with the binding of this variant to S-protein, determined by titration calorimetry in the temperature range 10-40 degrees C, are reported and compared to values previously reported [Varadarajan, R., Connelly, P. R., Sturtevant, J. M., & Richards, F. M. (1992) Biochemistry 31, 1421-1426] for other position 13 analogs. The differences in the free energy and enthalpy of binding between the Met and Nle peptides are 0.6 and 7.9 kcal/mol at 25 degrees C, respectively. These differences are slightly larger than, but comparable to, the differences in the values for the Met/Ile and Met/Leu pairs. The structure of the mutant complex was determined to 1.85 Angstrom resolution and refined to an R-factor of 17.4% The structures of mutant and wild-type complexes are practically identical although the Nle side chain has a significantly higher average B-factor than the corresponding Met side chain. In contrast, the B-factors of the atoms of the cage of residues surrounding position 13 are all somewhat lower in the Nle variant than in the Met wild-type. Thus, the large differences in the binding enthalpy appear to reside entirely in the difference in chemical properties or dynamic behavior of the -S- and -CH2- groups and not in differences in the geometry of the side chains or the internal cavity surface. In addition, a novel method of obtaining protein stability data by means of isothermal titration calorimetry is introduced.

Synthetic, spectroscopic and structural studies on uranium and thorium complexes of diphosphazane dioxides

Co-ordination complexes of the diphosphazane dioxides Ph(2)P(O)N(Pr-i)P(O)Ph(2) L(1). Ph(2)P(O)N(Pr-i)P(O)Ph(OC(6)H(4)Me-4) L(2) and Ph(2)P(O)N(Pr-i)P(O)(O2C12H8) L(3) with UO22+ or Th4+ ions have been synthesised and characterised by IR and NMR spectroscopy. The structures of [UO2(NO3)(2)L(1)] and [Th(NO3)(2)L(3)(1)][Th(NO3)(6)] are established by X-ray crystallography. In the former, the uranyl ion is bonded to two bidentate nitrate groups and the two phosphoryl groups of the ligand L(1); the co-ordination polyhedron around the metal is a hexagonal bipyramid. The cationic moiety in the thorium complex contains three bidentate diphosphazane dioxide ligands and two bidentate nitrate groups around the ten-co-ordinated metal.

An ethnobotanical survey of medicinal plants in the Eastern Himalayan zone of Arunachal Pradesh, India

Aim of the study: The medicinal plants are integral source of easily available remedy used in rural healthcare system. This study was conducted among three major ethnic groups namely the Nocte, the Nyishi and the Adi in the Eastern Himalayan region of Arunachal Pradesh to evaluate their comparative knowledge on medicinal plants. Materials and methods: The three remote districts of Arunachal Pradesh namely the Tirap, the Dibang Valley and the Papum Pare were surveyed through interviewing of randomly selected 237 participants using semi-structured questionnaire and regular field visits to selected districts. Results: We recorded the traditional use of 74 medicinal plants species belonging to 41 taxonomic plant families used for treating a total of 25 different diseases/ailments. The informant consensus factor (ICF) values demonstrated that local people tend to agree more with each other in terms of the plants used to treat malaria (0.71), jaundice (0.62), urological problems (0.56), dermatological disorders (0.45), pain (0.30), and respiratory disorder (0.33), and while the general health (0.15) and gastro-intestinal disorders category (0.28) were found low ICF values. Conclusion: Of the total 74 species recorded, the highest number of medicinal plants (36 species) was reported from the Adi of Lower Dibang Valley followed by the Nocte of the Tirap (25 species) and the Nyishi ethnic groups of Papum Pare districts (13 species). In the present study, we found that the men, elder people and illiterate ones had better knowledge on medicinal plants as compared to women, younger and literate people. Findings of this documentation study can be used as an ethnopharmacological basis for selecting plants for future phytochemical and pharmaceutical studies. (C) 2010 Elsevier Ireland Ltd. All rights reserved.

Creation of a Huge Annotated Database for Tamil and Kannada OHR

This paper describes the efforts at MILE lab, IISc, to create a 100,000-word database each in Kannada and Tamil for the design and development of Online Handwritten Recognition. It has been collected from over 600 users in order to capture the variations in writing style. We describe features of the scripts and how the number of symbols were reduced to be able to effectively train the data for recognition. The list of words include all the characters, Kannada and Indo-Arabic numerals, punctuations and other symbols. A semi-automated tool for the annotation of data from stroke to word level is used. It segments each word into stroke groups and also acts as a validation mechanism for segmentation. The tool displays the stroke, stroke groups and aksharas of a word and hence can be used to study the various styles of writing, delayed strokes and for assigning quality tags to the words. The tool is currently being used for annotating Tamil and Kannada data. The output is stored in a standard XML format.

Aggregation and mesomorphic properties of 'double-headed' carbohydrate amphiphiles

Sugar-based amphiphiles, consisting of two sugar head groups and an alkylene chain within the molecules, are synthesized and their aggregation and mesomorphic properties are evaluated. The hydrophilic sugar head groups, constituted with β-D-glucopyranoside units, and the lyophilic alkylene units, are coupled to a glycerol backbone to afford the ‘double-headed’ sugar amphiphiles. Aggregation studies in aqueous solutions provided their critical micellar concentrations and the aggregation numbers. Mesophase characterizations by polarizing optical microscopy and differential scanning calorimetry (DSC) revealed the phase-transition behaviour of these new ‘double-headed’ glycolipids.

2,3-Unsaturated enoses. A Pummerer rearrangement route to sugar vinyl sulfides and synthesis of 3-deoxy-3-alkyl/arylsulfinyl pyranosides

A Pummerer rearrangement of 2,3-dideoxy-3-alkyl/arylsulfinyl-arabino-hexopyranosides is reported. Treatment of sulfinyl-arabino-hexopyranoside derivatives, obtained through oxidation of the corresponding thio-derivatives, with trifluoroacetic anhydride (TFAA)/pyridine led to a facile formation of 2,3-dideoxy-3-alkyl/arylthio-hex-2-enopyranosides. Upon conversion of sugar vinyl sulfides to vinyl sulfoxides, conjugate addition reactions were conducted with alkoxides, to afford 3-deoxy-3-alkyl/arylsulfinyl pyranosides, in the manno-configuration exclusively. Whereas the conjugate addition reaction did not proceed with ether protecting groups, ester protecting groups and free hydroxyl groups in the sugar vinyl sulfoxide permitted the reaction. (C) 2012 Elsevier Ltd. All rights reserved.

Orthogonal biofunctionalization of magnetic nanoparticles via ``clickable'' poly(ethylene glycol) silanes: a ``universal ligand'' strategy to design stealth and target-specific nanocarriers

The present work demonstrates a novel strategy to synthesize orthogonally bio-engineered magnetonanohybrids (MNPs) through the design of versatile, biocompatible linkers whose structure includes: (i) a robust anchor to bind with metal-oxide surfaces; (ii) tailored surface groups to act as spacers and (iii) a general method to implement orthogonal functionalizations of the substrate via ``click chemistry''. Ligands that possess the synthetic generality of features (i)-(iii) are categorized as ``universal ligands''. Herein, we report the synthesis of a novel, azido-terminated poly(ethylene glycol) (PEG) silane that can easily self-assemble on MNPs through hetero-condensation between surface hydroxyl groups and the silane end of the ligand, and simultaneously provide multiple clickable sites for high density, chemoselective bio-conjugation. To establish the universal-ligand-strategy, we clicked alkyl-functionalized folate onto the surface of PEGylated MNPs. By further integrating a near-infrared fluorescent (NIRF) marker (Alexa-Fluor 647) with MNPs, we demonstrated their folate-receptor mediated internalization inside cancer cells and subsequent translocation into lysosomes and mitochondria. Ex vivo NIRF imaging established that the azido-PEG-silane developed in course of the study can effectively reduce the sequestration of MNPs by macrophage organs (viz. liver and spleen). These folate-PEG-MNPs were not only stealth and noncytotoxic but their dual optical and magnetic properties aided in tracking their whereabouts through combined magnetic resonance and optical imaging. Together, these results provided a strong motivation for the future use of the ``universal ligand'' strategy towards development of ``smart'' nanohybrids for theragnostic applications.

NMR Analysis of Cross Strand Aromatic Interactions in an 8 Residue Hairpin and a 14 Residue Three Stranded beta-Sheet Peptide

Cross strand aromatic interactions between a facing pair of phenylalanine residues in antiparallel beta-sheet structures have been probed using two structurally defined model peptides. The octapeptide Boc-(LFVPPLFV)-P-D-P-L-OMe (peptide 1) favors the beta-hairpin conformation nucleated by the type II' beta-turn formed by the (D)Pro-(L)Pro segment, placing Phe2 and Phe7 side chains in proximity. Two centrally positioned (D)Pro-(L)Pro segments facilitate the three stranded beta-sheet formation in the 14 residue peptide Boc-LFV(D)P(L)PLFVA(D)P(L)PLFV-OMe (peptide 2) in which the Phe2/Phe7 orientations are similar to that in the octapeptide. The anticipated folded conformations of peptides 1 and 2 are established by the delineation of intramolecularly hydrogen bonded NH groups and by the observation of specific cross strand NOEs. The observation of ring current shifted aromatic protons is a diagnostic of close approach of the Phe2 and Phe7 side chains. Specific assignment of aromatic proton resonances using HSQC and HSQC-TOCSY methods allow an analysis of interproton NOEs between the spatially proximate aromatic rings. This approach facilitates specific assignments in systems containing multiple aromatic rings in spectra at natural abundance. Evidence is presented for a dynamic process which invokes a correlated conformational change about the C-alpha-C-beta(chi(1)) bond for the pair of interacting Phe residues. NMR results suggest that aromatic ring orientations observed in crystals are maintained in solution. Anomalous temperature dependence of ring current induced proton chemical shifts suggests that solvophobic effects may facilitate aromatic ring clustering in apolar solvents.

Low temperature CO oxidation and water gas shift reaction over Pt/Pd substituted in Fe/TiO2 catalysts

We demonstrate the activity of Ti0.84Pt0.01Fe0.15O2-delta and Ti0.73Pd0.02Fe0.25O2-delta catalysts towards the CO oxidation and water gas shift (VMS) reaction. Both the catalysts were synthesized in the nano crystalline form by a low temperature sonochemical method and characterized by different techniques such as XRD, FT-Raman, TEM, FT-IR, XPS and BET surface analyzer. H-2-TPR results corroborate the intimate contact between noble metal and Fe ions in the both catalysts that facilitates the reducibility of the support. In the absence of feed CO2 and H-2, nearly 100% conversion of CO to CO2 with 100% H-2 selectivity was observed at 300 degrees C and 260 degrees C respectively, for Ti0.84Pt0.01Fe0.15O2-delta and Ti0.73Pd0.02Fe0.25O2-delta catalyst. However, the catalytic performance of Ti0.73Pd0.02Fe0.25O2-delta deteriorates in the presence of feed CO2 and H-2. The change in the support reducibility is the primary reason for the significant increase in the activity for CO oxidation and WGS reaction. The effect of Fe addition was more significant in Ti0.73Pd0.02Fe0.25O2-delta than Ti0.84Pt0.01Fe0.15O2-delta. Based on the spectroscopic evidences and surface phenomena, a hybrid reaction scheme utilizing both surface hydroxyl groups and the lattice oxygen was hypothesized over these catalysts for WGS reaction. The mechanisms based on the formate and redox pathway were used to fit the ldnetic data. The analysis of experimental data shows the redox mechanism is the dominant pathway over these catalysts. Copyright (C) 2012, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.