Selective detection of single-enantiomer spectrum of chiral molecules aligned in the polypeptide liquid crystalline solvent: Transition selective one-dimensional H-1-H-1 COSY

One-dimensional (1D) proton NMR spectra of enantiomers are generally undecipherable in chiral orienting poly-gamma-benzyl-L-glutamate (PBLG)/CDCl3 solvent. This arises due to large number of couplings, in addition to superposition of spectra from both the enantiomers, severely hindering the H-1 detection. On the other hand in the present study the benefit is derived front the presence of several couplings among the entire network of interacting protons. Transition selective 1D H-1-H-1 correlation experiment (1D-COSY) which utilizes the Coupling assisted transfer of magnetization not only for unraveling the overlap but also for the selective detection of enantiopure spectrum is reported. The experiment is simple, easy to implement and provides accurate eanantiomeric excess in addition to the determination of the proton-proton couplings of an enantiomer within a short experimental time (few minutes). (C) 2009 Elsevier Inc. All rights reserved.

MIPS: metal interactions in protein structures

MIPS (metal interactions in protein structures) is a database of metals in the three-dimensional acromolecular structures available in the Protein Data Bank. Bound metal ions in proteins have both catalytic and structural functions. The proposed database serves as an open resource for the analysis and visualization of all metals and their interactions with macromolecular (protein and nucleic acid) structures. MIPS can be searched via a user-friendly interface, and the interactions between metals and protein molecules, and the geometric parameters, can be viewed in both textual and graphical format using the freely available graphics plug-in Jmol. MIPS is updated regularly, by means of programmed scripts to find metal-containing proteins from newly released protein structures. The database is useful for studying the properties of coordination between metals and protein molecules. It also helps to improve understanding of the relationship between macromolecular structure and function. This database is intended to serve the scientific community working in the areas of chemical and structural biology, and is freely available to all users, around the clock, at http://dicsoft2.physics.iisc.ernet.in/mips/.

Immunospecific binding of tRNA precursors containing N6-(delta 2-isopentenyl) adenosine

Antibodies specific for N6-(delta 2-isopentenyl) adenosine (i6A) were immobilized on Sepharose and this adsorbent (Sepharose-anti-i6A) was used to selectively isolate bacteriophage T4 tRNA precursors containing i6A/ms2i6A from an unfractionated population of 32P-labeled T4 RNAs. The results showed that antibodies to i6A selectively bound only those tRNA precursors containing i6A/ms2i6A. Binding of tRNA precursors by antibody and specificity of the binding was assessed by membrane binding using 32P-labeled tRNA precursor. Binding was highly specific for i6A/ms2i6A residues in the tRNA precursors. This binding can be used to separate modified from unmodified precursor RNAs and to study the biosynthetic pathways of tRNA precursors.

Facile preparation and some applications of an affinity matrix with a cleavable connector arm containing a disulfide bond

A versatile affinity matrix in which the ligand of interest is linked to the matrix through a connector arm containing a disulfide bond is described. It can be synthesized from any amino-substituted matrix by successive reaction with 2-imino-thio-lane, 5, 5'-dithiobis(2-nitrobenzoic acid), and a thiol derivative of the ligand of choice. The repertoire of ligands can be significantly increased by the appropriate use of avidin-biotin bridges. After adsorption of the material to be fractionated, elution can be effected by reducing the disulfide bond in the connector arm with dithiothreitol. Examples of the preparation and use of various affinity matrices based on amino-substituted Sepharose 6MB are given. One involves the immobilization of the Fab' fragment of a monoclonal antibody against Aspergillus oryzae β-galactosidase and the specific binding of that enzyme to the resulting immunoaffinity matrix. Another involves the immobilization of N-biotinyl-2-thioethylamine followed by complex formation with avidin. The resulting avidin-substituted matrix was used for the selective adsorption and subsequent recovery of mouse hybridoma cells producing anti-avidin antibodies. By further complexing the avidin-substituted matrix with appropriate biotinylated antigens, it should be possible to fractionate cells producing antibodies against a variety of antigens.

The 310 helical conformation of a pentapeptide containing a-aminoisobutyric acid (Aib): X-ray crystal structure of Tos-(Aib)5 OMe

The pentapeptide Tos-(Aib)5-OMe adopts a 310 helical conformation in the solid state, with three consecutive Type III B-turns stabilized by intramolecular hydrogen bonds.

H N.M.R. studies of protected alpha-aminoisobutyric acid containing peptides. Chemical shift nonequivalence of benzyloxycarbonyl methylene protons

The benzylic methylene protons in a large number of benzyloxycarbonyl alpha-aminoisobutyric acid (Z-Aib) containing peptides, show chemical shift nonequivalence. The magnitude of the geminal nonequivalence is correlated with the involvement of the urethane carbonyl group, in an intramolecular hydrogen bond. Studies of the model compounds Z-Aib-Aib-Ala-NHMe, and Z-Aib-Aib-Aib-Pro-OMe clearly establish the presence of intramolecular hydrogen bonds, involving the urethane CO group. In both compounds marked anisochrony of the benzylic methylene protons is demonstrated. In Z-Aib-Aib-Pro-OMe, where a 4 leads to 1 hydrogen bonded beta-turn is not possible, the benzylic-CH2-protons appear as a singlet in CDCl3 and have a very small chemical shift difference in (CD3)2SO. The observation of such nonequivalence is of value in establishing whether the amino terminal Aib-Pro beta-turn is retained in large peptide-fragments of alamethicin.

Diffusion of flexible, charged, nanoscopic molecules in solution: Size and pH dependence for PAMAM dendrimer

In order to understand self-diffusion (D) of a charged, flexible, and porous nanoscopic molecule in water, we carry out very long, fully atomistic molecular dynamics simulation of PAMAM dendrimer up to eight generations in explicit salt water under varying pH. We find that while the radius of gyration (R-g) varies as N-1/3, the self-diffusion constant (D) scales, surprisingly, as N-alpha, with alpha=0.39 at high pH and 0.5 at neutral pH, indicating a dramatic breakdown of Stokes-Einstein relation for diffusion of charged nanoscopic molecules. The variation in D as a function of radius of gyration demonstrates the importance of treating water and ions explicitly in the diffusion process of a flexible nanoscopic molecule. In agreement with recent experiments, the self-diffusion constant increases with pH, revealing the importance of dielectric friction in the diffusion process. The shape of a dendrimer is found to fluctuate on a nanosecond time scale. We argue that this flexibility (and also the porosity) of the dendrimer may play an important role in determining the mean square displacement of the dendrimer and the breakdown of the Stokes-Einstein relation between diffusion constant and the radius.

Conformation of di-n-propylglycine residues (Dpg) in peptides: crystal structures of a type I-turn forming tetrapeptide and an -helical tetradecapeptide

The crystal structures of two oligopeptides containing di-n-propylglycine (Dpg) residues, Boc-Gly-Dpg-Gly-Leu-OMe (1) and Boc-Val-Ala-Leu-Dpg-Val-Ala-Leu-Val-Ala-Leu-Dpg-Val-Ala-Leu-OMe (2) are presented. Peptide 1 adopts a type I-turn conformation with Dpg(2)-Gly(3) at the corner positions. The 14-residue peptide 2 crystallizes with two molecules in the asymmetric unit, both of which adopt -helical conformations stabilized by 11 successive 5 1 hydrogen bonds. In addition, a single 4 1 hydrogen bond is also observed at the N-terminus. All five Dpg residues adopt backbone torsion angles (, ) in the helical region of conformational space. Evaluation of the available structural data on Dpg peptides confirm the correlation between backbone bond angle NCC() and the observed backbone , values. For > 106° , helices are observed, while fully extended structures are characterized by < 106° . The mean values for extended and folded conformations for the Dpg residue are 103.6° ± 1.7° and 109.9° ± 2.6° , respectively.

Hybrid peptide design. Hydrogen bonded conformations in peptides containing the stereochemically constrained gamma-amino acid residue, gabapentin

he crystal structure of 12 peptides containing the conformationally constrained 1-(aminomethyl)cyclohexaneacetic acid, gabapentin (Gpn), are reported. In all the 39 Gpn residues conformationally characterized so far, the torsion angles about the C-alpha-C-beta and C-beta-C-gamma bonds are restricted to the gauche conformation (+/- 60 degrees). The Gpn residue is constrained to adopt folded conformations resulting in the formation of intramolecularly hydrogen-bonded structures even in short peptides. The peptides Boc-Ac(6)c-Gpn-OMe 1 and Boc-Gpn-Aib-Gpn-Aib-OMe 2 provide examples of C-7 conformation; peptides Boc-Gpn-Aib-OH 3, Boc-Ac(6)c-Gpn-OH 4, Boc-Val-Pro-Gpn-OH 5, Piv-Pro-Gpn-Val-OMe 6, and Boc-Gpn-Gpn-Leu-OMe 7 provide examples of C-9 conformation; peptide Boc-Ala-Aib-Gpn-Aib-Ala-OMe 8 provides an example of C-12 conformation and peptides Boc-beta Leu-Gpn-Val-OMe 9 and Boc-beta Phe-Gpn-Phe-OMe 10 provide examples of C-13 conformation. Gpn peptides provide examples of backbone expanded mimetics for canonical alpha-peptide turns like the gamma (C-7) and the beta (C-10) turns. The hybrid beta gamma sequences provide an example of a mimetic of the C-13 alpha-turn formed by three contiguous alpha-amino acid residues. Two examples of folded tripeptide structures, Boc-Gpn-beta Phe-Leu-OMe 11 and Boc-Aib-Gpn-beta Phg-NHMe 12, lacking internal hydrogen bonds are also presented. An analysis of available Gpn residue conformations provides the basis for future design of folded hybrid peptides.

Synthesis of Diketopyrrolopyrrole Containing Copolymers: A Study of Their Optical and Photovoltaic Properties

The diketopyrrolopyrrole-based copolymers PDPP-BBT and TDPP-BBT were synthesized and used as donor for bulk heterojunction photovoltaic devices. The photophysical properties of these polymers showed absorption in the range 500-600 nm with a maximum peak around 563 nm, while TDPP-BBT showed broadband absorption in the range 620 - 800 nm with a peak around 656 nm. The power conversion efficiencies (PCE) of the polymer solar cells based on these copolymers and [6,6]-phenyl C61 butyric acid methyl ester (PCBM) were 0.68% (as cast PDPP-BBT:PCBM), 1.51% (annealed PDPP-BBT:PCBM), 1.57% (as cast TDPPBBT: PCBM), and 2.78% (annealed TDPP-BBT:PCBM), under illumination of AM 1.5 (100 mW/cm2). The higher PCE for TDPP-BBT-based polymer solar cells has been attributed to the low band gap of this copolymer as compared to PDPP-BBT, which increases the numbers of photogenerated excitons and corresponding photocurrent of the device. These results indicate that PDPP-BBT and TDPP-BBT act as excellent electron donors for bulk heterojunction devices.

From the {Cu(μ2-S)N}4 butterfly architecture to the {Cu(μ3-S)N}12 double wheel

Copper(I) complexes with {Cu(μ2-S)N}4 and {Cu(μ3-S)N}12 core portions of butterfly-shaped or double wheel architectures have been isolated in the reaction of Cu(I) with the Schiff base ligand C6H4(CHNC6H4S)2, aiso-abtâ, under different conditions. View the MathML source containing the tetranuclear electroneutral complex View the MathML source is formed by the reaction of CuI in acetonitrilic solution and recrystallization from DMF, whereas View the MathML source containing dodecanuclear View the MathML source wheels is accessible starting from CuBF4. Complexes 2 and 4 represent the first examples of cyclic complexes with the same overall stoichiometry but different ring sizes. The ligand induces two different coordination environments around copper(I) by switching between μ2- and μ3-sulfur bridging modes.

Enhanced Tetrahedral Ordering of Water Molecules in Minor Grooves of DNA: Relative Role of DNA Rigidity, Nanoconfinement, and Surface Specific Interactions

Confinement and Surface specific interactions call induce Structures otherwise unstable at that temperature and pressure. Here we Study the groove specific water dynamics ill the nucleic acid sequences, poly-AT and poly-GC, in long B-DNA duplex chains by large scale atomistic molecular dynamics simulations, accompanied by thermodynamic analysis. While water dynamics in the major groove remains insensitive to the sequence differences, exactly the opposite is true for the minor groove water. Much slower water dynamics observed in the minor grooves (especially in the AT minor) call be attributed to all enhanced tetrahedral ordering (< t(h)>) of water. The largest value of < t(h)> in the AT minor groove is related to the spine of hydration found in X-ray Structure. The calculated configurational entropy (S-C) of the water molecules is found to be correlated with the self-diffusion coefficient of water in different region via Adam-Gibbs relation D = A exp(-B/TSC), and also with < t(h)>.

Two- and Three-Dimensional Open-Framework Uranium Arsenates: Synthesis, Structure, and Characterization

Hydrothermal reactions between uranium salts and arsenic pentoxide in the presence of two different amines yielded six new uranium arsenate phases exhibiting open-framework structures, ethylenediamine (en): [C2N2H9]-[(UO2)(ASO(4))] I; [C2N2H10][(UO2)F(HASO(4))]2 center dot 4H(2)O, II; [C2N2H9][U2F5(HASO(4))(2)], III; [C2N2H9][UF2(ASO(4))], IV; diethylenetriamine (DETA), [C4N3H16][U2F3(ASO(4))(2)(HAsO4)] V; and [C4N3H16][U2F6(AsO4)(HAsO4)], VI. The structures were determined using single crystal studies, which revealed two- (I, II, V) and three-dimensional (III, IV, VI) structures for the uranium arsenates. The uranium atom, in these compounds, exhibits considerable variations in the coordination (6 to 9) that appears to have some correlation with the synthetic conditions. The water molecules in [C2N2H10][(UO2)F(HAsO4)](2 center dot)4H(2)O, II, could be reversibly removed, and the dehydrated phase, [C2N2H10][(UO2)F(HAsO4)](2), IIa, was also characterized using single crystal studies. The observation of many mineralogical structures in the present compounds suggests that the hydrothermal method could successfully replicate the geothermal conditions. As part of this study, we have observed autunite, Ca[(UO2)(PO4)](2)(H2O)(11), metavauxite, [Fe(H2O)(6)][Al(OH)(H2O)(PO4)](2), finarite, PbCU(SO4)(OH)(2), and tancoite, LiNa2H[Al(PO4)(2)(OH)], structures. The repeated observation of the secondary building unit, SBU-4, in many of the uranium arsenate structures suggests that these are viable building units. Optical studies on the uranium arsenate compound, [C4N3H16][U2F6(AsO4)(HASO(4))), VI, containing uranium in the +4 oxidation state indicates a blue emission through an upconversion process. The compound also exhibits antiferromagnetic behavior.

Performance of RT-PCR-ELISA for the detection of peste des petits ruminants virus

A highly sensitive and specific reverse transcription polymerase chain reaction enzyme linked immunosorbent assay (RT-PCR-ELISA) was developed for the objective detection of nucleoprotein (N) gene of peste des petits ruminants (PPR) virus from field outbreaks or experimentally infected sheep. Two primers (IndF and Np4) and one probe (Sp3) available or designed for the amplification/probing of the 'N' gene of PPR virus, were chosen for labeling and use in RT-PCR-ELISA based on highest analytical sensitivity of detection of infective virus or N-gene containing recombinant plasmid, higher nucleotide homology at the primer binding sites of the 'N' gene sequences available and the ability to amplify PPR viral genome from different sources of samples. RT-PCR was performed with unlabeled IndF and Np4 digoxigenin labeled primers followed by a microplate hybridization probe reaction with biotin labeled Sp3 probe. RT-PCR-ELISA was found to be 10-fold more sensitive than the conventional RT-PCR followed by agarose gel based detection of PCR product. Based on the Mean (mean +/- 3S.D.) optical density (OD) values of 47 RT-PCR negative samples, OD values above 0.306 were considered positive in RT-PCR-ELISA. A total of 82 oculo-nasal swabs and tissue samples from suspected PPR cases were analyzed by RT-PCR and RT-PCR-ELISA, which revealed 54.87 and 58.54% positivity, respectively. From an experimentally infected sheep, both RT-PCR and RT-PCR-ELISA could detect the virus from 6 days post-infection up to 9 days in oculo-nasal swabs. On post-mortem, PPR viral genome was detected in spleen, lymph node, lung, heart and liver. The correlation co-efficient between RT-PCR-ELISA OD values and either TCID50 of virus or molecules of DNA was 0.622 and 0.657, respectively. The advantages of RT-PCR-ELISA over the conventional agarose gel based detection of RT-PCR products are discussed. (c) 2006 Elsevier B.V. All rights reserved.

Phosphorus Partition between Liquid Steel and CaO-SiO2-P2O5-MgO Slag Containing Low FeO

CaO-SiO2-FeOx-P2O5-MgO bearing slags are typical in the basic oxygen steelmaking (BOS) process. The partition ratio of phosphorus between slag and steel is an index of the phosphorus holding capacity of the slag, which determines the phosphorus content achievable in the finished steel. The influences of FeO concentration and basicity on the equilibrium phosphorus partition ratios were experimentally determined at temperatures of 1873 and 1923 K, for conditions of MgO saturation. The partition ratio initially increased with basicity but attained a constant value beyond basicity of 2.5. An increase in FeO concentration up to approximately 13 to 14 mass pet was beneficial for phosphorus partition.