Structural and molecular basis of interaction of HCV non-structural protein 5A with human casein kinase 1 alpha and PKR

Background: Interaction of non-structural protein 5A (NS5A) of Hepatitis C virus (HCV) with human kinases namely, casein kinase 1 alpha (ck1 alpha) and protein kinase R (PKR) have different functional implications such as regulation of viral replication and evasion of interferon induced immune response respectively. Understanding the structural and molecular basis of interactions of the viral protein with two different human kinases can be useful in developing strategies for treatment against HCV. Results: Serine 232 of NS5A is known to be phosphorylated by human ck1 alpha. A structural model of NS5A peptide containing phosphoacceptor residue Serine 232 bound to ck1 alpha has been generated using the known 3-D structures of kinase-peptide complexes. The substrate interacting residues in ck1 alpha has been identified from the model and these are found to be conserved well in the ck1 family. ck1 alpha - substrate peptide complex has also been used to understand the structural basis of association between ck1 alpha and its other viral stress induced substrate, tumour suppressor p53 transactivation domain which has a crystal structure available. Interaction of NS5A with another human kinase PKR is primarily genotype specific. NS5A from genotype 1b has been shown to interact and inhibit PKR whereas NS5A from genotype 2a/3a are unable to bind and inhibit PKR efficiently. This is one of the main reasons for the varied response to interferon therapy in HCV patients across different genotypes. Using PKR crystal structure, sequence alignment and evolutionary trace analysis some of the critical residues responsible for the interaction of NS5A 1b with PKR have been identified. Conclusions: The substrate interacting residues in ck1 alpha have been identified using the structural model of kinase substrate peptide. The PKR interacting NS5A 1b residues have also been predicted using PKR crystal structure, NS5A sequence analysis along with known experimental results. Functional significance and nature of interaction of interferon sensitivity determining region and variable region 3 of NS5A in different genotypes with PKR which was experimentally shown are also supported by the findings of evolutionary trace analysis. Designing inhibitors to prevent this interaction could enable the HCV genotype 1 infected patients respond well to interferon therapy.

DNA Binding and Oxidative Cleavage Activity of Ternary (alpha-Lipoic Acid) Copper(II) Complex of Heterocyclic Base

Ternary copper(II) complex Cu(a-lipo)(phen)(Cl)](NO3) where a-lipo = a-lipoic acid, phen is N, N-donor heterocyclic base, 1,10-phenanthroline was synthesized, characterized, and its DNA binding and cleavage activity were studied. Binding interactions of the complex with calf thymus (CT) DNA has been investigated by emission, viscosity, and DNA melting studies. The complex shows efficient oxidative cleavage of SC-DNA in the presence of 3-mercaptopropionic acid involving hydroxyl radical species, and results of control experiments exhibit the inhibition of DNA cleavage in the presence of hydroxyl radical scavengers, viz. DMSO and KI.

Wheeler-Feynman absorber revisited: a useful technique to calculate decay rates and lifetimes in small scale optical systems

The Wheeler-Feynman (WF) absorber theory of radiation though no more of interest in explaining self interaction of an electron, can be very useful in today's research in small scale optical systems. The significance of the WF absorber is the use of time-symmetrical solution of Maxwell's equations as opposed to only the retarded solution. The radiative coupling of emitters to nano wires in the near field and change in their lifetimes due to small mode volume enclosures have been elucidated with the retarded solutions before. These solutions have also been shown to agree with quantum electrodynamics, thus allowing for classical electromagnetic approaches in such problems. It is here assumed that the radiative coupling of the emitter with a body is in proportion to its contribution to the classical force of radiative reaction as derived in the WF absorber theory. Representing such nano structures as a partial WF absorber acting on the emitter makes the computations considerably easier than conventional electromagnetic solutions for full boundary conditions.

Structural, EPR, optical and magnetic properties of alpha-Fe2O3 nanoparticles

alpha-Fe2O3 nanoparticles were synthesized by a low temperature solution combustion method. The structural, magnetic and luminescence properties were studied. Powder X-ray diffraction (PXRD) pattern of alpha-Fe2O3 exhibits pure rhombohedral structure. SEM micrographs reveal the dumbbell shaped particles. The EPR spectrum shows an intense resonance signal at g approximate to 5.61 corresponding to isolated Fe3+ ions situated in axially distorted sites, whereas the g approximate to 2.30 is due to Fe3+ ions coupled by exchange interaction. Raman studies show A(1g) (225 cm(-1)) and E-g (293 and 409 cm(-1)) phonon modes. The absorption at 300 nm results from the ligand to metal charge transfer transitions whereas the 540 nm peak is mainly due to the (6)A(1) + (6)A(1) —> T-4(1)(4G) + T-4(1)(4G) excitation of an Fe3+-Fe3+ pair. A prominent TL glow peak was observed at 140 C at heating rate of 5 degrees C s(-1). The trapping parameters namely activation energy (E), frequency factor (s) and order of kinetics (b) were evaluated and discussed. (C) 2012 Elsevier B.V. All rights reserved.

Discrimination of alpha-Amino Acids Using Green Tea Flavonoid (-)-Epigallocatechin Gallate as a Chiral Solvating Agent

We report a special, hitherto-unexplored property of (-)-epigallocatechin gallate (EGCG) as a chiral solvating agent for enantiodiscrimination of alpha-amino acids in the polar solvent DMSO. This phenomenon has been investigated by H-1 NMR spectroscopy. The mechanism of the interaction property of EGCG with alpha-amino acids has been understood as arising out of hydrogen-bonded noncovalent interactions, where the -OH groups of two phenyl rings of EGCG play dominant roles. The conversion of the enantiomeric mixture into diastereomers yielded well-resolved peaks for D and L amino acids permitting the precise measurement of enantiomeric composition. Often one encounters complex situations when the spectra are severely overlapped or partially resolved hampering the testing of enantiopurity and the precise measurement of enantiomeric excess (ee). Though higher concentration of EGCG yielded better discrimination, the use of lower concentration being economical, we have exploited an appropriate 2D NMR experiment in overcoming such problems. Thus, in the present study we have successfully demonstrated the utility of the bioflavonoid (-)-EGCG, a natural product as a chiral solvating agent for the discrimination of large number of alpha-amino acids in a polar solvent DMSO. Another significant advantage of this new chiral sensing agent is that it is a natural product and does not require tedious multistep synthesis unlike many other chiral auxiliaries.

Total synthesis and determination of the absolute configuration of 5,6-Dihydro-alpha-pyrone natural product synargentolide B

Enantiospecific total synthesis and determination of the absolute stereochemistry of the alpha-pyrone-containing natural product synargentolide B were accomplished. The absolute stereochemistry of the natural product was established by synthesizing the possible diastereomers and comparison of the data with those reported for the natural product. During the process, total synthesis of the putative structure of related natural product 6R-1S,2R,SR,6S-(tetraacetyloxy)-3E-heptenyl]-5,6-dihydro-2H-pyran-2-o ne was also accomplished and confirmed by X-ray crystal structure analysis. Wittig-Horner reaction of a chiral phosphonate derived from (S)-lactic acid and ring-closing metathesis were the key reactions during the course of the total synthesis.

Designed three-stranded beta-sheet in an alpha/beta hybrid peptide

The incorporation of beta-amino acid residues into the antiparallel beta-strand segments of a multi-stranded beta-sheet peptide is demonstrated for a 19-residue peptide, Boc-LV(beta)FV(D)PGL(beta)FVVL(D)PGLVL(beta)FVV-OMe (BBH19). Two centrally positioned (D)Pro-Gly segments facilitate formation of a stable three-stranded beta-sheet, in which beta-phenylalanine ((beta)Phe) residues occur at facing positions 3, 8 and 17. Structure determination in methanol solution is accomplished by using NMR-derived restraints obtained from NOEs, temperature dependence of amide NH chemical shifts, rates of H/D exchange of amide protons and vicinal coupling constants. The data are consistent with a conformationally well-defined three-stranded beta-sheet structure in solution. Cross-strand interactions between (beta)Phe3/(beta)Phe17 and (beta)Phe3/Val15 residues define orientations of these side-chains. The observation of close contact distances between the side-chains on the N- and C-terminal strands of the three-stranded beta-sheet provides strong support for the designed structure. Evidence is presented for multiple side-chain conformations from an analysis of NOE data. An unusual observation of the disappearance of the Gly NH resonances upon prolonged storage in methanol is rationalised on the basis of a slow aggregation step, resulting in stacking of three-stranded beta-sheet structures, which in turn influences the conformational interconversion between type I' and type II' beta-turns at the two (D)Pro-Gly segments. Experimental evidence for these processes is presented. The decapeptide fragment Boc-LV(beta)FV(D)PGL(beta)FVV-OMe (BBH10), which has been previously characterized as a type I' beta-turn nucleated hairpin, is shown to favour a type II' beta-turn conformation in solution, supporting the occurrence of conformational interconversion at the turn segments in these hairpin and sheet structures.

Synthesis and characterization of porous flowerlike alpha-Fe2O3 nanostructures for supercapacitor application

Porous flower-like alpha-Fe2O3 nanostructures synthesized by an ethylene glycol mediated self-assembly process are crystalline and porous with BET surface area of 64.6 m(2) g(-1). The discharge capacitance is 127 F g(-1) when the electrodes are cycled in 0.5 M Na2SO3 at a current density of 1 A g(-1). Capacitance retention after 1000 cycles is about 80% of the initial capacitance. The high discharge capacitance and its retention are attributed to high surface area and porosity of the iron oxide. As the iron oxides are inexpensive, the nano alpha-Fe2O3 is expected to be of potential use for supercapacitor application.

Microstructure and texture evolution during sub-transus thermomechanical processing of Ti-6Al-4V-0.1B alloy: part I. hot rolling in (alpha plus beta) phase field

In the current study, the evolution of microstructure and texture has been studied for Ti-6Al-4V-0.1B alloy during sub-transus thermomechanical processing. This part of the work deals with the deformation response of the alloy by rolling in the (alpha + beta) phase field. The (alpha + beta) annealing behavior of the rolled specimen is communicated in part II. Rolled microstructures of the alloys exhibit either kinked or straight alpha colonies depending on their orientations with respect to the principal rolling directions. The Ti-6Al-4V-0.1B alloy shows an improved rolling response compared with the alloy Ti-6Al-4V because of smaller alpha lamellae size, coherency of alpha/beta interfaces, and multiple slip due to orientation factors. Accelerated dynamic globularization for this alloy is similarly caused by the intralamellar transverse boundary formation via multiple slip and strain accumulation at TiB particles. The (0002)(alpha) pole figures of rolled Ti-6Al-4V alloy shows ``TD splitting'' at lower rolling temperatures because of strong initial texture. Substantial beta phase mitigates the effect of starting texture at higher temperature so that ``RD splitting'' characterizes the basal pole figure. Weak starting texture and easy slip transfer for Ti-6Al-4V-0.1B alloy produce simultaneous TD and RD splittings in basal pole figures at all rolling temperatures.

Microstructure and texture evolution during sub-transus thermo-mechanical processing of Ti-6Al-4V-0.1B alloy: part II. static annealing in (alpha plus beta) regime

The first part of this study describes the evolution of microstructure and texture in Ti-6Al-4V-0.1B alloy during sub-transus rolling vis-A -vis the control alloy Ti-6Al-4V. In the second part, the static annealing response of the two alloys at self-same conditions is compared and the principal micromechanisms are analyzed. Faster globularization kinetics has been observed in the Ti-6Al-4V-0.1B alloy for equivalent annealing conditions. This is primarily attributed to the alpha colonies, which leads to easy boundary splitting via multiple slip activation in this alloy. The other mechanisms facilitating lamellar to equiaxed morphological transformations, e.g., termination migration and cylinderization, also start early in the boron-modified alloy due to small alpha colony size, small aspect ratio of the alpha lamellae, and the presence of TiB particles in the microstructure. Both the alloys exhibit weakening of basal fiber (ND||aOE (c) 0001 >) and strengthening of prism fiber (RD||aOE (c) aOE(a)) upon annealing. A close proximity between the orientations of fully globularized primary alpha and secondary alpha phases during alpha -> beta -> alpha transformation has accounted for such a texture modification.

Probing the indefinite CP nature of the Higgs boson through decay distributions in the process e(+)e(-) -> t(t)over-bar Phi

The recently discovered scalar resonance at the Large Hadron Collider is now almost confirmed to be a Higgs boson, whose CP properties are yet to be established. At the International Linear Collider with and without polarized beams, it may be possible to probe these properties at high precision. In this work, we study the possibility of probing departures from the pure CP-even case, by using the decay distributions in the process e(+)e(-) -> t (t) over bar Phi, with Phi mainly decaying into a b (b) over bar pair. We have compared the case of a minimal extension of the Standard Model case (model I) with an additional pseudoscalar degree of freedom, with a more realistic case namely the CP-violating two-Higgs doublet model (model II) that permits a more general description of the couplings. We have considered the International Linear Collider with root s = 800 GeV and integrated luminosity of 300 fb(-1). Our main findings are that even in the case of small departures from the CP-even case, the decay distributions are sensitive to the presence of a CP-odd component in model II, while it is difficult to probe these departures in model I unless the pseudoscalar component is very large. Noting that the proposed degrees of beam polarization increase the statistics, the process demonstrates the effective role of beam polarization in studies beyond the Standard Model. Further, our study shows that an indefinite CP Higgs would be a sensitive laboratory to physics beyond the Standard Model.

Fluctuations in the alpha-effect and grand solar minima

The parameters of a special type of alpha-effect known in dynamo theory as the Babcock-Leighton mechanism are estimated using the data of sunspot catalogs. The estimates support the presence of the Babcock-Leighton alpha-effect on the Sun. Fluctuations of the alpha-effect are also estimated. The fluctuation amplitude appreciably exceeds themean value, and the characteristic time for the fluctuations is comparable to the period of the solar rotation. Fluctuations with the parameters found are included in a numericalmodel for the solar dynamo. Computations show irregular changes in the amplitudes of the magnetic cycles on time scales of centuries and millennia. The calculated statistical characteristics of the grand solar minima and maxima agree with the data on solar activity over the Holocene.

Odd-even effect in the elastic modulii of alpha,omega-Alkanedicarboxylic acids

Nanoindentation studies on alpha,omega-alkanedicarboxylic acids reveal that the elastic modulus, E, shows an odd-even alternation in exactly the same manner as the melting temperature, T-m. The results are consistent with the hypothesis that the strained molecular conformations in the odd diacids are the reasons for these alternations in T-m. The same packing features that lower T-m in the odd acids lead to easy accommodation of the deformation during nanoindentation and hence their low E.