Structural Basis of Drug Resistance by Genetic Variants of HIV Type 1 Clade C Protease from India

Using computer modeling of three-dimensional structures and structural information available on the crystal structures of HIV-1 protease, we investigated the structural effects of mutations, in treatment-naive and treatment-exposed individuals from India and postulated mechanisms of resistance in clade C variants. A large number of models (14) have been generated by computational mutation of the available crystal structures of drug bound proteases. Localized energy minimization was carried out in and around the sites of mutation in order to optimize the geometry of interactions present. Most of the mutations result in structural differences at the flap that favors the semiopen state of the enzyme. Some of the mutations were also found to confer resistance by affecting the geometry of the active site. The E35D mutation affects the flap structure in clade B strains and E35N and E35K mutation, seen in our modeled strains, have a more profound effect. Common polymorphisms at positions 36 and 63 in clade C also affected flap structure. Apart from a few other residues Gln-58, Asn-83, Asn-88, and Gln-92 and their interactions are important for the transition from the closed to the open state. Development of protease inhibitors by structure-based design requires investigation of mechanisms operative for clade C to improve the efficacy of therapy.

Biochemical characterization of the intracellular domain of the human guanylyl cyclase C receptor provides evidence for a catalytically active homotrimer

Guanylyl cyclase C (GCC) is the receptor for the family of guanylin peptides and bacterial heat-stable enterotoxins (ST). The receptor is composed of an extracellular, ligand-binding domain and an intracellular domain with a region of homology to protein kinases and a guanylyl cyclase catalytic domain. We have expressed the entire intracellular domain of GCC in insect cells and purified the recombinant protein, GCC-IDbac, to study its catalytic activity and regulation. Kinetic properties of the purified protein were similar to that of full-length GCC, and high activity was observed when MnGTP was used as the substrate. Nonionic detergents, which stimulate the guanylyl cyclase activity of membrane-associated GCC, did not appreciably increase the activity of GCC-IDbac, indicating that activation of the receptor by Lubrol involved conformational changes that required the transmembrane and/or the extracellular domain. The guanylyl cyclase activity of GCC-IDbac was inhibited by Zn2+, at concentrations shown to inhibit adenylyl cyclase, suggesting a structural homology between the two enzymes. Covalent crosslinking of GCC-IDbac indicated that the protein could associate as a dimer, but a large fraction was present as a trimer. Gel filtration analysis also showed that the major fraction of the protein eluted at a molecular size of a trimer, suggesting that the dimer detected by cross-linking represented subtle differences in the juxtaposition of the individual polypeptide chains. We therefore provide evidence that the trimeric state of GCC is catalytically active, and sequences required to generate the trimer are present in the intracellular domain of GCC.

Fluorescence quenching of biologically active carboxamide by aniline and carbon tetrachloride in different solvents using Stern-Volmer plots

Fluorescence quenching of biologically active carboxamide namely (E)-2-(4-chlorobenzylideneamino)-N-(2-chlorophenyl)-4,5,6,7-tetrahydrobe nzo[b]thiophene-3-carboxamide [ECNCTTC] by aniline and carbon tetrachloride (CCl(4)) quenchers in different solvents using steady state method and time resolved method using only one solvent has been carried out at room temperature to understand the role of quenching mechanisms. The Stern-Volmer plot has been found to be linear for all the solvents studied. The probability of quenching per encounter p (p') was determined in all the solvents and was found to be less than unity. Further, from the studies of rate parameters and life time measurements in n-heptane and cyclohexane with aniline and carbon tetrachloride as quenchers have been shown that, the phenomenon of quenching is generally governed by the well-known Stern-Volmer (S-V) plot. The activation energy E(a) (or E(a)') of quenching was determined using the literature values of activation energy of diffusion E(d) and the experimentally determined values of p (or p'). It has been found that, the activation energy E(a) (E(a)') is greater than the activation energy for diffusion E(d) in all solvents. Hence, from the magnitudes of E(a) (or E(a)') as well as p (or p') infer that, the quenching mechanism is not solely due to the material diffusion, but there is also contribution from the activation energy. (C) 2011 Elsevier B.V. All rights reserved.

Solvent effect on the fluorescence quenching of biologically active carboxamide by aniline and carbon tetrachloride in different solvents using S-V plots

The fluorescence quenching studies of carboxamide namely (E)-N-(3-Chlorophenyl)-2-(3,4,5-trimethoxybenzylideneamino)-4,5,6,7 tetrahydrobenzob]thiophene-3-carboxamide ENCTTTC] by aniline and carbon tetrachloride in six different solvents namely toluene, cyclohexane, n-hexane, n-heptane, n-decane and n-pentane have been carried out at room temperature with a view to understand the quenching mechanisms. The Stern-Volmer (S-V) plots have been found to be nonlinear with a positive deviation for all the solvents studied. In order to interpret these results we have invoked the ground state complex formation and sphere of action static quenching models. Using these models various quenching rate parameters have been determined. The magnitudes of these parameters suggest that sphere of action static quenching model agrees well with the experimental results. Hence the positive deviation is attributed to the static and dynamic quenching. Further, with the use of Finite Sink approximation model, it was possible to check these bimolecular reactions as diffusion-limited and to estimate independently distance parameter R' and mutual diffusion coefficient D. Finally an effort has been made to correlate the values of R' and D with the values of the encounter distance R and the mutual coefficient D determined using the Edward's empirical relation and Stokes Einstein relation. (C) 2011 Elsevier B.V. All rights reserved.

Hyperexpression of biologically active human chorionic gonadotropin using the methylotropic yeast, Pichia pastoris

Human chorionic gonadotropin (hCG), a heterodimeric glycoprotein hormone, is composed of an alpha subunit noncovalentlv associated with the hormone-specific beta subunit. The objective of the present study was recombinant expression of properly folded, biologically active hCG and its subunits using an expression system that could be used for structure-function studies while providing adequate quantities of the hormone for immunocontraceptive studies. We report here expression of biologically active hCG and its subunits using a yeast expression system, Pichia pastoris. The recombinant hGG alpha and hCG beta subunits were secreted into the medium and the levels of expression achieved at shake culture level were 24 and 2.7-3 mg/l secretory medium respectively. Go-expression of both subunits in the same cell resulted in secretion of heterodimeric hGG into the medium. The pichia-expressed hCG was immunologically similar to the native hormone, capable of binding to the LH receptors and stimulating a biological response in vitro. Surprisingly, the maximal response obtained was twice that obtained with the native hGG. The le level of expression of hCG achieved was 12-16 mg/l secretory medium and is expected to increase several-fold in a fermenter. Thus the Pichia expression system is capable of hyperexpressing properly folded, biologically active hGG and is suitable for structure-function studies of the hormone.

A theoretical model for the magnetic helicity of solar active regions

Active regions on the solar surface are known to possess magnetic helicity, which is predominantly negative in the northern hemisphere and positive in the southern hemisphere. Choudhuri et al. [Choudhuri, A.R. On the connection between mean field dynamo theory and flux tubes. Solar Phys. 215, 31–55, 2003] proposed that the magnetic helicity arises due to the wrapping up of the poloidal field of the convection zone around rising flux tubes which form active regions. Choudhuri [Choudhuri, A.R., Chatterjee, P., Nandy, D. Helicity of solar active regions from a dynamo model. ApJ 615, L57–L60, 2004] used this idea to calculate magnetic helicity from their solar dynamo model. Apart from getting broad agreements with observational data, they also predict that the hemispheric helicity rule may be violated at the beginning of a solar cycle. Chatterjee et al. [Chatterjee, P., Choudhuri, A.R., Petrovay, K. Development of twist in an emerging magnetic flux tube by poloidal field accretion. A&A 449, 781–789, 2006] study the penetration of the wrapped poloidal field into the rising flux tube due to turbulent diffusion using a simple 1-d model. They find that the extent of penetration of the wrapped field will depend on how weak the magnetic field inside the rising flux tube becomes before its emergence. They conclude that more detailed observational data will throw light on the physical conditions of flux tubes just before their emergence to the photosphere.

Conformation of the flexible bent helix of Leu1-zervamicin in crystal C and a possible gating action for ion passage

The membrane channel-forming polypeptide, Leu(1)-zervamicin, Ac-Leu-Ile-Gln-Iva-Ile(5)-Thr-Aib-Leu-Aib-Hyp(10) -Gln-Aib-Hyp-Aib-Pro(15)-Phol (Aib: alpha-aminoisobutyric acid; Iva: isovaline; Hyp: 4-hydroxyproline; Phol: phenylalininol) has been analyzed by x-ray diffraction in a third crystal form. Although the bent helix is quite similar to the conformations found in crystals A and B, the amount of bending is more severe with a bending angle approximate to 47 degrees, The water channel formed by the convex polar faces of neighboring helices is larger at the mouth than in crystals A and B, and the water sites have become disordered. The channel is interrupted in the middle by a hydrogen bond between the OH of Hyp(10) and the NH2 of the Gln(11) of a neighboring molecule. The side chain of Gln(11) is wrapped around the helix backbone in an unusual fashion in order that it can augment the polar side of the helix. In the present crystal C there appears to be an additional conformation for the Gln(11) side chain (with approximate to 20% occupancy) that opens the channel for possible ion passage. Structure parameters for C85H140N18O22.xH(2)O.C2H5OH are space group P2(1)2(1)2(1), a = 10.337 (2) Angstrom, b = 28.387 (7) Angstrom, c = 39.864 (11) Angstrom, Z = 4, agreement factor R = 12.99% for 3250 data observed > 3 sigma(F), resolution = 1.2 Angstrom. (C) 1994 John Wiley & Sons, Inc.

Cloning,overexpression and purification of functionally active Saccharomyces cerevisiae Hop1 protein from scherichia coli

One of the major limitations to the application of high-resolution biophysical techniques such as X-crystallography and spectroscopic analyses to structure-function studies of Saccharomyces cerevisiae Hop1 protein has been the non-availability of sufficient quantities of functionally active pure protein. This has, indeed, been the case of many proteins, including yeast synaptonemal complex proteins. In this study, we have performed expression screening in Escherichia coli host strains, capable of high-level expression of soluble S. cerevisiae Hop1 protein. A new protocol has been developed for expression and purification of S. cerevisiae Hop1 protein, based on the presence of hexa-histidine tag and double-stranded DNA-Cellulose chromatography. Recombinant S. cerevisiae Hop1 protein was >98% pure and exhibited DNA-binding activity with high-affinity to the Holliday junction. The availability of the recombinant HOP1 expression vector and active Hop1 protein would facilitate structure-function investigations as well as the generation of appropriate truncated and site-directed mutant proteins, respectively. (C) 2010 Elsevier Inc. All rights reserved.

Structure of N-nitroso-r-2,c-7-diphenylhexahydro-1,4-diazepin-5-one

C17H17N3O2, M(r) = 295.34, orthorhombic, P2(1)2(1)2(1), a = 7.659 (1), b = 12.741 (1), c = 15.095 (1) angstrom, V = 1473.19 (2) angstrom 3, Z = 4, D(m) = 1.33, D(x) = 1.32 Mg m-3, lambda(Cu K-alpha) = 1.5418 angstrom, mu = 0.68 mm-1, F(000) = 624, T = 295 K, R = 0.031 for 1549 unique observed reflections with I > 2.5-sigma(I). The seven-membered heterocyclic ring adopts a boat conformation flattened at the nitroso end of the ring. The substituent phenyl rings occupy pseudo-axial positions and the nitroso group is coplanar with the C(2), N(1), C(7) plane of the central ring. The crystal structure is stabilized by intermolecular N-H...O and weak C-H...O hydrogen bonds.

Influence of Si-C bond density on the properties of a-Si(1-x)C(x) thin films

Amorphous silicon carbide (a-Si(1-x)C(x)) films were deposited on silicon (100) and quartz substrates by pulsed DC reactive magnetron sputtering of silicon in methane (CH(4))-Argon (Ar) atmosphere. The influence of substrate temperature and target power on the composition, carbon bonding configuration, band gap, refractive index and hardness of a-SiC films has been investigated. Increase in substrate temperature results in slightly decreasing the carbon concentration in the films but favors silicon-carbon (Si-C) bonding. Also lower target powers were favorable towards Si-C bonding. X-ray photoelectron spectroscopy (XPS) results agree with the Fourier Transform Infrared (FTIR), UV-vis spectroscopy results. Increase in substrate temperature resulted in increased hardness of the thin films from 13 to 17 GPa and the corresponding bandgap varied from 2.1 to 1.8 eV. (C) 2011 Elsevier B.V. All rights reserved.

Molybdenum trioxide catalyzed oxidative cross-dehydrogenative coupling of benzylic sp(3) C-H bonds: synthesis of alpha-aminophosphonates under aerobic conditions

Molybdenum trioxide (MoO3) catalyzed efficient oxidative cross-dehydrogenative-coupling (CDC) method for C-H functionalization of N-aryl tetrahydroisoquinolines has been explored. This user-friendly method of synthesizing alpha-aminophosphonates employs 1.1 equiv of dialkyl-H-phosphonate under aerobic condition. Formation of new C-P bonds from unfunctionalized starting materials under environmentally benign conditions provides an excellent avenue for the synthesis of biologically active alpha-aminophosphonates. (C) 2012 Elsevier Ltd. All rights reserved.

Molecular topology of three ring nematogens from C-13-H-1 dipolar couplings

Molecules in their liquid crystalline phase undergo rotational motion about the long axis of the molecule and the shape adopted by the rotating molecule plays an important role in influencing the mesophase morphology. In this context, obtaining the topology and the relative orientation of the different sub-units are important steps. For studying the liquid crystalline phase, C-13 NMR spectroscopy is a convenient method and for certain specifically designed nematogens, 2-dimensional separated local field (2D-SLF) NMR spectroscopy provides a particularly simple and straightforward means of arriving at the molecular topology. We demonstrate this approach on two three ring based nematogens designed with a phenyl or a thiophene ring at one of the termini. From the C-13-H-1 dipolar couplings of the terminal carbon obtained using the 2D-SLF NMR technique, the order parameter of the local symmetry axis of the terminal phenyl ring as well as of the long molecular axis could be easily estimated. For the thiophene nematogen, the lack of symmetry of the thiophene moiety necessitates some additional computational steps. The results indicate that the thiophene unit has its local ordering axis oriented away from the long molecular axis by a small angle, consistent with a bent structure expected in view of the thiophene geometry. The experiment also demonstrates the ability of 2D-SLF NMR to provide high resolution spectra by separation of several overlapped resonances in terms of their C-13-H-1 dipolar couplings. The results are consistent with a rod-like topology of the core of the investigated mesogens. The investigation demonstrates the potential of 2D-SLF NMR C-13 spectroscopy for obtaining atomistic level information and its utility for topological studies of different mesogens.

Co-liposomes of redox-active alkyl-ferrocene modified low MW branched PEI and DOPE for efficacious gene delivery in serum

Herein, we present six new lipopolymers based on low molecular weight, branched polyethylenimine (BPEI 800 Da) which are hydrophobically modified using ferrocene terminated alkyl tails of variable lengths. The effects of degree of grafting, spacer length and the redox state of ferrocene in the lipopolymers on the self assembly properties were investigated in detail by TEM, AFM, DLS and zeta potential measurements. The assemblies displayed an oxidation induced increase in the size of the aggregates. The co-liposomes comprising the lipopolymer and a helper lipid, 1,2-dioleoyl phosphatidyl ethanolamine (DOPE), showed excellent gene (pDNA) delivery capability in a serum containing environment in two cancer cell lines (HeLa and U251 cells). Optimized formulations showed remarkably higher transfection activity than BPEI (25 kDa) and were also significantly better than a commercial transfection reagent, Lipofectamine 2000 as evidenced from both the luciferase activity and GFP expression analysis. Oxidation of ferrocene in the lipopolymers led to drastically reduced levels of gene transfection which was substantiated by reduced cellular internalization of fluorescently labelled pDNA as detected using confocal microscopy and flow cytometry. Moreover, the transfection inactive oxidized lipopolyplexes could be turned transfection active by exposure to ascorbic acid (AA) in cell culture medium during transfection. Endocytosis inhibition experiments showed that gene expression mediated by reduced formulations involved both clathrin and caveolae mediated pathways while the oxidized formulations were routed via the caveolae. Cytotoxicity assays revealed no obvious toxicity for the lipopolyplexes in the range of optimized transfection levels in both the cell lines studied. Overall, we have exploited the redox activity of ferrocene in branched PEI-based efficient polymeric gene carriers whose differential transfection activities could be harnessed for spatial or temporal cellular transfections.

Microwave Spectrum of Hexafluoroisopropanol and Torsional Behavior of Molecules with a CF3-C-CF3 Group

This paper presents the first microwave spectroscopic investigation on hexafluoroisopropanol (HFIP). A pulsed nozzle Fourier transform microwave spectrometer has been used to determine the rotational constants for HFIP as A = 2105.12166(18) MHz, B = 1053.99503(12) MHz, and C = 932.33959(13) MHz. In addition, five isotopologues of HFIP have been observed experimentally to determine the accurate structure of HFIP. The observed spectrum could be assigned to the most stable conformer of HFIP, called antiperiplanar. Available spectroscopic information and ab initio calculations on five prototype molecules helped in exploring the torsional behavior of molecules having a CF3-C-CF3 group. Two-dimensional potential energy surfaces have been analyzed for all molecules, which explained the presence/absence of doubling in the rotational transitions. With the help of natural bond orbital (NBO) analysis, reasons for the conformational preference of HFIP have been explained.