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.

Common-mode filter design for PWM rectifier-based motor drives

A common-mode (CM) filter based on the LCL filter topology is proposed in this paper, which provides a parallel path for ground currents and which also restricts the magnitude of the EMI noise injected into the grid. The CM filter makes use of the components of a line to line LCL filter, which is modified to address the CM voltage with minimal additional components. This leads to a compact filtering solution. The CM voltage of an adjustable speed drive using a PWM rectifier is analyzed for this purpose. The filter design is based on the CM equivalent circuit of the drive system. The filter addresses the adverse effects of the PWM rectifier in an adjustable speed drive. Guidelines are provided on the selection of the filter components. Different variants of the filter topology are evaluated to establish the effectiveness of the proposed circuit. Experimental results based on EMI measurement on the grid side and the CM current measurement on the motor side are presented. These results validate the effectiveness of the filter.

A common epitope of beta-lactoglobulin and serum retinol-binding proteins: Elucidation of its core sequence using synthetic peptides

One of the monoclonal antibodies raised against bovine beta-lactoglobulin reacted with human serum retinol binding protein. The finding that this monoclonal antibody also reacted with the serum retinol binding proteins isolated from other animals, suggested that this epitopic conformation is conserved among these proteins. Using ELISA and various synthetic peptides of defined sequence, we show in this paper that the epitope defined by this monoclonal antibody comprises of the highly conserved core sequence of DTDY present in beta-lactoglobulin and retinol binding proteins.

Studies on the variants of the protein toxins ricin and abrin

his study elucidates some structural and biological features of galactose-binding variants of the cytotoxic proteins ricin and abrin. An isolation procedure is reported for ricin variants from Ricinus communis seeds by using lactamyl-Sepharose affinity matrix, similar to that reported previously for variants of abrin from Abrus precatorius seeds [Hegde, R., Maiti, T. K. & Podder, S. K. (1991) Anal. Biochem. 194, 101–109]. Ricin variants, subfractionated on carboxymethyl-Sepharose CL-6B ion-exchange chromatography, were characterized further by SDS/PAGE, IEF and a binding assay. Based on the immunological cross-reactivity of antibody raised against a single variant of each of ricin and abrin, it was established that all the variants of the corresponding type are immunologically indistinguishable. Analysis of protein titration curves on an immobilized pH gradient indicated that variants of abrin I differ from other abrin variants, mainly in their acidic groups and that variance in ricin is a cause of charge substitution. Detection of subunit variants of proteins by two-dimensional gel electrophoresis showed that there are twice as many subunit variants as there are variants of holoproteins, suggesting that each variant has a set of subunit variants, which, although homologous, are not identical to the subunits of any other variant with respect to pI. Seeds obtained from polymorphic species of R. communis showed no difference in the profile of toxin variants, as analyzed by isoelectric focussing. Toxin variants obtained from red and white varieties of A. precatorius, however, showed some difference in the number of variants as well as in their relative intensities. Furthermore, variants analyzed from several single seeds of A. precatorius red type revealed a controlled distribution of lectin variants in three specific groups, indicating an involvement of at least three genes in the production of Abrus lectins. The complete absence or presence of variants in each group suggested a post-translational differential proteolytic processing, a secondary event in the production of abrin variants.

Mapping the common antigenic determinants in avidin and streptavidin

An epitope scan analysis of the whole sequence of avidin and core streptavidin using polyclonal antibodies to these two antigens reveal the presence of multiple common epitopes in both the proteins. These antigenic determinants consist mostly of either identical or similar residues. The antibody recognition sites in both antigens are shown to be localized to homologous regions.

Mutational analysis of active-site residues in the Mycobacterium leprae RecA intein, a LAGLIDADG homing endonuclease: Asp(122) and Asp(193) are crucial to the double-stranded DNA cleavage activity whereas Asp(218) is not

Mycobacterium leprae recA harbors an in-frame insertion sequence that encodes an intein homing endonuclease (PI-MleI). Most inteins (intein endonucleases) possess two conserved LAGLIDADG (DOD) motifs at their ctive center. A common feature of LAGLIDADG-type homing endonucleases is that they recognize and cleave the same or very similar DNA sequences. However, PI-MleI is distinctive from other members of the family of LAGLIDADG-type HEases for its modular structure with functionally separable domains for DNA-binding and cleavage, each with distinct sequence preferences. Sequence alignment analyses of PI-MleI revealed three putative LAGLIDADG motifs; however, there is conflicting bioinformatics data in regard to their identity and specific location within the intein polypeptide. To resolve this conflict and to determine the active-site residues essential for DNA target site recognition and double-stranded DNA cleavage, we performed site-directed mutagenesis of presumptive catalytic residues in the LAGLIDADG motifs. Analysis of target DNA recognition and kinetic parameters of the wild-type PI-MleI and its variants disclosed that the two amino acid residues, Asp(122) (in Block C) and Asp(193) (in functional Block E), are crucial to the double-stranded DNA endonuclease activity, whereas Asp(218) (in pseudo-Block E) is not. However, despite the reduced catalytic activity, the PI-MleI variants, like the wild-type PI-MleI, generated a footprint of the same length around the insertion site. The D122T variant showed significantly reduced catalytic activity, and D122A and D193A mutations although failed to affect their DNA-binding affinities, but abolished the double-stranded DNA cleavage activity. On the other hand, D122C variant showed approximately twofold higher double-stranded DNA cleavage activity, compared with the wild-type PI-MleI. These results provide compelling evidence that Asp(122) and Asp(193) in DOD motif I and II, respectively, are bona fide active-site residues essential for DNA cleavage activity. The implications of these results are discussed in this report.

Functional diversity of human protein kinase splice variants marks significant expansion of human kinome

Background: Protein kinases are involved in diverse spectrum of cellular processes. Availability of draft version of the human genomic data in the year 2001 enabled recognition of repertoire of protein kinases. However, over the years the human genomic data is being refined and the current release of human genomic data has helped us to recognize a larger repertoire of over 900 human protein kinases represented mainly by splice variants. Results: Many of these identified protein kinases are alternatively spliced products. Interestingly, some of the human kinase splice variants appear to be significantly diverged in terms of their functional properties as represented by incorporation or absence of one or more domains. Many sets of protein kinase splice variants have substantially different domain organization and in a few sets of splice variants kinase domains belong to different subfamilies of kinases suggesting potential participation in different signal transduction pathways. Conclusions: Addition or deletion of a domain between splice variants of multi-domain kinases appears to be a means of generating differences in the functional features of otherwise similar kinases. It is intriguing that marked sequence diversity within the catalytic regions of some of the splice variant kinases result in kinases belonging to different subfamilies. These human kinase splice variants with different functions might contribute to diversity of eukaryotic cellular signaling.

Perpetuation of immunological memory through common MHC-I binding modes of peptidomimic and antigenic peptides

Understanding the molecular mechanisms of immunological memory assumes importance in vaccine design. We had earlier hypothesized a mechanism for the maintenance of immunological memory through the operation of a network of idiotypic and anti-idiotypic antibodies (Ab2). Peptides derived from an internal image carrying anti-idiotypic antibody are hypothesized to facilitate the perpetuation of antigen specific T cell memory through similarity in peptide-MHC binding as that of the antigenic peptide. In the present work, the existence of such peptidomimics of the antigen in the Ab2 variable region and their similarity of MHC-I binding was examined by bioinformatics approaches. The analysis employing three known viral antigens and one tumor-associated antigen shows that peptidomimics from Ab2 variable regions have structurally similar MHC-I binding patterns as compared to antigenic peptides, indicating a structural basis for memory perpetuation. (C)) 2007 Elsevier Inc. All rights reserved.

Three-level inverter fed open-end winding IM drive with common mode voltage elimination and reduced power device count

A three-level space phasor generation scheme with common mode elimination and with reduced power device count is proposed for an open end winding induction motor in this paper. The open end winding induction motor is fed by the three-level inverters from both sides. Each two level inverter is formed by cascading two two-level inverters. By sharing the bottom inverter for the two three-level inverters on either side, the power device count is reduced. The switching states with zero common mode voltage variation are selected for PWM switching so that there is no alternating common mode voltage in the pole voltages as well as in phase voltages. Only two isolated DC-links, with half the voltage rating of a conventional three-level neutral point clamped inverter, are needed for the proposed scheme.

A novel fibre-coated sorbent for rapid removal of heavy metals from wastewater. Sorption of Zinc(II) from dilute aqueous solutions in the presence of high concentrations of common salts

The commercial acrylic fibre "Cashmilon" was partially hydrolyzed to convert a fraction of its nitrile (-CN) groups to carboxylic acid (-COOH) groups and then coated with polyethylenimine (PEI) resin and cross-linked with glutaraldehyde to produce a novel gel-coated fibrous sorbent with multiple functionalities of cationic, anionic and chelating types, and significantly faster sorption kinetics than bead-form sorbents. The sorption properties of the fibrous sorbent were measured using Zn(II) in aqueous solution as the sorbate to determine the effects of pH and the presence of common ions in the solution on the sorption capacity. The rate of sorption on the gel-coated fibre was measured in comparison with that on Amberlite IRA-68 weak-base resin beads, to demonstrate the marked difference between fibre and bead-form sorbents in their kinetic behaviour.

Secondary flow induced by the rotation of two concentric spheres about their common diameter in micropolar fluids

In this paper, we have studied the secondary flow induced in a micropolar fluid by the rotation of two concentric spheres about a fixed diameter. The secondary flow exhibits behaviour commonly observed in visco-elastic fluids. In particular we have obtained the expressions for microrotation vector. Numerical results have been obtained for a number of values of relative rotations of the two spheres for a chosen set of values of fluid parameters. The results are presented graphically and compared with the previous investigations.

A novel fibre-coated sorbent for rapid removal of heavy metals from wastewater. Sorption of Zinc(II) from dilute aqueous solutions in the presence of high concentrations of common salts

The commercial acrylic fibre "Cashmilon" was partially hydrolyzed to convert a fraction of its nitrile (-CN) groups to carboxylic acid (-COOH) groups and then coated with polyethylenimine (PEI) resin and cross-linked with glutaraldehyde to produce a novel gel-coated fibrous sorbent with multiple functionalities of cationic, anionic and chelating types, and significantly faster sorption kinetics than bead-form sorbents. The sorption properties of the fibrous sorbent were measured using Zn(II) in aqueous solution as the sorbate to determine the effects of pH and the presence of common ions in the solution on the sorption capacity. The rate of sorption on the gel-coated fibre was measured in comparison with that on Amberlite IRA-68 weak-base resin beads, to demonstrate the marked difference between fibre and bead-form sorbents in their kinetic behaviour.

Low Power continuous time common mode sensing for common mode feedback circuits

Continuous common mode feedback (CMFB) circuits having high input impedance and low distortion are proposed. The proposed circuits are characterized for 0.18 mu m CMOS process with 1.8 V supply. Simulation results indicate that the proposed common mode detector consumes no standby power and CMFB circuit consumes 27-34% less power than previous high swing CMFB circuits.

X-ray Crystallographic Analysis of the Complexes of Enoyl Acyl Carrier Protein Reductase of Plasmodium falciparum with Triclosan Variants to Elucidate the Importance of Different Functional Groups in Enzyme Inhibition

Triclosan, a well-known inhibitor of Enoyl Acyl Carrier Protein Reductase (ENR) from several pathogenic organisms, is a promising lead compound to design effective drugs. We have solved the X-ray crystal structures of Plasmodium falciparum ENR in complex with triclosan variants having different substituted and unsubstituted groups at different key functional locations. The structures revealed that 4 and 2' substituted compounds have more interactions with the protein, cofactor, and solvents when compared with triclosan. New water molecules were found to interact with some of these inhibitors. Substitution at the 2' position of triclosan caused the relocation of a conserved water molecule, leading to an additional hydrogen bond with the inhibitor. This observation can help in conserved water-based inhibitor design. 2' and 4' unsubstituted compounds showed a movement away from the hydrophobic pocket to compensate for the interactions made by the halogen groups of triclosan. This compound also makes additional interactions with the protein and cofactor which compensate for the lost interactions due to the unsubstitution at 2' and 4'. In cell culture, this inhibitor shows less potency, which indicates that the chlorines at 2' and 4' positions increase the ability of the inhibitor to cross multilayered membranes. This knowledge helps us to modify the different functional groups of triclosan to get more potent inhibitors. (C) 2010 IUBMB IUBMB Life, 62(6): 467-476.

Elimination of common mode voltage and fifth and seventh harmonics in a multilevel inverter fed IM drive using 12-sided polygonal voltage spacephasor

A multilevel inverter with 12-sided polygonal voltage space vector structure is proposed in this paper. The present scheme provides elimination of common mode voltage variation and 5(th) and 7(th) order harmonics in the entire operating range of the drive. The proposed multi level structure is achieved by cascading only the conventional two-level inverters with asymmetrical DC link voltages. The bandwidths problems associated with conventional hexagonal voltage space vector structure current controllers, due to the presence of 5(th) and 7(th) harmonics, in the over modulation region, is absent in the present 12-sided structure. So a linear voltage control up to 12-step operation is possible, from the present twelve sided scheme, with less current control complexity. An open-end winding structure is used for the induction motor drive.