High-efficiency gene transfer into nontransformed cells: utility for studying gene regulation and analysis of potential therapeutic targets

The elucidation of the signalling pathways involved in inflammatory diseases, such as rheumatoid arthritis, could provide long sought after targets for therapeutic intervention. Gene regulation is complex and varies depending on the cell type, as well as the signal eliciting gene activation. However, cells from certain lineages, such as macrophages, are specialised to degrade exogenous material and consequently do not easily transfect. Methods for high-efficiency gene transfer into primary cells of various lineages and disease states are desirable, as they remove the uncertainties associated with using transformed cell lines. Significant research has been undertaken into the development of nonviral and viral vectors for basic research, and as vehicles for gene therapy. We briefly review the current methods of gene delivery and the difficulties associated with each system. Adenoviruses have been used extensively to examine the role of various cytokines and signal transduction molecules in the pathogenesis of rheumatoid arthritis. This review will focus on the involvement of different signalling molecules in the production of tumour necrosis factor alpha by macrophages and in rheumatoid synovium. While the NF-kappaB pathway has proven to be a major mediator of tumour necrosis factor alpha production, it is not exclusive and work evaluating the involvement of other pathways is ongoing.     

Studies on chromium(VI) adsorption-desorption using immobilized fungal biomass

The aim of this study was to investigate the Cr(VI) biosorption potential of immobilized Rhizopus nigricans and to screen a variety of non-toxic desorbing agents, in order to find out possible application in multiple sorption-desorption cycles. The biomass was immobilized by various mechanisms and evaluated for removal of Cr(VI) from aqueous solution, mechanical stability to desorbents, and reuse in successive cycles. The finely powdered biomass, entrapped in five different polymeric matrices viz. calcium alginate, polyvinyl alcohol (PVA), polyacrylamide, polyisoprene, and polysulfone was compared for biosorption efficiency and stability to desorbents. Physical immobilization to polyurethane foam and coir fiber was less efficient than polymer entrapment methods. Of the different combinations (%, w/v) of biomass dose compared for each matrix, 8% (calcium alginate), 6% (polyacrylamide and PVA), 12% (polyisoprene), and 10% (polysulfone) were found to be the optimum. The Cr sorption capacity (mg Cr/g sorbent) of all immobilized biomass was lesser than the native, powdered biomass. The Cr sorption capacity decreased in the order of free biomass (119.2) > polysulfone entrapped (101.5) > polyisoprene immobilized (98.76) > PVA immobilized (96.69) > calcium alginate entrapped (84.29) > polyacrylamide (45.56), at 500 mg/l concentration of Cr(VI). The degree of mechanical stability and chemical resistance of the immobilized systems were in the order of polysulfone > polyisoprene > PVA > polyacrylamide > calcium alginate. The bound Cr(VI) could be eluted successfully using 0.01 N NaOH, NaHCO3, and Na2CO3. The adsorption data for the native and the immobilized biomass was evaluated by the Freundlich isotherm model. The successive sorption-desorption studies employing polysulfone entrapped biomass indicated that the biomass beads could be regenerated and reused in more than 25 cycles and the regeneration efficiency was 75-78%.     

Molecular dynamics studies on HIV-1 protease drug resistance and folding pathways

Drug resistance to HIV-1 protease involves the accumulation of multiple mutations in the protein. We investigate the role of these mutations by using molecular dynamics simulations that exploit the influence of the native-state topology in the folding process. Our calculations show that sites contributing to phenotypic resistance of FDA-approved drugs are among the most sensitive positions for the stability of partially folded states and should play a relevant role in the folding process. Furthermore, associations between amino acid sites mutating under drug treatment are shown to be statistically correlated. The striking correlation between clinical data and our calculations suggest a novel approach to the design of drugs tailored to bind regions crucial not only for protein function, but for folding as well.     

Inhibitory effect of ATP analogs and actin on the modification of myosin subfragment 1 with 9-anthroylnitrile

The fluorescent probe, 9-anthroylnitrile (ANN), can selectively attach to Ser-180 at the ATP-binding site of subfragment 1 (S1) of skeletal muscle myosin [J. Biol. Chem. 278 (2003) 31891]. We have found that MgATP, MgATPgammaS, MgADP.AlF(4) or MgPP(i), but not MgADP, inhibit the incorporation of ANN into S1. The inhibitory effect of the nucleotide gamma-phosphate group (or its analog) on the modification of S1 with ANN can be explained by the contribution of Ser-180 to the binding of the nucleotide gamma-phosphate at the active site of S1. We have also observed that the incorporation of ANN into S1.MgADP complex is inhibited by actin. These experimental data strongly support the existence of nucleotide-promoted conformational changes revealed by crystal structures of S1 complexes with various nucleotide analogs. They also convincingly show an effect of actin on the environment of Ser-180 at the nucleotide binding site of S1.     

Comparative analysis of HIV-1 Tat variants

HIV-1 Tat protein is a crucial element for viral replication; therefore, its inhibition might be exploited against the AIDS infection. To gain insights on the natural variability of this protein, we present a comparative investigation on the relationship between the primary sequences and the experimentally available three-dimensional structures from the HIV-1 Tat variants Z2, BRU, and MAL. Our computational tools include sequence conservation algorithms, structural analysis, electrostatic modeling, and molecular dynamics (MD) simulations. We find that two regions located between residues 10-18 and 41-52 display the highest primary sequence conservation, while the most conserved region among the available structures corresponds approximately to the segment between positions approximately 44 and 50. Furthermore, in spite of their large structural divergence, Tat variants share a common mode for long-range intramolecular interactions. Finally, the flexibility of the Z2, BRU, and MAL variants, as emerging from multinanosecond MD simulations, is rather similar. Based on this work, we conclude that the turnlike region between amino acids 44 and 50 is structurally most conserved, emerging as an important motif for pharmaceutical targeting aimed toward inhibiting Tat action.     

Crystal structures of Escherichia coli KDO8P synthase complexes reveal the source of catalytic irreversibility

The enzyme 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase (KDO8PS) catalyses the condensation of arabinose 5-phosphate (A5P) and phosphoenol pyruvate (PEP) to obtain 3-deoxy-D-manno-2-octulosonate-8-phosphate (KDO8P). We have elucidated initial modes of ligand binding in KDO8PS binary complexes by X-ray crystallography. Structures of the apo-enzyme and of binary complexes with the substrate PEP, the product KDO8P and the catalytically inactive 1-deoxy analog of arabinose 5-phosphate (1dA5P) were obtained. The KDO8PS active site resembles an irregular funnel with positive electrostatic potential situated at the bottom of the PEP-binding sub-site, which is the primary attractive force towards negatively charged phosphate moieties of all ligands. The structures of the ligand-free apo-KDO8PS and the binary complex with the product KDO8P visualize for the first time the role of His202 as an active-site gate. Examination of the crystal structures of KDO8PS with the KDO8P or 1dA5P shows these ligands bound to the enzyme in the PEP-binding sub-site, and not as expected to the A5P sub-site. Taken together, the structures presented here strengthen earlier evidence that this enzyme functions predominantly through positional catalysis, map out the roles of active-site residues and provide evidence that explains the total lack of catalytic reversibility.