The binding of divalent metal ions to polyelectrolytes in mixed counterion systems. I. The dye spectrophotometric method

The dye spectrophotometric method for the measurement of the activity of divalent metal ions in polyelectrolyte solutions containing added electrolytes is discussed.The method is applied to mixtures containing the dextransulfate polyanion, NaCl, and MgCl2 or Ca2. A two wavelength ratio method as applied to polyelectrolyte solutions is compared to the standard method which makes use of the previous determination of the dye-metal ion formation constant. The ratio method is found to be a convenient and reliable method which is not influenced by decomposition of the dye or by statistical errors in the extrapolation procedure. The activity coefficients as determined by the two wavelength dye spectrophotometric method are compared to results of Donnan exclusion measurements, and of EMF measurements using a calcium ion selective electrode. The results of the spectrophotometric method are equal to those of the two other methods within the limits of error in the latter. The spectrophotometric measurements can extend to much lower ion activaties than the other two methods, and can be done in the presence of a large excess of added electrolyte, yielding results of considerably improved precision when compared to Donnan and EMF methods.     

The binding of divalent metal ions to polyelectrolytes in mixed counterion systems. II. Dextransulfate-Mg2+ and dextransulfate-Ca2+ in solutions containing added NaCl or KCl

Measurements of magnesium and calcium ion activities in solutions of the polyelectrolyte dextransulfate, with added sodium chloride or potassium chloride are presented. A two wavelength dye spectrophotometric method is used. Dextransulfate concentrations Cp (expressed as moles sulfate ion/litre) vary between 0.001 and 0.007, total ionic strengths between 0.005 and 0.08 mole/XXX. Divalent metal ion concentrations are varied between 0 and 1.2 Cp. The results for the metal ion activities are expressed in the form of parameters theta2 = C2/Cp (C(2bp) = bound divalent metal ion concentration) and K2 = theta2/(C2-C2b). For each divalent/univalent counterion pair the values obtained for theta2 and K2 as a function of C2,Cp, and ionic strength are compared to predictions of the "two variable theory" developed for these mixed counterion systems by Manning. This comparison shows that the observed decrease in theta2 with increasing ionic strength at fixed C2 and Cp is generally well predicted by the two variable theory. The extent of divalent ion binding at a given C2, Cp, and ionic strength is largest for the Ca/Na counterion combination, and lowest for the Mg/K combination.     

Single amino acid substitution in HIV-1 integrase catalytic core causes a dramatic shift in inhibitor selectivity

HIV-1 integrase (IN) mediates the insertion of viral cDNA into the cell genome, a vital process for replication. This step is catalyzed by two separate DNA reaction events, termed 3'-processing and strand transfer. Here, we show that six inhibitors from five structurally different classes of compounds display a selectivity shift towards preferential strand transfer inhibition over the 3'-processing activity of IN when a single serine is substituted at position C130. Even though IN utilizes the same active site for both reactions, this finding suggests a distinct conformational dissimilarity in the mechanistic details of each IN catalytic event.     

Characterization and optimization of a simple, repeatable system for the long term in vitro culture of aligned myotubes in 3D

Increased recent research activity in exercise physiology has dramatically improved our understanding of skeletal muscle development and physiology in both health and disease. Advances in bioengineering have enabled the development of biomimetic 3D in vitro models of skeletal muscle which have the potential to further advance our understanding of the fundamental processes that underpin muscle physiology. As the principle structural protein of the extracellular matrix, collagen-based matrices are popular tools for the creation of such 3D models but the custom nature of many reported systems has precluded their more widespread adoption. Here we present a simple, reproducible iteration of an established 3D in vitro model of skeletal muscle, demonstrating both the high levels of reproducibility possible in this system and the improved cellular architecture of such constructs over standard 2D cell culture techniques. We have used primary rat muscle cells to validate this simple model and generate comparable data to conventional established cell culture techniques. We have optimized culture parameters for these cells which should provide a template in this 3D system for using muscle cells derived from other donor species and cell lines.     

Pharmacophore modelling and atom-based 3D-QSAR studies on N-methyl pyrimidones as HIV-1 integrase inhibitors

Pharmacophore modelling and atom-based 3D-QSAR studies were carried out for a series of compounds belonging to N-methyl pyrimidones as HIV-1 integrase inhibitors. Based on the ligand-based pharmacophore model, we got 5-point pharmacophore model AADDR, with two hydrogen bond acceptors (A), two hydrogen bond donors (D) and one aromatic ring (R). The generated pharmacophore-based alignment was used to derive a predictive atom-based 3D-QSAR model for the training set (r²?=?0.92, SD?=?0.16, F?=?84.8, N?=?40) and for test set (Q²?=?0.71, RMSE?=?0.06, Pearson R?=?0.90, N?=?10). From these results, AADDR pharmacophore feature was selected as best common pharmacophore hypothesis, and atom-based 3D-QSAR results also support the outcome by means of favourable and unfavourable regions of hydrophobic and electron-withdrawing groups for the most potent compound 30. These results can be useful for further design of new and potent HIV-1 IN inhibitors.     

Oligonucleotide-based assays for integrase activity

Oligonucleotide assays have been invaluable for elucidation of the molecular mechanisms of retroviral integrases. A suite of rapid and sensitive fluorescence assays to measure the DNA binding, processing, and joining activities of integrase (IN) is described here. The assays are especially useful for characterizing the major activities of the enzyme, and for handling large numbers of samples efficiently. They can greatly facilitate further biochemical and structural analyses for HIV-1 and other IN proteins. The assays can also be adapted for moderate-high throughput testing of various inhibitory compounds.     

HIV-1 Protease Uses Bi-Specific S2/S2′ Subsites to Optimize Cleavage of Two Classes of Target Sites

Retroviral proteases (PRs) have a unique specificity that allows cleavage of sites with or without a P1′ proline. A P1′ proline is required at the MA/CA cleavage site due to its role in a post-cleavage conformational change in the capsid protein. However, the HIV-1 PR prefers to have large hydrophobic amino acids flanking the scissile bond, suggesting that PR recognizes two different classes of substrate sequences. We analyzed the cleavage rate of over 150 combinations of six different HIV-1 cleavage sites to explore rate determinants of cleavage. We found that cleavage rates are strongly influenced by the two amino acids flanking the amino acids at the scissile bond (P2–P1/P1′–P2′), with two complementary sets of rules. When P1′ is proline, the P2 side chain interacts with a polar region in the S2 subsite of the PR, while the P2′ amino acid interacts with a hydrophobic region of the S2′ subsite. When P1′ is not proline, the orientations of the P2 and P2′ side chains with respect to the scissile bond are reversed; P2 residues interact with a hydrophobic face of the S2 subsite, while the P2′ amino acid usually engages hydrophilic amino acids in the S2′ subsite. These results reveal that the HIV-1 PR has evolved bi-functional S2 and S2′ subsites to accommodate the steric effects imposed by a P1′ proline on the orientation of P2 and P2′ substrate side chains. These results also suggest a new strategy for inhibitor design to engage the multiple specificities in these subsites.