Side-chain interactions form late and cooperatively in the binding reaction between disordered peptides and PDZ domains

Intrinsically disordered proteins are very common and mediate numerous protein-protein and protein-DNA interactions. While it is clear that these interactions are instrumental for the life of the mammalian cell, there is a paucity of data regarding their molecular binding mechanisms. Here we have used short peptides as a model system for intrinsically disordered proteins. Linear free energy relationships based on rate and equilibrium constants for the binding of these peptides to ordered target proteins, PDZ domains, demonstrate that native side-chain interactions form mainly after the rate-limiting barrier for binding and in a cooperative fashion. This finding suggests that these disordered peptides first form a weak encounter complex with non-native interactions. The data do not support the recent notion that the affinities of intrinsically disordered proteins toward their targets are generally governed by their association rate constants. Instead, we observed the opposite for peptide-PDZ interactions, namely, that changes in K(d) correlate with changes in k(off).     

Supramolecular solvent microextraction of Sudan blue II in environmental samples prior to its spectrophotometric determination

A liquid phase microextraction method-based conformation of supramolecular assembly was developed for the separation and preconcentration of trace levels of Sudan blue II. Various analytical parameters such as pH, supramolecular solvent type and volume, sample volume and matrix effect etc. were optimised. Sudan blue II concentration in the extraction phase was determined by UV-visible spectrophotometer. Under the optimised conditions, detection limit and preconcentration factor was found as 2.16 µg L^?1 and 80, respectively. Relative standard deviation value was found 5%. The developed procedure was successfully applied for the determination of trace levels of Sudan blue II in environmental samples.     

Synthesis and characterization of a double photochromic initiator for cationic polymerization

A novel cationic photoinitiator namely, 2-benzyl-2-(N,N-dimethyl-2-oxo-2-phenylethyl) ammonium hexafluoroantimonate-1-(4-morpholinophenyl)-butane-1-one (BDMPP⁺ ), carrying two photochromophoric groups was synthesized and characterized. Theoretical absorption characteristics of the salt were studied and compared with those obtained experimentally. Photoinitiation activity of this salt was demonstrated by polymerization of various monomers at λ = 350 nm. Upon irradiation by UV light, cationic species formed from homolytic dissociation followed by electron transfer or directly by heterolytic scission initiate cationic polymerization.     

Speciation of antimony using chromosorb 102 resin as a retention medium.

The selective retention of the Sb(III) chelate with ammonium pyrrolidine dithiocarbamate (APDC) on a column of Chromosorb 102 resin from a buffered sample solution including Sb(V) was used for the determination of Sb(III). The retained antimony was eluted with acetone. The retention of the Sb(III)-iodide compounds with sodium iodide on the Chromosorb 102 resin column from the same solution after reducing Sb(V) to Sb(III) by iodide in acidic solution was used to preconcentrate the total antimony. The retained antimony was eluted with 0.25 mol l(-1) HNO3. The antimony in the effluent was determined by flame atomic-absorption spectrometry. Also, the total antimony was determined directly by graphite-furnace atomic absorption spectrometry. The Sb(V) concentration could be calculated by the difference. The recoveries were > or = 95%. The detection limits of a combination of the column procedure and flame AAS for antimony were 6 - 61 microg l(-1) and comparable to 4 microg l(-1) for a direct GFAAS measurement. The relative standard deviations were <6%. The procedure was applied to the determination of Sb(III) and Sb(V) in spiked tap water, waste-water samples and a certified copper metal with the satisfactory results.     

Electrochemical Determination and in silico Studies of Fludarabine on NH2 Functionalized Multiwalled Carbon Nanotube Modified Glassy Carbon Electrode

A sensitive voltammetric technique has been developed for the determination of Fludarabine using amine‐functionalized multi walled carbon nanotubes modified glassy carbon electrode (NH₂‐MWCNTs/GCE). Molecular dynamics simulations, an in silico technique, were employed to examine the properties including chemical differences of Fludarabine‐ functionalized MWCNT complexes. The redox behavior of Fludarabine was examined by cyclic, differential pulse and square wave voltammetry in a wide pH range. Cyclic voltammetric investigations emphasized that Fludarabine is irreversibly oxidized at the NH₂‐MWCNTs/GCE. The electrochemical behavior of Fludarabine was also studied by cyclic voltammetry to evaluate both the kinetic (k_s and E_a) and thermodynamic (ΔH, ΔG and ΔS) parameters on NH₂‐MWCNTs/GCE at several temperatures. The mixed diffusion‐adsorption controlled electrochemical oxidation of Fludarabine revealed by studies at different scan rates. The experimental parameters, such as pulse amplitude, frequency, deposition potential optimized for square‐wave voltammetry. Under optimum conditions in phosphate buffer (pH 2.0), a linear calibration curve was obtained in the range of 2×10^?7 M–4×10^?6 M solution using adsorptive stripping square wave voltammetry. The limit of detection and limit of quantification were calculated 2.9×10^?8 M and 9.68×10^?8 M, respectively. The developed method was applied to the simple and rapid determination of Fludarabine from pharmaceutical formulations.     

Helical Propensity in an Intrinsically Disordered Protein Accelerates Ligand Binding

Many intrinsically disordered proteins fold upon binding to other macromolecules. The secondary structure present in the well‐ordered complex is often formed transiently in the unbound state. The consequence of such transient structure for the binding process is, however, not clear. The activation domain of the activator for thyroid hormone and retinoid receptors (ACTR) is intrinsically disordered and folds upon binding to the nuclear coactivator binding domain (NCBD) of the CREB binding protein. A number of mutants was designed that selectively perturbs the amount of secondary structure in unbound ACTR without interfering with the intermolecular interactions between ACTR and NCBD. Using NMR spectroscopy and fluorescence‐monitored stopped‐flow kinetic measurements we show that the secondary structure content in helix 1 of ACTR indeed influences the binding kinetics. The results thus support the notion of preformed secondary structure as an important determinant for molecular recognition in intrinsically disordered proteins.