Resolving Multiple Protein–Peptide Binding Events: Implication for HLA-DQ2 Mediated Antigen Presentation in Celiac Disease

Techniques that can effectively separate protein–peptide complexes from free peptides have shown great value in major histocompatibility complex (MHC)–peptide binding studies. However, most of the available techniques are limited to measuring the binding of a single peptide to an MHC molecule. As antigen presentation in vivo involves both endogenous ligands and exogenous antigens, the deconvolution of multiple binding events necessitates the implementation of a more powerful technique. Here we show that capillary electrophoresis coupled to fluorescence detection (CE–FL) can resolve multiple MHC–peptide binding events owing to its superior resolution and the ability to simultaneously monitor multiple emission channels. We utilized CE–FL to investigate competition and displacement of endogenous peptides by an immunogenic gluten peptide for binding to HLA-DQ2. Remarkably, this immunogenic peptide could displace CLIP peptides from the DQ2 binding site at neutral but not acidic pH. This unusual ability of the gluten peptide supports a direct loading mechanism of antigen presentation in extracellular environment, a property that could explain the antigenicity of dietary gluten in celiac disease.     

Dye and its removal from aqueous solution by adsorption: A review

In this review article the authors presented up to-date development on the application of adsorption in the removal of dyes from aqueous solution. This review article provides extensive literature information about dyes, its classification and toxicity, various treatment methods, and dye adsorption characteristics by various adsorbents. One of the objectives of this review article is to organise the scattered available information on various aspects on a wide range of potentially effective adsorbents in the removal of dyes. Therefore, an extensive list of various adsorbents such as natural materials, waste materials from industry, agricultural by-products, and biomass based activated carbon in the removal of various dyes has been compiled here. Dye bearing waste treatment by adsorption using low cost alternative adsorbent is a demanding area as it has double benefits i.e. water treatment and waste management. Further, activated carbon from biomass has the advantage of offering an effected low cost replacement for non-renewable coal based granular activated carbon provided that they have similar or better adsorption on efficiency. The effectiveness of various adsorbents under different physico-chemical process parameters and their comparative adsorption capacity towards dye adsorption has also been presented. This review paper also includes the affective adsorption factors of dye such as solution pH, initial dye concentration, adsorbent dosage, and temperature. The applicability of various adsorption kinetic models and isotherm models for dye removal by wide range of adsorbents is also reported here. Conclusions have been drawn from the literature reviewed and few suggestions for future research are proposed.     

PtII Coordination to N1 of 9‐Methylguanine: Why it Facilitates Binding of Additional Metal Ions to the Purine Ring

The preparation and X‐ray crystal structure analysis of {trans‐[Pt(MeNH₂)₂(9‐MeG‐N1)₂]} ? {3 K₂[Pt(CN)₄]} ? 6 H₂O ( 3 a ) (with 9‐MeG being the anion of 9‐methylguanine, 9‐MeGH) are reported. The title compound was obtained by treating [Pt(dien)(9‐MeGH‐N7)]²⁺ ( 1 ; dien=diethylenetriamine) with trans‐[Pt(MeNH₂)₂(H₂O)₂]²⁺ at pH 9.6, 60 °C, and subsequent removal of the [(dien)Pt^II] entities by treatment with an excess amount of KCN, which converts the latter to [Pt(CN)₄]^2?. Cocrystallization of K₂[Pt(CN)₄] with trans‐[Pt(MeNH₂)₂(9‐MeG‐N1)₂] is a consequence of the increase in basicity of the guanine ligand following its deprotonation and Pt coordination at N1. This increase in basicity is reflected in the pK_a values of trans‐[Pt(MeNH₂)₂(9‐MeGH‐N1)₂]²⁺ (4.4±0.1 and 3.3±0.4). The crystal structure of 3 a reveals rare (N7,O6 chelate) and unconventional (N2,C2,N3) binding patterns of K⁺ to the guaninato ligands. DFT calculations confirm that K⁺ binding to the sugar edge of guanine for a N1‐platinated guanine anion is a realistic option, thus ruling against a simple packing effect in the solid‐state structure of 3 a . The linkage isomer of 3 a , trans‐[Pt(MeNH₂)₂(9‐MeG‐N7)₂] ( 6 a ) has likewise been isolated, and its acid–base properties determined. Compound 6 a is more basic than 3 a by more than 4 log units. Binding of metal entities to the N7 positions of 9‐MeG in 3 a has been studied in detail for [(NH₃)₃Pt^II], trans‐[(NH₃)₂Pt^II], and [(en)Pd^II] (en=ethylenediamine) by using ¹H NMR spectroscopy. Without exception, binding of the second metal takes place at N7, but formation of a molecular guanine square with trans‐[(Me₂NH₂)Pt^II] cross‐linking N1 positions and trans‐[(NH₃)₂Pt^II] cross‐linking N7 positions could not be confirmed unambiguously, despite the fact that calculations are fully consistent with its existence.     

A small molecule discrimination map of the antibiotic resistance kinome

Kinase-mediated resistance to antibiotics is a significant clinical challenge. These enzymes share a common protein fold characteristic of Ser/Thr/Tyr protein kinases. We screened 14 antibiotic resistance kinases against 80 chemically diverse protein kinase inhibitors to map resistance kinase chemical space. The screens identified molecules with both broad and narrow inhibition profiles, proving that protein kinase inhibitors offer privileged chemical matter with the potential to block antibiotic resistance. One example is the flavonol quercetin, which inhibited a number of resistance kinases in vitro and in vivo. This activity was rationalized by determination of the crystal structure of the aminoglycoside kinase APH(2″)-IVa in complex with quercetin and its antibiotic substrate kanamycin. Our data demonstrate that protein kinase inhibitors offer chemical scaffolds that can block antibiotic resistance, providing leads for co-drug design.     

Analysis of the ketosynthase-chain length factor heterodimer from the fredericamycin polyketide synthase

The pentadecaketide fredericamycin has the longest carbon chain backbone among polycyclic aromatic polyketide antibiotics whose biosynthetic genes have been sequenced. This backbone is synthesized by the bimodular fdm polyketide synthase (PKS). Here, we demonstrate that the bimodular fdm PKS as well as its elongation module alone synthesize undecaketides and dodecaketides. Thus, unlike other homologs, the fdm ketosynthase-chain length factor (KS-CLF) heterodimer does not exclusively control the backbone length of its natural product. Using sequence- and structure-based approaches, 48 CLF multiple mutants were engineered and analyzed. Unexpectedly, the I134F mutant was unable to turn over but could initiate and partially elongate the polyketide chain. This unprecedented mutant suggests that the KS-CLF heterodimer harbors an as yet uncharacterized chain termination mechanism. Together, our findings reveal fundamental mechanistic differences between the fdm PKS and its well-studied homologs.     

A 'microfluidic pinball' for on-chip generation of Layer-by-Layer polyelectrolyte microcapsules

Inspired by the game of "pinball" where rolling metal balls are guided by obstacles, here we describe a novel microfluidic technique which utilizes micropillars in a flow channel to continuously generate, encapsulate and guide Layer-by-Layer (LbL) polyelectrolyte microcapsules. Droplet-based microfluidic techniques were exploited to generate oil droplets which were smoothly guided along a row of micropillars to repeatedly travel through three parallel laminar streams consisting of two polymers and a washing solution. Devices were prototyped in PDMS and generated highly monodisperse and stable 45±2 μm sized polyelectrolyte microcapsules. A total of six layers of hydrogen bonded polyelectrolytes (3 bi-layers) were adsorbed on each droplet within <3 minutes and a fluorescent intensity measurement confirmed polymer film deposition. AFM analysis revealed the thickness of each polymer layer to be approx. 2.8 nm. Our design approach not only provides a faster and more efficient alternative to conventional LbL deposition techniques, but also achieves the highest number of polyelectrolyte multilayers (PEMs) reported thus far using microfluidics. Additionally, with our design, a larger number of PEMs can be deposited without adding any extra operational or interfacial complexities (e.g. syringe pumps) which are a necessity in most other designs. Based on the aforementioned advantages of our device, it may be developed into a great tool for drug encapsulation, or to create capsules for biosensing where deposition of thin nanofilms with controlled interfacial properties is highly required.     

Accelerated iterative strategy for the divergent synthesis of dendritic macromolecules using a combination of living radical polymerization and an irreversible terminator multifunctional initiator

Our laboratory has reported the elaboration of an iterative strategy for the synthesis of dendritic macromolecules from conventional monomers. This synthetic method involves a combination of self‐regulated metal‐catalyzed living radical polymerization initiated from arenesulfonyl chlorides and an irreversible terminator multifunctional initiator (TERMINI). The previous TERMINI, (1,1‐dimethylethyl)[[1‐[3,5‐bis(S‐phenyl‐4‐N,N′ diethylthiocarbamate)phenyl]ethenyl]oxy]dimethylsilane, was prepared in nine reaction steps. The replacement of the previous TERMINI with one that requires only three steps for its synthesis, diethylthiocarbamic acid S‐{3‐[1‐(tert‐butyl‐dimethyl‐silanyloxy)‐vinyl]‐5‐diethylcarbamoylsulfanyl‐phenyl} ester, and the use of the more reactive Cu₂S/2,2′‐bipyridine rather than the Cu₂O/2,2′‐bipyridine self‐regulated catalyst have generated an accelerated method for the synthesis of dendritic macromolecules. This method provides rational design strategies for the synthesis of dendritic macromolecules with different compaction by the use of a single monomer. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 4894–4906, 2005     

Effect of the three-body force on trinucleon bound systems consideringS andS′-state admixture

We report the calculation of binding energy, charge form factor and point-like proton density of both³H and³He by the hyperspherical harmonics method with the inclusion of two-pion exchange three-nucleon force (Fujita-Miyazawa type). For the two-body force theN-N Afnan-Tang S-3 potential is taken. Coulomb and three-body forces are treated nonperturbatively. In this calculation the mixed symmetryS′-state of the trinucleon ground state is considered along with the space totally symmetricS-state.     

Chemical,Thermal and X-Ray Analysis of Some Clays

Chemical, Dehydration, Differential Thermal and X-ray analysis of some clays has been carried out to study their mineralogical composition. All the clay samples appear to be basically montmorillonites. While in one of the clays, montmorillonite is the predominent phase, the other two also contain illites besides other clay mineral impurities.