Small molecule affinity fingerprinting. A tool for enzyme family subclassification,target identification,and inhibitor design

Classifying proteins into functionally distinct families based only on primary sequence information remains a difficult task. We describe here a method to generate a large data set of small molecule affinity fingerprints for a group of closely related enzymes, the papain family of cysteine proteases. Binding data was generated for a library of inhibitors based on the ability of each compound to block active-site labeling of the target proteases by a covalent activity based probe (ABP). Clustering algorithms were used to automatically classify a reference group of proteases into subfamilies based on their small molecule affinity fingerprints. This approach was also used to identify cysteine protease targets modified by the ABP in complex proteomes by direct comparison of target affinity fingerprints with those of the reference library of proteases. Finally, experimental data were used to guide the development of a computational method that predicts small molecule inhibitors based on reported crystal structures. This method could ultimately be used with large enzyme families to aid in the design of selective inhibitors of targets based on limited structural/function information.     

Automated annotation of microbial proteomes in SWISS-PROT

Large-scale sequencing of prokaryotic genomes demands the automation of certain annotation tasks currently manually performed in the production of the SWISS-PROT protein knowledgebase. The HAMAP project, or 'High-quality Automated and Manual Annotation of microbial Proteomes', aims to integrate manual and automatic annotation methods in order to enhance the speed of the curation process while preserving the quality of the database annotation. Automatic annotation is only applied to entries that belong to manually defined orthologous families and to entries with no identifiable similarities (ORFans). Many checks are enforced in order to prevent the propagation of wrong annotation and to spot problematic cases, which are channelled to manual curation. The results of this annotation are integrated in SWISS-PROT, and a website is provided at http://www.expasy.org/sprot/hamap/.     

Redox protein-polymer films for simultaneous determination of ascorbic Acid and hydrogen peroxide

Layer by layer films of protein and redox polymer were constructed and used to simultaneously analyze ascorbic acid and hydrogen peroxide. The films were made using hemoglobin and poly[4-vinylpyridine Os(bipyridine)(2)Cl]-co-ethylamine (Pos-Ea). The film growth was monitored using cyclic voltammetry, quartz crystal microbalance (QCM) and atomic force microscopy (AFM). Reversible pairs of oxidation-reduction peaks were observed using cyclic voltammetry corresponding to the Os(II)/Os(III) from redox polymer and HbFe(III)/HbFe(II) redox couples at 0.35 and -0.25 V vs. Ag/AgCl, respectively. The two redox centers were independent of each other. This enabled the simultaneous and independent determination of ascorbic acid and hydrogen. Peak currents were linearly related to concentration for both analytes in a mixture. The linear range of ascorbic acid was 0 - 1 mM (R(2) = 0.9996, n = 5) at scan rate of 50 mV s(-1) (sensitivity 3.5 microA/mM) while hydrogen peroxide linear range was 1.0 - 10.0 microM (R(2) = 0.991, n = 6) with sensitivity of 1.85 microA/microM.     

Annulation of pyrrole: application to the synthesis of indolizidine alkaloids

The nucleophilicity of pyrrole has been exploited to rapidly assemble the bicyclic skeleton of the indolizidine alkaloids. The key sequence is the annulation of a second ring onto pyrrole from a γ-lactone and has been exploited in the synthesis of the natural products (±)-monomorine and (±)-indolizidine 209D.     

Simple One‐Pot Syntheses of Water‐Soluble Bis(acyl)phosphane Oxide Photoinitiators and Their Application in Surfactant‐Free Emulsion Polymerization

The sodium salt of the new bis(mesitoyl)phosphinic acid (BAPO‐OH) can be prepared in a very efficient one‐pot synthesis. It is well soluble in water and hydrolytically stable for at least several weeks. Remarkably, it acts as an initiating agent for the surfactant‐free emulsion polymerization (SFEP) of styrene to yield monodisperse, spherical nanoparticles. Time‐resolved electron paramagnetic resonance (TR‐EPR) and chemically induced electron polarisation (CIDEP) indicate preliminary mechanistic insights.

     

Pyridine modified polyethylene copolymer compatibilizer for melt blended carbon nanotube composites: effects of chain structure and matrix viscosity

The electrical percolation threshold of different polyethylene/carbon nanotube nanocomposites was studied as a function of chain structure, matrix viscosity, and the effect of compatibilizer. The lower the viscosity of the matrix the lower is the percolation threshold, regardless of the chain architecture and degree of crystallization. To improve dispersion a series of acrylic acid copolymer are introduced into the system. The highest concentration of acid co‐monomer that maintain miscibility with the polyethylene matrix is 5 wt.%. The compatibilizer in its pristine form does not have a significant effect on dispersion and on volume resistivity. When the acidic copolymer was modified with aminomethylpyridine, in order to facilitate π–π interaction with the nanotubes, a 4‐decade reduction was recorder for the high viscosity matrices at 10 wt.% compatibilizer loading. Copyright © 2014 John Wiley & Sons, Ltd.