Engineering protein therapeutics: predictive performances of a structure-based virtual affinity maturation protocol

The implementation of a structure based virtual affinity maturation protocol and evaluation of its predictivity are presented. The in silico protocol is based on conformational sampling of the interface residues (using the Dead End Elimination/A* algorithm), followed by the estimation of the change of free energy of binding due to a point mutation, applying MM/PBSA calculations. Several implementations of the protocol have been evaluated for 173 mutations in 7 different protein complexes for which experimental data were available: the use of the Boltzamnn averaged predictor based on the free energy of binding (ΔΔG(*)) combined with the one based on its polar component only (ΔΔE(pol*)) led to the proposal of a subset of mutations out of which 45% would have successfully enhanced the binding. When focusing on those mutations that are less likely to be introduced by natural in vivo maturation methods (99 mutations with at least two base changes in the codon), the success rate is increased to 63%. In another evaluation, focusing on 56 alanine scanning mutations, the in silico protocol was able to detect 89% of the hot-spots.     

A fluorescently labeled dendronized polymer-enzyme conjugate carrying multiple copies of two different types of active enzymes

A hybrid structure of a synthetic dendronized polymer, two different types of enzymes (superoxide dismutase and horseradish peroxidase), and a fluorescent dye (fluorescein) was synthesized. Thereby, a single polymer chain carried multiple copies of the two enzymes and the fluorescein. The entire attachment chemistry is based on UV/vis-quantifiable bis-aryl hydrazone bond formation that allows direct quantification of bound molecules: 60 superoxide dismutase, 120 horseradish peroxidase, and 20 fluorescein molecules on an average polymer chain of 2000 repeating units. To obtain other enzyme ratios the experimental conditions were altered accordingly. Moreover, it could be shown that both enzymes remained fully active and catalyzed a two-step cascade reaction.     

Synthesis and characterization of well‐defined ABC‐type triblock copolymers via atom transfer radical polymerization and stable free‐radical polymerization

An asymmetric difunctional initiator 2‐phenyl‐2‐[(2,2,6,6 tetramethylpiperidino)oxy] ethyl 2‐bromo propanoate ( 1 ) was used for the synthesis of ABC‐type methyl methacrylate (MMA)‐tert‐butylacrylate (tBA)‐styrene (St) triblock copolymers via a combination of atom transfer radical polymerization (ATRP) and stable free‐radical polymerization (SFRP). The ATRP‐ATRP‐SFRP or SFRP‐ATRP‐ATRP route led to ABC‐type triblock copolymers with controlled molecular weight and moderate polydispersity (M_w/M_n < 1.35). The block copolymers were characterized by gel permeation chromatography and ¹H NMR. The retaining chain‐end functionality and the applying halide exchange afforded high blocking efficiency as well as maintained control over entire routes. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 2025–2032, 2002     

Photoresponsive poly(methyl methacrylate)2–(polystyrene)2 miktoarm star copolymer containing an azobenzene moiety at the core

We prepared a novel miktoarm star copolymer with an azobenzene unit at the core via combination of atom transfer radical polymerization (ATRP) and nitroxide‐mediated free radical polymerization (NMP) routes. For this purpose, first, mikto‐functional initiator, 3 , with tertiary bromide (for ATRP) and 2,2,6,6‐tetramethylpiperidin‐1‐yloxy (TEMPO) (for NMP) functionalities and an azobenzene moiety at the core was synthesized. The initiator 3 thus obtained was used in the subsequent living radical polymerization routes such as ATRP of MMA and NMP of St, respectively, to give A₂B₂ type miktoarm star copolymer, (PMMA)₂‐(PSt)₂ with an azobenzene unit at the core with controlled molecular weight and low polydispersity (M_w/M_n < 1.15). The photoresponsive properties of 3 and (PMMA)₂‐(PSt)₂ miktoarm star copolymer were investigated. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 1396–1403, 2006     

The determination of β-agonist residues in bovine tissues using liquid chromatography–tandem mass spectrometry

We aimed to develop a rapid, simple and reproducible method based on LC–tandem mass spectrometry (LC–MS/MS) to analyze β-agonist residues (clenbuterol, zilpaterol, ractopamine and isoxsuprine) in bovine tissues. The method was validated in accordance with the European Council Decision 2002/657/EC. The samples were homogenized, and then 10 mL of an acetate buffer was added to a 5-g sample. The sample was then centrifuged at 12,000 rpm and filtered. Sodium hydroxide (2 m ) was added to adjust pH of the sample that was centrifuged again. The extract was filtered through a solid-phase extraction column. The residue was re-dissolved in 250 μL acetonitrile and then subjected to LC–MS/MS. The separation was done on a C₁₈ column. The mobile phase consisted of 0.1% formic acid in deionized water and 0.1% formic acid in methanol. The mean recoveries of β-agonists were in the range of 84.3%–119.1% with relative standard deviations (%RSDs) of 0.683%–4.05%. Decision limits and detection capabilities of the analytes ranged from 0.0960 to 4.9349 μg/kg and from 0.0983 to 5.0715, respectively. This method was used to detect four β-agonists in 100 bovine muscle, 100 liver and 100 kidney tissues from a slaughterhouse. No residue was found above the maximum residue limit level.     

Projective dimension of the universal modules for the product of a hypersurface and affine t-space

The main result in this paper is that the. projective dimension of the nth order universal module of the. coordinate ring of the product of a reduced hypersurface and an affine t-spa.ee is finite. This question appears in [1]. We have seen this by showing that projective dimension of the nth order universal module of the ring corresponding to a reduced hypersurface is finite. At the end we present some examples related to projective dimension of the universal modules of the product of variaties.