MHC class II binding prediction:a little help from a friend

Vaccines are the greatest single instrument of prophylaxis against infectious diseases, with immeasurable benefits to human wellbeing. The accurate and reliable prediction of peptide-MHC binding is fundamental to the robust identification of T-cell epitopes and thus the successful design of peptide- and protein-based vaccines. The prediction of MHC class II peptide binding has hitherto proved recalcitrant and refractory. Here we illustrate the utility of existing computational tools for in silico prediction of peptides binding to class II MHCs. Most of the methods, tested in the present study, detect more than the half of the true binders in the top 5% of all possible nonamers generated from one protein. This number increases in the top 10% and 15% and then does not change significantly. For the top 15% the identified binders approach 86%. In terms of lab work this means 85% less expenditure on materials, labour and time. We show that while existing caveats are well founded, nonetheless use of computational models of class II binding can still offer viable help to the work of the immunologist and vaccinologist.

EpiTOP—a proteochemometric tool for MHC class II binding prediction

Motivation: T-cell epitope identification is a critical immunoinformatic problem within vaccine design. To be an epitope, a peptide must bind an MHC protein. Results: Here, we present EpiTOP, the first server predicting MHC class II binding based on proteochemometrics, a QSAR approach for ligands binding to several related proteins. EpiTOP uses a quantitative matrix to predict binding to 12 HLA-DRB1 alleles. It identifies 89% of known epitopes within the top 20% of predicted binders, reducing laboratory labour, materials and time by 80%. EpiTOP is easy to use, gives comprehensive quantitative predictions and will be expanded and updated with new quantitative matrices over time.

Special classes of iron(II) azole spin-crossover compounds

In this chapter, selected results obtained so far on Fe(II) spin crossover compounds of 1,2,4-triazole, isoxazole and tetrazole derivatives are summarized and analysed. These materials include the only compounds known to have Fe(II)N6 spin crossover chromophores consisting of six chemically identical heterocyclic ligands. Particular attention is paid to the coordination modes for substituted 1,2,4-triazole derivatives towards Fe(II) resulting in polynuclear and mononuclear compounds exhibiting Fe(II) spin transitions. Furthermore, the physical properties of mononuclear Fe(II) isoxazole and 1-alkyl-tetrazole compounds are discussed in relation to their structures. It will also be shown that the use of α,β- and α,ω-bis(tetrazol-1-yl)alkane type ligands allowed a novel strategy towards obtaining polynuclear Fe(II) spin crossover materials.

Cleavage initiation in the intercritically reheated coarse-grained heat affected zone:Part II. Failure criteria and statistical effects

In part 1 of this article, cleavage initiation in the intercritically reheated coarse-grained heat affected zone (IC CG HAZ) of high-strength low-alloy (HSLA) steels was determined to occur between two closely spaced blocky MA particles. Blunt notch, crack tip opening displacement (CTOD), and precracked Charpy testing were used in this investigation to determine the failure criteria required for cleavage initiation to occur by this mechanism in the IC CG HAZ. It was found that the attainment of a critical level of strain was required in addition to a critical level of stress. This does not occur in the case of high strain rate testing, for example, during precracked Charpy testing. A different cleavage initiation mechanism is then found to operate. The precise fracture criteria and microstructural requirements (described in part I of this article) result in competition between potential cleavage initiation mechanisms in the IC CG HAZ.

Isothermal fatigue of an aluminide-coated single-crystal superalloy:Part II. Effects of brittle precracking

The effect of brittle coating precracking on the fatigue behavior of a high-activity aluminide-coated single-crystal nickel-base superalloy has been studied using hollow cylindrical specimens at test temperatures of 600 °C, 800 °C, and 1000 °C. Three types of precrack were studied: narrow precracks formed at room temperature, wide precracks formed at room temperature, and narrow precracks formed at elevated temperature. The effect of precracking on fatigue life at 600 °C was found to depend strongly on the type of precrack. No failure was observed for specimens with narrow room-temperature precracks because of crack arrest via an oxidation-induced crack closure mechanism, while the behavior of wide precracks and precracks formed at elevated temperature mirrored the non-precracked behavior. Crack retardation also occurred for narrow room-temperature precracks tested at 800 °C - in this case, fatigue cracks leading to failure initiated in a layer of recrystallized grains on the inside surface of the specimen. A significant reduction in fatigue life at 800 °C relative to non-precracked specimens was observed for wide precracks and elevated temperature precracks. The presence of precracks bypassed the initiation and growth of coating fatigue cracks necessary for failure in non-precracked material. No effect of precracking was observed at 1000 °C.

Amine-functionalised hexagonal mesoporous silica as support for copper(II) acetylacetonate catalyst

Copper(II) acetylacetonate was anchored onto a hexagonal mesoporous silica (HMS) material using a two-step procedure: (i) functionalisation of the surface hydroxy groups with (3-aminopropyl)triethoxysilane (AMPTSi) and then (ii) anchoring of the copper(II) complex through Schiff condensation with free amine groups, using two different metal complex loadings. Upon the first step, nitrogen elemental analysis, XPS and DRIFT showed the presence of amine groups on the surface of the HMS material, and porosimetry indicated that the structure of the mesoporous material remained unchanged, although a slight decrease in surface area was observed. Atomic absorption, XPS and DRIFT showed that copper(II) acetylacetonate was anchored onto the amine-functionalised HMS by Schiff condensation between the free amine groups and the carbonyl groups of the copper(II) complex; using EPR an NO3 coordination sphere was proposed for the anchored copper(II) complex. The new [Cu(acac)2]-AMPTSi/HMS materials were tested in the aziridination of styrene at room temperature, using PhI=NTs as nitrogen source and acetonitrile as solvent. The styrene conversion and total TON of the heterogeneous phase reaction are higher than those of the same reaction catalysed in homogeneous phase by [Cu(acac)2]; nevertheless, the initial activity decreases and the reaction time increases due to substrate and product diffusion limitations. The heterogeneous catalyst showed a successive slight decrease in catalytic activity when reused for two more times. © Wiley-VCH Verlag GmbH & Co. KGaA, 2006.

Spin transition of 1D, 2D and 3D iron(II) complex polymers - the tug-of-war between elastic interaction and a shock-absorber effect

The structures of linear chain Fe(II) spin-crossover compounds of α,β- and α,ω-bis (tetrazol-1-yl)alkane type ligands are described in relation to their magnetic properties. The first threefold interlocked 3-D catenane Fe(II) spin-transition system, [μ-tris(1,4-bis(tetrazol-1-yl)butane-N1,N1′) iron(II)] bis(perchlorate), will be discussed. An analysis is made among the structures and the cooperativity of the spin-crossover behaviour of polynuclear Fe(II) spin-transition materials.

Preparation of a poly(L-lactide-co-caprolactone) copolymer using a novel tin(II) alkoxide initiator and its fiber processing for potential use as an absorbable monofilament surgical suture

A poly(L-lactide-co-caprolactone) copolymer, P(LL-co-CL), of composition 75:25 mol% was synthesized via the bulk ring-opening copolymerization of L-lactide and ε-caprolactone using a novel bis[tin(II) monooctoate] diethylene glycol coordination-insertion initiator, OctSn-OCH2CH2OCH2CH2O-SnOct. The P(LL-co-CL) copolymer obtained was characterized by a combination of analytical techniques, namely nuclear magnetic resonance spectroscopy, gel permeation chromatography, dilute-solution viscometry, differential scanning calorimetry, and thermogravimetric analysis. For processing into a monofilament fiber, the copolymer was melt spun with minimal draw to give a largely amorphous and unoriented as-spun fiber. The fiber's oriented semicrystalline morphology, necessary to give the required balance of mechanical properties, was then developed via a sequence of controlled offline hot-drawing and annealing steps. Depending on the final draw ratio, the fibers obtained had tensile strengths in the region of 200–400 MPa.