The performance of poly(styrene)-block-poly(2-vinyl pyridine)-block- poly(styrene) triblock copolymers as pH-driven actuators

Poly(styrene)-block-poly(2-vinyl pyridine)-block-poly(styrene) (PS-b-P2VP-b-PS) triblock copolymers were synthesised by anionic polymerisation. Thick films were cast from solution and their structure analysed by small angle X-ray scattering (SAXS). Longer annealing times led to more ordered structures whereas short evaporation times effectively "lock" the polymer chains in a disordered state by vitrification. Well-ordered structures not only provide an isotropic network, which reduces localised stress within the material, but are also essential for fundamental studies of soft matter because their activity on the molecular scale must be analysed and understood prior to their use in technological applications. Well-characterised PS-b-P2VP-b-PS materials have been coupled to a pH-oscillating reaction and their potential application as responsive actuators is discussed. This journal is © The Royal Society of Chemistry.

A predictor of membrane class:discriminating α-helical and β-barrel membrane proteins from non-membranous proteins

Accurate protein structure prediction remains an active objective of research in bioinformatics. Membrane proteins comprise approximately 20% of most genomes. They are, however, poorly tractable targets of experimental structure determination. Their analysis using bioinformatics thus makes an important contribution to their on-going study. Using a method based on Bayesian Networks, which provides a flexible and powerful framework for statistical inference, we have addressed the alignment-free discrimination of membrane from non-membrane proteins. The method successfully identifies prokaryotic and eukaryotic α-helical membrane proteins at 94.4% accuracy, β-barrel proteins at 72.4% accuracy, and distinguishes assorted non-membranous proteins with 85.9% accuracy. The method here is an important potential advance in the computational analysis of membrane protein structure. It represents a useful tool for the characterisation of membrane proteins with a wide variety of potential applications.

Alpha helical trans-membrane proteins:enhanced prediction using a Bayesian approach

Membrane proteins, which constitute approximately 20% of most genomes, are poorly tractable targets for experimental structure determination, thus analysis by prediction and modelling makes an important contribution to their on-going study. Membrane proteins form two main classes: alpha helical and beta barrel trans-membrane proteins. By using a method based on Bayesian Networks, which provides a flexible and powerful framework for statistical inference, we addressed alpha-helical topology prediction. This method has accuracies of 77.4% for prokaryotic proteins and 61.4% for eukaryotic proteins. The method described here represents an important advance in the computational determination of membrane protein topology and offers a useful, and complementary, tool for the analysis of membrane proteins for a range of applications.

Beta barrel trans-membrane proteins:enhanced prediction using a Bayesian approach

Membrane proteins, which constitute approximately 20% of most genomes, form two main classes: alpha helical and beta barrel transmembrane proteins. Using methods based on Bayesian Networks, a powerful approach for statistical inference, we have sought to address beta-barrel topology prediction. The beta-barrel topology predictor reports individual strand accuracies of 88.6%. The method outlined here represents a potentially important advance in the computational determination of membrane protein topology.

Combining algorithms to predict bacterial protein sub-cellular location:parallel versus concurrent implementations

We describe a novel and potentially important tool for candidate subunit vaccine selection through in silico reverse-vaccinology. A set of Bayesian networks able to make individual predictions for specific subcellular locations is implemented in three pipelines with different architectures: a parallel implementation with a confidence level-based decision engine and two serial implementations with a hierarchical decision structure, one initially rooted by prediction between membrane types and another rooted by soluble versus membrane prediction. The parallel pipeline outperformed the serial pipeline, but took twice as long to execute. The soluble-rooted serial pipeline outperformed the membrane-rooted predictor. Assessment using genomic test sets was more equivocal, as many more predictions are made by the parallel pipeline, yet the serial pipeline identifies 22 more of the 74 proteins of known location.

Controlled growth of poly(2-(diethylamino)ethyl methacrylate) brushes via atom transfer radical polymerisation on planar silicon surfaces

Progress in making pH-responsive polyelectrolyte brushes with a range of different grafting densities is reported. Polymer brushes of poly(2-(diethylamino)ethyl methacrylate) were synthesised via atom transfer radical polymerisation on silicon wafers using a 'grafted from' approach. The [11-(2-bromo-2-methyl) propionyloxy]undecyl trichlorosilane initiator was covalently attached to the silicon via silylation, from which the brushes were grown using a catalytic system of copper(I) chloride and pentamethyldiethylenetriamine in tetrahydrofuran at 80°C. X-ray reflectivity was used to assess the initiator surfaces and an upper limit on the grafting density of the polymer was determined. The quality of the brushes produced was analysed using ellipsometry and atomic force microscopy, which is also discussed.

Multi-class subcellular location prediction for bacterial proteins

Two algorithms, based onBayesian Networks (BNs), for bacterial subcellular location prediction, are explored in this paper: one predicts all locations for Gram+ bacteria and the other all locations for Gram- bacteria. Methods were evaluated using different numbers of residues (from the N-terminal 10 residues to the whole sequence) and residue representation (amino acid-composition, percentage amino acid-composition or normalised amino acid-composition). The accuracy of the best resulting BN was compared to PSORTB. The accuracy of this multi-location BN was roughly comparable to PSORTB; the difference in predictions is low, often less than 2%. The BN method thus represents both an important new avenue of methodological development for subcellular location prediction and a potentially value new tool of true utilitarian value for candidate subunit vaccine selection.

LIPPRED:a web server for accurate prediction of lipoprotein signal sequences and cleavage sites

Bacterial lipoproteins have many important functions and represent a class of possible vaccine candidates. The prediction of lipoproteins from sequence is thus an important task for computational vaccinology. Naïve-Bayesian networks were trained to identify SpaseII cleavage sites and their preceding signal sequences using a set of 199 distinct lipoprotein sequences. A comprehensive range of sequence models was used to identify the best model for lipoprotein signal sequences. The best performing sequence model was found to be 10-residues in length, including the conserved cysteine lipid attachment site and the nine residues prior to it. The sensitivity of prediction for LipPred was 0.979, while the specificity was 0.742. Here, we describe LipPred, a web server for lipoprotein prediction; available at the URL: http://www.jenner.ac.uk/LipPred/. LipPred is the most accurate method available for the detection of SpaseIIcleaved lipoprotein signal sequences and the prediction of their cleavage sites.

Controlled RAFT polymerization and zinc binding performance of catechol-inspired homopolymers

Incorporation of catechols into polymers has long been of interest due to their ability to chelate heavy metals and their use in the design of adhesives, metal-polymer nanocomposites, antifouling coatings, and so on. This paper reports, for the first time, the reversible addition-fragmentation chain transfer (RAFT) polymerization of a protected catechol-inspired monomer, 3,4-dimethoxystyrene (DMS), using commercially available trithiocarbonate, 2-(dodecylthiocarbonothioylthio)-2-methylpropionic acid (DDMAT), as a chain transfer agent. Our identified RAFT system produces well-defined polymers across a range of molecular weights (5-50 kg/mol) with low molar mass dispersities (Mw/Mn < 1.3). Subsequent facile demethylation of poly(3,4-dimethoxystyrene) (PDMS) yields poly(3,4-dihydroxystyrene) (PDHS), a catechol-bearing polymer, in quantitative yields. Semiquantitative zinc binding capacity analysis of both polymers using SEM/EDXA has demonstrated that both PDMS and PDHS have considerable surface binding (65% and 87%, respectively), although the films deposited from PDMS are of a better quality and processability due to solubility and lower processing temperatures. © 2014 American Chemical Society.

Controlled synthesis and processing of a poly(L-lactide-co-ε-caprolactone) copolymer for biomedical use as an absorbable monofilament surgical suture

Poly(L-lactide-co-ε-caprolactone) 75:25% mol, P(LL-co-CL), was synthesized via bulk ring-opening polymerisation (ROP) using a novel tin(II)alkoxide initiator, [Sn(Oct)]2DEG, at 130oC for 48 hrs. The effectiveness of this initiator was compared withthe well-known conventional tin(II) octoateinitiator, Sn(Oct)2. The P(LL-co-CL) copolymersobtained were characterized using a combination of analytical technique including: nuclear magnetic resonance spectroscopy (NMR), differential scanning calorimetry (DSC), thermogravimetry (TG) and gel permeation chromatography (GPC). The P(LL-co-CL) was melt-spun into monofilament fibres of uniform diameter and smooth surface appearance. Modification of the matrix morphology was then built into the as-spun fibresvia a series of controlled off-line annealing and hot-drawing steps. © (2014) Trans Tech Publications, Switzerland.

Design, synthesis and RAFT polymerisation of a quinoline-based monomer for use in metal-binding composite microfibres

Metal-binding polymer fibres have attracted major attention for diverse applications in membranes for metal sequestration from waste waters, non-woven wound dressings, matrices for photocatalysis, and many more. This paper reports the design and synthesis of an 8-hydroxyquinoline-based zinc-binding styrenic monomer, QuiBoc. Its subsequent polymerisation by reversible addition–fragmentation chain transfer (RAFT) yielded well-defined polymers, PQuiBoc, of controllable molar masses (6 and 12 kg mol−1) with low dispersities (Đ, Mw/Mn < 1.3). Protected (PQuiBoc) and deprotected (PQuiOH) derivatives of the polymer exhibited a high zinc-binding capacity, as determined by semi-quantitative SEM/EDXA analyses, allowing the electrospinning of microfibres from a PQuiBoc/polystyrene (PS) blend without the need for removal of the protecting group. Simple “dip-coating” of the fibrous mats into ZnO suspensions showed that PQuiBoc/PS microfibres with only 20% PQuiBoc content had almost three-fold higher loadings of ZnO (29%) in comparison to neat PS microfibres (11%).

BPROMPT:a consensus server for membrane protein prediction

Protein structure prediction is a cornerstone of bioinformatics research. Membrane proteins require their own prediction methods due to their intrinsically different composition. A variety of tools exist for topology prediction of membrane proteins, many of them available on the Internet. The server described in this paper, BPROMPT (Bayesian PRediction Of Membrane Protein Topology), uses a Bayesian Belief Network to combine the results of other prediction methods, providing a more accurate consensus prediction. Topology predictions with accuracies of 70% for prokaryotes and 53% for eukaryotes were achieved. BPROMPT can be accessed at http://www.jenner.ac.uk/BPROMPT.

Unravelling the photodegradation mechanisms of a low bandgap polymer by combining experimental and modeling approaches

Large-scale introduction of Organic Solar Cells (OSCs) onto the market is currently limited by their poor stability in light and air, factors present in normal working conditions for these devices. Thus, great efforts have to be undertaken to understand the photodegradation mechanisms of their organic materials in order to find solutions that mitigate these effects. This study reports on the elucidation of the photodegradation mechanisms occurring in a low bandgap polymer, namely, Si-PCPDTBT (poly[(4,4′-bis(2-ethylhexyl)dithieno[3,2-b:2′,3′-d]silole)-2,6-diyl-alt-(4,7-bis(2-thienyl)-2,1,3-benzothiadiazole)-5,5′-diyl]). Complementary analytical techniques (AFM, HS-SPME-GC-MS, UV-vis and IR spectroscopy) have been employed to monitor the modification of the chemical structure of the polymer upon photooxidative aging and the subsequent consequences on its architecture and nanomechanical properties. Furthermore, these different characterization techniques have been combined with a theoretical approach based on quantum chemistry to elucidate the evolution of the polymer alkyl side chains and backbone throughout exposure. Si-PCPDTBT is shown to be more stable against photooxidation than the commonly studied p-type polymers P3HT and PCDTBT, while modeling demonstrated the benefits of using silicon as a bridging atom in terms of photostability. (Figure Presented).

Mechanism for cross-linking polychloroprene with ethylene thiourea and zinc oxide

An investigation into the mechanism by which ethylene thiourea (ETU) cross-links polychloroprene (CR) in combination with zinc oxide (ZnO) was undertaken. This was achieved through an examination of the mechanisms of crosslinking CR with ETU and ZnO separately and in unison. Spectroscopic and physical characterization techniques were employed to probe the cross-linking mechanisms of CRusing other standard rubber accelerators and model compounds with analogous structures and functionalities to ETU. These investigations have resulted in the proposal of a new mechanism by which ETU and ZnO can synergistically cross-link CR, in addition to providing new evidence to support concomitant mechanisms already published for cross-linking CR.

Controlled synthesis of poly(neopentyl p-styrene sulfonate) via reversible addition-fragmentation chain transfer polymerisation

The controlled synthesis of poly(neopentyl p-styrene sulfonate) (PNSS) using RAFT polymerisation has been studied. Selected experimental conditions led to the production of PNSS with variable molecular weights and low dispersities (D{stroke}≤1.50). The controlled synthesis of poly(neopentyl p-styrene sulfonate) (PNSS) using reversible addition-fragmentation chain transfer polymerisation has been studied under a wide range of experimental conditions. PNSS can be used as an organic-soluble, thermally labile precursor for industrially valuable poly(p-styrene sulfonate), widely employed in technologies such as ionic exchange membranes and organic electronics. The suitability of two different chain transfer agents, three solvents, three different monomer concentrations and two different temperatures for the polymerisation of neopentyl p-styrene sulfonate is discussed in terms of the kinetics of the process and characteristics of the final polymer. Production of PNSS with systematically variable molecular weights and low dispersities (D{stroke} ≤1.50 in all cases) has been achieved using 2-azidoethyl 2-(dodecylthiocarbonothioylthio)-2-methylpropionate in anisole at 75°C, with an initial monomer concentration of 4.0molL-1. Finally, a poly(neopentyl p-styrene sulfonate)-b-polybutadiene-b-poly(neopentyl p-styrene sulfonate) (PNSS-b-PBD-b-PNSS) triblock copolymer has been synthesised via azide-alkyne click chemistry. Moreover, subsequent thermolysis of the PNSS moieties generated poly(p-styrene sulfonate) end blocks. This strategy allows the fabrication of amphiphilic copolymer films from single organic solvents without the need for post-deposition chemical treatment.