A brief review of coarse-grained and other computational studies of molecularly imprinted polymers

Molecular imprinting is an established method for the creation of artificial recognition sites in synthetic materials through polymerization and cross-linking in the presence of template molecules. Removal of the templates leaves cavities that are complementary to the template molecules in size, shape, and functionality. In recent years, various theoretical and computational models have been developed as tools to aid in the design of molecularly imprinted polymers (MIPs) or to provide insight into the features that determine MIP performance. These studies can be grouped into two general approaches-screening for possible functional monomers for particular templates and macromolecular models focusing on the structural characterization of the imprinted material. In this review, we pay special attention to coarse-grained models that characterize the functional heterogeneity in imprinted pores, but also cover recent advances in atomistic and first principle studies. We offer a critical assessment of the potential impact of the various models towards improving the state-of-the-art of molecular imprinting.     

Mean-field model of immobilized enzymes embedded in a grafted polymer layer

Two-dimensional mean-field lattice theory is used to model immobilization and stabilization of an enzyme on a hydrophobic surface using grafted polymers. Although the enzyme affords biofunctionality, the grafted polymers stabilize the enzyme and impart biocompatibility. The protein is modeled as a compact hydrophobic-polar polymer, designed to have a specific bulk conformation reproducing the catalytic cleft of natural enzymes. Three scenarios are modeled that have medical or industrial importance: 1), It is shown that short hydrophilic grafted polymers, such as polyethylene glycol, which are often used to provide biocompatibility, can also serve to protect a surface-immobilized enzyme from adsorption and denaturation on a hydrophobic surface. 2), Screening of the enzyme from the surface and nonspecific interactions with biomaterial in bulk solution requires a grafted layer composed of short hydrophilic polymers and long triblock copolymers. 3), Hydrophilic polymers grafted on a hydrophobic surface in contact with an organic solvent form a dense hydrophilic nanoenvironment near the surface that effectively shields and stabilizes the enzyme against both surface and solvent.     

Toxicity of propylene oxide at low pressure against life stages of four species of stored product insects

The relative toxicity of propylene oxide (PPO) at a low pressure of 100 mm Hg to four species of stored product insect at 30 degrees C over a 4-h exposure period was investigated. PPO at 100 mm Hg was toxic to all four species tested: Tribolium castaneum (Herbst), Plodia interpunctella (Hübner), Ephestia cautella (Wlk.), and Oryzaephilus surinamensis (L.). There were differences in susceptibility between the life stages of the tested insect species. Mortality tests on all life stages of the insects resulted in LD99 values ranging from 4.7 to 26.1 mg/liter. The pupal stage of E. cautella, O. surinamensis, and T. castaneum was the most tolerant stage with LD99 values of 14.4, 26.1, and 25.7 mg/liter, respectively. For P. interpunctella, the egg stage was most tolerant, with a LD99 value of 15.3 mg/liter. Generally, PPO at 100 mm Hg was more toxic to P. interpunctella and E. cautella than to O. surinamensis and T. castaneum. A 99% mortality of all life stages of the tested species was achieved at a concentrations x time product of 104.4 mg h/liter. These findings indicate that a combination of PPO with low pressure can render the fumigant a potential alternative to methyl bromide for rapid disinfestation of commodities.     

MiRNA-mediated control of HLA-G expression and function

HLA-G is a non-classical HLA class-Ib molecule expressed mainly by the extravillous cytotrophoblasts (EVT) of the placenta. The expression of HLA-G on these fetal cells protects the EVT cells from immune rejection and is therefore important for a healthy pregnancy. The mechanisms controlling HLA-G expression are largely unknown. Here we demonstrate that miR-148a and miR-152 down-regulate HLA-G expression by binding its 3'UTR and that this down-regulation of HLA-G affects LILRB1 recognition and consequently, abolishes the LILRB1-mediated inhibition of NK cell killing. We further demonstrate that the C/G polymorphism at position +3142 of HLA-G 3'UTR has no effect on the miRNA targeting of HLA-G. We show that in the placenta both miR-148a and miR-152 miRNAs are expressed at relatively low levels, compared to other healthy tissues, and that the mRNA levels of HLA-G are particularly high and we therefore suggest that this might enable the tissue specific expression of HLA-G.     

The Relation between α-Helical Conformation and Amyloidogenicity

Amyloid fibrils are stable aggregates of misfolded proteins and polypeptides that are insoluble and resistant to protease activity. Abnormal formation of amyloid fibrils in vivo may lead to neurodegenerative disorders and other systemic amyloidosis, such as Alzheimer’s, Parkinson’s, and atherosclerosis. Because of their clinical importance, amyloids are under intense scientific research. It is believed that short polypeptide segments within proteins are responsible for the transformation of correctly folded proteins into parts of larger amyloid fibrils and that this transition is modulated by environmental factors, such as pH, salt concentration, interaction with the cell membrane, and interaction with metal ions. Most studies on amyloids focus on the amyloidogenic sequences. The focus of this study is on the structure of the amyloidogenic α-helical segments because the α-helical secondary structure has been recognized to be a key player in different stages of the amyloidogenesis process. We have previously shown that the α-helical conformation may be expressed by two parameters (θ and ρ) that form orthogonal coordinates based on the Ramachandran dihedrals (φ and ψ) and provide an illuminating interpretation of the α-helical conformation. By performing statistical analysis on α-helical conformations found in the Protein Data Bank, an apparent relation between α-helical conformation, as expressed by θ and ρ, and amyloidogenicity is revealed. Remarkably, random amino acid sequences, whose helical structures were obtained from the most probable dihedral angles, revealed the same dependency of amyloidogenicity, suggesting the importance of α-helical structure as opposed to sequence.     

Potential defence from herbivory by ‘dazzle effects’ and ‘trickery coloration’ of leaf variegation

The very conspicuous dazzle coloration invented for naval defence during World War I was used in pre‐radar days to mislead attackers of naval units about vessel size, type, speed, and direction. Among several potential types of defences, it is proposed that zebra‐like white leaf variegation may defend leaves and other plant organs from herbivory as a result of dazzle effects. Two different dazzle effects may be involved in defending plants from herbivory, making it hard for herbivores (1) to decide where, in a three‐dimensional space, to bite the leaves (large herbivores) and (2) to land on them (insects). In addition, the related types of leaf coloration described in the present study, comprising parallels of military defensive trickery naval painting, may also deceive herbivores about the actual shape, location, and identity of leaves. Some of these visual defences may operate at the same time as other visual defences, such as aposematism, or serve various physiological functions. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 692–697.     

Unripe red fruits may be aposematic

The unripe fruits of certain species are red. Some of these species disperse their seeds by wind (Nerium oleander, Anabasis articulata), others by adhering to animals with their spines (Emex spinosa) or prickles (Hedysarum spinosissimum). Certainly neither type uses red coloration as advertisement to attract the seed dispersing agents. Fleshy-fruited species (Rhamnus alaternus, Rubus sanguineus and Pistacia sp.), which disperse their seeds via frugivores, change fruit color from green to red while still unripe and then to black or dark blue upon ripening. The red color does not seem to function primarily in dispersal (unless red fruits form advertisement flags when there are already black ripe fruits on the plant) because the red unripe fruits of these species are poisonous, spiny, or unpalatable. The unripe red fruits of Nerium oleander are very poisonous, those of Rhamnus alaternus and Anabasis articulata are moderately poisonous, those of Rubus sanguineus are very sour, those of Pistacia sp. contain unpalatable resin and those of Emex spinosa and Hedysarum spinosissimum are prickly. We propose that these unripe red fruits are aposematic, protecting them from herbivory before seed maturation.