What makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces

Investigation of the non-covalent interaction of biomolecules with aqueous graphene interfaces is a rapidly expanding area. However, reliable exploitation of these interfaces in many applications requires that the links between the sequence and binding of the adsorbed peptide structures be clearly established. Molecular dynamics (MD) simulations can play a key role in elucidating the conformational ensemble of peptides adsorbed at graphene interfaces, helping to elucidate these rules in partnership with experimental characterisation. We apply our recently-developed polarisable force-field for biomolecule-graphene interfaces, GRAPPA, in partnership with advanced simulation approaches, to probe the adsorption behaviour of peptides at aqueous graphene. First we determine the free energy of adsorption of all twenty naturally occurring amino acids (AAs) via metadynamics simulations, providing a benchmark for interpreting peptide-graphene adsorption studies. From these free energies, we find that strong-binding amino acids have flat and/or compact side chain groups, and we relate this behaviour to the interfacial solvent structuring. Second, we apply replica exchange with solute tempering simulations to efficiently and widely sample the conformational ensemble of two experimentally-characterised peptide sequences, P1 and its alanine mutant P1A3, in solution and adsorbed on graphene. For P1 we find a significant minority of the conformational ensemble possesses a helical structure, both in solution and when adsorbed, while P1A3 features mostly extended, random-coil conformations. In solution this helical P1 configuration is stabilised through favourable intra-peptide interactions, while the adsorbed structure is stabilised via interaction of four strongly-binding residues, identified from our metadynamics simulations, with the aqueous graphene interface. Our findings rationalise the performance of the P1 sequence as a known graphene binder.

Identification of a gene for an ancient cytokine, interleukin 15-like, in mammals; interleukins 2 and 15 co-evolved with this third family member, all sharing binding motifs for IL-15Rα

Interleukins 2 and 15 (IL-2 and IL-15) are highly differentiated but related cytokines with overlapping, yet also distinct functions, and established benefits for medical drug use. The present study identified a gene for an ancient third IL-2/15 family member in reptiles and mammals, interleukin 15-like (IL-15L), which hitherto was only reported in fish. IL-15L genes with intact open reading frames (ORFs) and evidence of transcription, and a recent past of purifying selection, were found for cattle, horse, sheep, pig and rabbit. In human and mouse the IL-15L ORF is incapacitated. Although deduced IL-15L proteins share only ~21 % overall amino acid identity with IL-15, they share many of the IL-15 residues important for binding to receptor chain IL-15Rα, and recombinant bovine IL-15L was shown to interact with IL-15Rα indeed. Comparison of sequence motifs indicates that capacity for binding IL-15Rα is an ancestral characteristic of the IL-2/15/15L family, in accordance with a recent study which showed that in fish both IL-2 and IL-15 can bind IL-15Rα. Evidence reveals that the species lineage leading to mammals started out with three similar cytokines IL-2, IL-15 and IL-15L, and that later in evolution (1) IL-2 and IL-2Rα receptor chain acquired a new and specific binding mode and (2) IL-15L was lost in several but not all groups of mammals. The present study forms an important step forward in understanding this potent family of cytokines, and may help to improve future strategies for their application in veterinarian and human medicine.

Amyloid peptide self assembly in protic ionic liquids

Overall, this thesis presents the novel approach of using carefully selected PILs to both control amyloid fibril formation and inhibit/dissolve Aβ fibrils through induced helical transitions. These results provide insights into future PIL-mediated protein studies and the potential application of PILs in AD pathogenesis.

A comprehensive analytical subdomain model and its field solutions for surface-mounted permanent magnet machines

This paper presents a comprehensive analytical subdomain model together with its field solutions for predicting the magnetic field distributions in surface-mounted permanent magnet (PM) machines. The tooth tips and slotting effects during open-circuit, armature reaction, and on-load conditions are considered when deriving the model and developing its solutions. The model derivations and field solutions are extended from a previous model, and can be applied to PM machines with any combinations of slot and pole numbers and any magnetization patterns in the magnets. This model is initially formulated according to Laplace's and Poisson's equations in 2-D polar coordinates by the separation of variables technique in four subdomains, such as magnet, airgap, winding slots, and slot-openings. The field solution of each subdomain is obtained applying the appropriate boundary conditions and interface conditions between every two subdomains, respectively, which can precisely account for the mutual influence between slots. Finite element analysis (FEA) is later deployed to validate the analytical results in a surface-mounted PM machine that has nonoverlapping winding arrangement. For validation purposes, PM machines having 3-slot/2-pole with parallel magnetization and 12-slot/10-pole with either parallel or radial magnetizations are used for comparisons. Computation of global quantities for the motor which include the phase back-EMF and cogging torque is also included. The results indicate that the proposed analytical model can accurately predict the magnetic field distributions in each subdomain and the motor's global quantities, which are in good agreement with those obtained from the FEA.

Children's implicit recall of junk food, alcohol and gambling sponsorship in Australian sport

BACKGROUND: In Australia, sport is saturated by the promotion of junk food, alcohol and gambling products. This is particularly evident on player jerseys. The effect of this advertising on children, who are exposed to these messages while watching sport, has not been thoroughly investigated. The aim of this research study was to investigate: (1) the extent to which children implicitly recalled shirt sponsors with the correct sporting team; (2) whether children associated some types of sponsors with certain sporting codes more than others; and (3) whether age of the children influenced the correct recall of sponsoring brands and teams. METHOD: This experimental study conducted in New South Wales, Australia used projective techniques to measure the implicit recall of team sponsorship relationships of 85 children aged 5-12 years. Participants were asked to arrange two sets of magnets - one which contained sporting teams and one which contained brand logos - in the manner deemed most appropriate by them. Children were not given any prompts relating to sporting sponsorship relationships. RESULTS: Three quarters (77 %) of the children were able to identify at least one correct shirt sponsor. Children associated alcohol and gambling brands more highly with the more popular sporting code, the National Rugby League compared to the Australian Football League sporting code. Results showed that age had an effect on number of shirt sponsors correctly recalled with 9-12 year olds being significantly more likely than 5-8 year olds to correctly identify team sponsors. CONCLUSIONS: Given children's ability to implicitly recall shirt sponsors in a sporting context, Australian sporting codes should examine their current sponsorship relationships to reduce the number of unhealthy commodity shirt sponsors. While there is some regulation that protects children from the marketing of unhealthy commodity products, these findings suggest that children are still exposed to and recall these sponsorship relationships. Results suggest that the promotion of unhealthy commodity products during sporting matches is contributing to increased awareness amongst children of unhealthy commodity brands. Further investigation is required to examine the extent and impact of marketing initiatives during televised sporting matches on children.

Complex coacervation between flaxseed protein isolate and flaxseed gum

Flaxseed protein isolate (FPI) and flaxseed gum (FG) were extracted, and the electrostatic complexation between these two biopolymers was studied as a function of pH and FPI-to-FG ratio using turbidimetric and electrophoretic mobility (zeta potential) tests. The zeta potential values of FPI, FG, and their mixtures at the FPI-to-FG ratios of 1:1, 3:1, 5:1, 10:1, 15:1 were measured over a pH range 8.0-1.5. The alteration of the secondary structure of FPI as a function of pH was studied using circular dichroism. The proportion of a-helical structure decreased, whereas both β-sheet structure and random coil structure increased with the lowering of pH from 8.0 to 3.0. The acidic pH affected the secondary structure of FPI and the unfolding of helix conformation facilitated the complexation of FPI with FG. The optimum FPI-to-FG ratio for complex coacervation was found to be 3:1. The critical pH values associated with the formation of soluble (pHc) and insoluble (pHΦ1) complexes at the optimum FPI-to-FG ratio were found to be 6.0 and 4.5, respectively. The optimum pH (pHopt) for the optimum complex coacervation was 3.1. The instability and dissolution of FPI-FG complex coacervates started (pHΦ2) at pH2.1. These findings contribute to the development of FPI-FG complex coacervates as delivery vehicles for unstable albeit valuable nutrients such as omega-3 fatty acids.