Existence and stability of multisite breathers in honeycomb and hexagonal lattices

We study the existence and stability of multisite discrete breathers in two prototypical non-square Klein-Gordon lattices, namely a honeycomb and a hexagonal one. In the honeycomb case we consider six-site configurations and find that for soft potential and positive coupling the out-of-phase breather configuration and the charge-two vortex breather are linearly stable, while the in-phase and charge-one vortex states are unstable. In the hexagonal lattice, we first consider three-site configurations. In the case of soft potential and positive coupling, the in-phase configuration is unstable and the charge-one vortex is linearly stable. The out-of-phase configuration here is found to always be linearly unstable. We then turn to six-site configurations in the hexagonal lattice. The stability results in this case are the same as in the six-site configurations in the honeycomb lattice. For all configurations in both lattices, the stability results are reversed in the setting of either hard potential or negative coupling. The study is complemented by numerical simulations which are in very good agreement with the theoretical predictions. Since neither the form of the on-site potential nor the sign of the coupling parameter involved have been prescribed, this description can accommodate inverse-dispersive systems (e. g. supporting backward waves) such as transverse dust-lattice oscillations in dusty plasma (Debye) crystals or analogous modes in molecular chains.

Molecular Modeling on Inhibitor Complexes and Active-Site Dynamics of Cytochrome P450 C17, a Target for Prostate Cancer Therapy

A molecular model for the P450 enzyme cytochrome P450 C17 (CYP17) is presented based on sequence alignments of multiple template structures and homology modeling. This enzyme plays a central role in the biosynthesis of testosterone and is emerging as a major target in prostate cancer, with the recently developed inhibitor abiraterone currently in advanced clinical trials. The model is described in detail, together with its validation, by providing structural explanations to available site-directed mutagenesis data. The CYP17 molecule in this model is in the form of a triangular prism, with an edge of similar to 55 angstrom and a thickness of similar to 37 angstrom. It is predominantly helical, comprising 13 alpha helices interspersed by six 3(10) helices and 11 beta-sheets. Multinanosecond molecular dynamics simulations in explicit solvent have been carried out, and principal components analysis has been used to reveal the details of dynamics around the active site. Coarse-grained methods have also been used to verify low-frequency motions, which have been correlated with active-site gating. The work also describes the results of docking synthetic inhibitors, including the drug abiraterone and the natural substrate pregnenolone, in the CYP17 active site together with molecular dynamics simulations on the complexes. (C) 2010 Elsevier Ltd. All rights reserved.

Ginkgolide B and bilobalide block the pore of the 5-HT3 receptor at a location that overlaps the picrotoxin binding site

Extracts from the Ginkgo biloba tree are widely used as herbal medicines, and include bilobalide (BB) and ginkgolides A and B (GA and GB). Here we examine their effects on human 5-HT(3)A and 5-HT(3)AB receptors, and compare these to the effects of the structurally related compounds picrotin (PTN) and picrotoxinin (PXN), the two components of picrotoxin (PTX), a known channel blocker of 5-HT3, nACh and GABA(A) receptors. The compounds inhibited 5-HT-induced responses of 5-HT3 receptors expressed in Xenopus oocytes, with IC50 values of 470 mu M (BB), 730 mu M (GB), 470 mu M (PTN), 11 mu M (PXN) and > 1 mM (GA) in 5-HT(3)A receptors, and 3.1 mM (BB), 3.9 mM (GB), 2.7 mM (PTN), 62 mu M (PXN) and > 1 mM (GA) in 5-HT(3)AB receptors. Radioligand binding on receptors expressed in HEK 293 cells showed none of the compounds displaced the specific 5-HT3 receptor antagonist [H-3]granisetron, confirming that they do not act at the agonist binding site. Inhibition by GB at 5-HT(3)A receptors is weakly use-dependent, and recovery is activity dependent, indicating channel block. To further probe their site of action at 5-HT(3)A receptors, BB and GB were applied alone or in combination with PXN, and the results fitted to a mathematical model; the data revealed partially overlapping sites of action. We conclude that BB and GB block the channel of the 5-HT(3)A receptor. Thus these compounds have comparable, although less potent, behaviour than at some other Cys-loop receptors, demonstrating their actions are conserved across the family. (C) 2010 Published by Elsevier Ltd.

Probing magnetic order in ultracold lattice gases

A forthcoming challenge in ultracold lattice gases is the simulation of quantum magnetism. That involves both the preparation of the lattice atomic gas in the desired spin state and the probing of the state. Here we demonstrate how a probing scheme based on atom-light interfaces gives access to the order parameters of nontrivial quantum magnetic phases, allowing us to characterize univocally strongly correlated magnetic systems produced in ultracold gases. This method, which is also nondemolishing, yields spatially resolved spin correlations and can be applied to bosons or fermions. As a proof of principle, we apply this method to detect the complete phase diagram displayed by a chain of (rotationally invariant) spin-1 bosons.

Detection of DNA base variation and cytosine methylation at a single nucleotide site using a highly sensitive fluorescent probe

A fluorescent DNA probe containing an anthracene group attached via an anucleosidic linker can identify all four DNA bases at a single site as well as the epigenetic modification C/5-MeC via a hybridisation sensing assay.

Confined site construction: A qualitative review of issues regarding health and safety on-site

The construction industry is inherently hazardous, with a significant number of accidents and incidents occurring, particularly on confined construction sites. This research identifies, clarifies and tabulates the various managerial health and safety issues encountered on confined construction sites, based on a qualitative approach, to aid in the management of the complex health and safety concerns. The methodology is based on qualitative research incorporating case studies, interviews, causal loop diagrams and mind mapping. The key findings in the managerial issues in the management of health and safety on confined construction sites can be summarised as follows; (1) A lack of space, (2) Increased management of site personnel, (3) Overcrowding of the work place. The implication for the industry is that due to the sustained development of urban centres on a global scale, coupled with the increasing complexity of architectural designs, the majority of on-site project management professionals are faced with the onerous task of completing often intricate designs within a limited spatial environment, under strict health and safety parameters. The value of such research is to aid management professionals successfully identify the various managerial issues highlighted, resulting in the successful management of health and safety on a confined construction site.

Confined Site Construction: A qualitative investigation of critical issues affecting management of Health and Safety

The construction industry is inherently risky, with a significant number of accidents and disasters occurring, particularly on confined construction sites. This research investigates and identifies the various issues affecting successful management of health and safety in confined construction sites. The rationale is that identifying the issues would assist the management of health and safety particularly in inner city centres which are mostly confined sites. Using empiricism epistemology, the methodology was based on qualitative research approach by means of multiple case studies in three different geographical locations of Ireland, UK and USA. Data on each case study were collected through individual interviews and focus group discussion with project participants. The findings suggest that three core issues are the underlying factors affecting management of health and safety on confined construction sites. It include, (i) lack of space, (ii) problem of co-ordination and management of site personnel, and (iii) overcrowding of workplace. The implication of this is that project teams and their organisations should see project processes from a holistic point of view, as a unified single system, where quick intervention in solving a particular issue should be the norm, so as not to adversely affect interrelated sequence of events in project operations. Proactive strategies should be devised to mitigate these issues and may include detail project programming, space management, effective constructability review and efficient co-ordination of personnel, plant and materials among others. The value of this research is to aid management and operation of brownfield sites by identifying issues impacting on health and safety management in project process.

Increased Promiscuity of Human Galactokinase Following Alteration of a Single Amino Acid Residue Distant from the Active Site

Galactokinase catalyses the site-and stereospecific phosphorylation of galactose at the expense of ATP. The specificity of bacterial galactokinase enzymes can be broadened by alteration of a tyrosine residue to a histidine. The effects of altering the equivalent residue in human galactokinase (Tyr379) were investigated by testing all 19 possible variants. All of these alterations, except Y379P, resulted in soluble protein on expression in Escherichia coli and all the soluble variants could catalyse the phosphorylation of galactose, except Y379A and Y379E. The variants Y379C, Y379K, Y379R, Y379S and Y379W were all able to catalyse the phosphorylation of a variety of monosaccharides, including ones that are not acted on by the wild-type enzyme. Novel substrates for these variant galactokinases included D-mannose and D-fructose. The latter monosaccharide is presumed to react in the pyranose configuration. Molecular modelling suggested that the alterations do not cause changes to the overall structure of the enzyme. However, alteration of Tyr379 increases the flexibility of the peptide backbone in regions surrounding the active site. Therefore, it is proposed that alteration of Tyr379 affects the substrate specificity by the propagation of changes in flexibility to the active site, permitting a broader range of compounds to be accommodated.

The role of the active site residues in human galactokinase: implications for the mechanisms of GHMP kinases.

Galactokinase catalyses the phosphorylation of galactose at the expense of ATP. Like other members of the GHMP family of kinases it is postulated to function through an active site base mechanism in which Asp-186 abstracts a proton from galactose. This asparate residue was altered to alanine and to asparagine by site-directed mutagenesis of the corresponding gene. This resulted in variant enzyme with no detectable galactokinase activity. Alteration of Arg-37, which lies adjacent to Asp-186 and is postulated to assist the catalytic base, to lysine resulted in an active enzyme. However, alteration of this residue to glutamate abolished activity. All the variant enzymes, except the arginine to lysine substitution, were structurally unstable (as judged by native gel electrophoresis in the presence of urea) compared to the wild type. This suggests that the lack of activity results from this structural instability, in addition to any direct effects on the catalytic mechanism. Computational estimations of the pK(a) values of the arginine and aspartate residues, suggest that Arg-37 remains protonated throughout the catalytic cycle whereas Asp-186 has an abnormally high pK(a) value (7.18). Quantum mechanics/molecular mechanics (QM/MM) calculations suggest that Asp-186 moves closer to the galactose molecule during catalysis. The experimental and theoretical studies presented here argue for a mechanism in which the C-1-OH bond in the sugar is weakened by the presence of Asp-186 thus facilitating nucleophilic attack by the oxygen atom on the gamma-phosphorus of ATP.