Rhodopsin and the Others: A Historical Perspective on Structural Studies of G Protein-Coupled Receptors

The role of rhodopsin as a structural prototype for the study of the whole superfamily of G protein-coupled receptors (GPCRs) is reviewed in an historical perspective. Discovered at the end of the nineteenth century, fully sequenced since the early 1980s, and with direct three-dimensional information available since the 1990s, rhodopsin has served as a platform to gather indirect information on the structure of the other superfamily members. Recent breakthroughs have elicited the solution of the structures of additional receptors, namely the beta 1- and beta 2-adrenergic receptors and the A(2A) adenosine receptor, now providing an opportunity to gauge the accuracy of homology modeling and molecular docking techniques and to perfect the computational protocol. Notably, in coordination with the solution of the structure of the A(2A) adenosine receptor, the first "critical assessment of GPCR structural modeling and docking" has been organized, the results of which highlighted that the construction of accurate models, although challenging, is certainly achievable. The docking of the ligands and the scoring of the poses clearly emerged as the most difficult components. A further goal in the field is certainly to derive the structure of receptors in their signaling state, possibly in complex with agonists. These advances, coupled with the introduction of more sophisticated modeling algorithms and the increase in computer power, raise the expectation for a substantial boost of the robustness and accuracy of computer-aided drug discovery techniques in the coming years.

Non-Prismatic Sub-Stiffening for Stiffened Panel Plates — Stability Behaviour and Performance Gains

Previous work has demonstrated the potential to introduce plate element sub-stiffening to increase the local stability and thus static strength performance of integrally machined aluminium alloy stiffened panels. The introduction of plate element prismatic sub-stiffening modifies local plate buckling behaviour and within realistic design constraints, may produce sizable performance gains with equivalent mass designs. This article examines through experimental and computational analysis the potential of non-prismatic sub-stiffening for tailoring local plate stability performance. Using non-prismatic sub-stiffening, the experimental work demonstrates potential initial buckling performance gains with equivalent mass designs (+185%), and computationally, potential mass savings with equivalent static strength performance designs (-9.4%). (C) 2010 Elsevier Ltd. All rights reserved.

Functional and Structural Diversification of the Anguimorpha Lizard Venom System

Venom has only been recently discovered to be a basal trait of the Anguimorpha lizards. Consequently, very little is known about the timings of toxin recruitment events, venom protein molecular evolution, or even the relative physical diversifications of the venom system itself. A multidisciplinary approach was used to examine the evolution across the full taxonomical range of this similar to 130 million-year-old clade. Analysis of cDNA libraries revealed complex venom transcriptomes. Most notably, three new cardioactive peptide toxin types were discovered (celestoxin, cholecystokinin, and YY peptides). The latter two represent additional examples of convergent use of genes in toxic arsenals, both having previously been documented as components of frog skin defensive chemical secretions. Two other novel venom gland-overexpressed modified versions of other protein frameworks were also recovered from the libraries (epididymal secretory protein and ribonuclease). Lectin, hyaluronidase, and veficolin toxin types were sequenced for the first time from lizard venoms and shown to be homologous to the snake venom forms. In contrast, phylogenetic analyses demonstrated that the lizard natriuretic peptide toxins were recruited independently of the form in snake venoms. The de novo evolution of helokinestatin peptide toxin encoding do-mains within the lizard venom natriuretic gene was revealed to be exclusive to the helodermatid/anguid subclade. New isoforms were sequenced for cysteine-rich secretory protein, kallikrein, and phospholipase A 2 toxins. Venom gland morphological analysis revealed extensive evolutionary tinkering. Anguid glands are characterized by thin capsules and mixed glands, serous at the bottom of the lobule and mucous toward the apex. Twice, independently this arrangement was segregated into specialized serous protein-secreting glands with thick capsules with the mucous lobules now distinct (Heloderma and the Lanthanotus/Varanus clade). The results obtained highlight the importance of utilizing evolution-based search strategies for biodiscovery and emphasize the largely untapped drug design and development potential of lizard venoms. Molecular & Cellular Proteomics 9:2369-2390, 2010.

Study of structural change in Wyodak coal in high pressure CO2 by small-angle neutron scattering

Small angle neutron scattering (SANS) has been applied to examine the effect of high pressure CO2 on the structure of Wyodak coal. Significant decrease in the scattering intensities upon exposure of the coal to high pressure CO2 showed that high pressure CO2 rapidly adsorbs on the coal and reaches to all pores in the structure. This is confirmed by strong and steep exothermic peaks observed on DSC scans during coal/ CO2 interactions. In situ small angle neutron scattering on coal at high pressure CO2 atmosphere showed an increase in scattering intensities with time suggesting that after adsorption, high pressure CO2 immediately begins to diffuse into the coal matrix, changes the macromolecular structure of the coal, swells the matrix and probably creates microporosity in coal structure by extraction of volatile components from coal. Significant decrease in the glass transition temperature of coal caused by high pressure CO2 also confirms that CO2 at elevated pressures dissolve in the coal matrix, results in significant plasticization and physical rearrangement of the coal’s macromolecular structure.

Molecular Dynamics of HIV1-Integrase in Complex with 93del - A Structural Perspective on the Mechanism of Inhibition

HIV1 integrase is an important target for the antiviral therapy. Guanine-rich quadruplex, such as 93del, have been shown to be potent inhibitors of this enzyme and thus representing a new class of antiviral agents. Although X-ray and NMR structures of HIV1 integrase and 93del have been reported, there is no structural information of the complex and the mechanism of inhibition still remains unexplored. A number of computational methods including automated protein-DNA docking and molecular dynamics simulation in explicit solvent were used to model the binding of 93del to HIV1 integrase. Analysis of the dynamic behaviour of the complex using principal components analysis and elastic network modelling techniques allow us to understand how the binding of 93del aptamer and its interactions with key residues affect the intrinsic motions of the catalytic loops by stabilising them in catalytically inactive conformations. Such insights into the structural mechanism of inhibition can aid in improving the design of anti-HIV aptamers.

Efficient modelling and optimisation of hybrid multilayered plates subject to ballistic impact

Among the key challenges present in the modelling and optimisation of composite structures against impact is the computational expense involved in setting up accurate simulations of the impact event and then performing the iterations required to optimise the designs. It is of more interest to find good designs given the limitations of the resources and time available rather than the best possible design. In this paper, low cost but sufficiently accurate finite element (FE) models were generated in LS Dyna for several experimentally characterised materials by semi-automating the modelling process and using existing material models. These models were then used by an optimisation algorithm to generate new hybrid offspring, leading to minimum weight and/or cost designs from a selection of isotropic metals, polymers and orthotropic fibre-reinforced laminates that countered a specified impact threat. Experimental validation of the optimal designs thus identified was then successfully carried out using a single stage gas gun. With sufficient computational hardware, the techniques developed in this pilot study can further utilise fine meshes, equations of state and sophisticated material models, so that optimal hybrid systems can be identified from a wide range of materials, designs and threats.

Lay-up optimization of composite plates to delay mode-jump instabilities

Experimental and numerical studies have shown that the occurrence of abrupt secondary instabilities, or mode-jumps, in a postbuckling stiffened composite panel may initiate structural failure. This study presents an optimisation methodology, using a genetic algorithm and finite element analysis for the lay-up optimisation of postbuckling composite plates to delay the onset of mode-jump instabilities. A simple and novel approach for detecting modejumps is proposed, based on the RMS value of out-of-plane pseudo-velocities at a number of locations distributed over the postbuckling structure

A Novel Bradykinin-Related Dodecapeptide (RVALPPGFTPLR) from the Skin Secretion of the Fujian Large-Headed Frog (Limnonectes fujianensis) Exhibiting Unusual Structural and Functional Features

Bradykinin-related peptides (BRPs) are significant components of the defensive skin secretions of many anuran amphibians, and these secretions represent the source of the most diverse spectrum of such peptides so far encountered in nature. Of the many families of bioactive peptides that have been identified from this source, the BRPs uniquely appear to represent homologues of counterparts that have specific distributions and receptor targets within discrete vertebrate taxa, ranging from fishes through mammals. Their broad spectra of actions, including pain and inflammation induction and smooth muscle effects, make these peptides ideal weapons in predator deterrence. Here, we describe a novel 12-mer BRP (RVALPPGFTPLR-RVAL-(L1, T6, L8)-bradykinin) from the skin secretion of the Fujian large-headed frog (Limnonectes fujianensis). The C-terminal 9 residues of this BRP (-LPPGFTPLR) exhibit three amino acid substitutions (L/R at Position 1, T/S at Position 6 and L/F at Position 8) when compared to canonical mammalian bradykinin (BK), but are identical to the kinin sequence present within the cloned kininogen-2 from the Chinese soft-shelled turtle (Pelodiscus sinensis) and differ from that encoded by kininogen-2 of the Tibetan ground tit (Pseudopodoces humilis) at just a single site (F/L at Position 8). These data would imply that the novel BRP is an amphibian defensive agent against predation by sympatric turtles and also that the primary structure of the avian BK, ornithokinin (RPPGFTPLR), is not invariant within this taxon. Synthetic RVAL-(L1, T6, L8)-bradykinin was found to be an antagonist of BK-induced rat tail artery smooth muscle relaxation acting via the B2-receptor.

Understanding aerospace composite components' supply chain carbon emissions

This paper examines a large structural component and its supply chain. The component is representative of that used in the production of civil transport aircraft and is manufactured from carbon fibre epoxy resin prepreg, using traditional hand layup and autoclave cure. Life cycle assessment (LCA) is used to predict the component’s production carbon emissions. The results determine the distribution of carbon emissions within the supply chain, identifying the dominant production processes as carbon fibre manufacture and composite part manufacture. The elevated temperature processes of material and part creation, and the associated electricity usage, have a significant impact on the overall production emissions footprint. The paper also demonstrates the calculation of emissions footprint sensitivity to the geographic location and associated energy sources of the supply chain. The results verify that the proposed methodology is capable of quantitatively linking component and supply chain specifics to manufacturing processes and thus identifying the design drivers for carbon emissions in the manufacturing life of the component.

Using Graph Components Derived from an Associative Concept Dictionary to Predict fMRI Neural Activation Patterns that Represent the Meaning of Nouns

In this study, we introduce an original distance definition for graphs, called the Markov-inverse-F measure (MiF). This measure enables the integration of classical graph theory indices with new knowledge pertaining to structural feature extraction from semantic networks. MiF improves the conventional Jaccard and/or Simpson indices, and reconciles both the geodesic information (random walk) and co-occurrence adjustment (degree balance and distribution). We measure the effectiveness of graph-based coefficients through the application of linguistic graph information for a neural activity recorded during conceptual processing in the human brain. Specifically, the MiF distance is computed between each of the nouns used in a previous neural experiment and each of the in-between words in a subgraph derived from the Edinburgh Word Association Thesaurus of English. From the MiF-based information matrix, a machine learning model can accurately obtain a scalar parameter that specifies the degree to which each voxel in (the MRI image of) the brain is activated by each word or each principal component of the intermediate semantic features. Furthermore, correlating the voxel information with the MiF-based principal components, a new computational neurolinguistics model with a network connectivity paradigm is created. This allows two dimensions of context space to be incorporated with both semantic and neural distributional representations.