Using Quest3D to Develop VES: a Tool for Enhancing Electrical Safety and Design in the Built Environment

This paper presents a novel desktop virtual reality model titled Virtual Electrical Services (VES), developed to enhance electrical safety and design in the built environment. The model developed using Quest3D has the potential to be used as an industry design tool or as an educational tool for third level students and represents a significant watershed in how electrical services engineers can potentially design buildings and interpret their design decisions. A description of the software development process of the virtual reality model is presented along with the applications that were developed within the model. Based on the early implementation of this prototype model, it would appear electrical services engineers perceive the prototype to be a useful tool and were receptive to using VES as a learning and design tool

Development and Evaluation of a Desktop VR System for Electrical Services Engineers

This paper presents a prototype desktop virtual reality model, developed to enhance electrical safety and design in the built environment. The model presented has the potential to be used as an educational tool for third level students, an industry design tool or as a virtual electrical safety manual for the general public. A description of the development of the virtual reality model is presented along with the applications that were developed within the model. Subsequently, a case study is carried out to evaluate the users’ attitudes toward VR learning environments and also the usability of the prototype model developed. Based on the development of this prototype model, it appears from the completed case study that the users perceive the prototype to be a useful tool and were receptive to using VR as a learning and design tool

Enhanced conformational space sampling improves the prediction of chemical shifts in proteins.

A biased-potential molecular dynamics simulation method, accelerated molecular dynamics (AMD), was combined with the chemical shift prediction algorithm SHIFTX to calculate (1)H(N), (15)N, (13)Calpha, (13)Cbeta, and (13)C' chemical shifts of the ankyrin repeat protein IkappaBalpha (residues 67-206), the primary inhibitor of nuclear factor kappa-B (NF-kappaB). Free-energy-weighted molecular ensembles were generated over a range of acceleration levels, affording systematic enhancement of the conformational space sampling of the protein. We have found that the predicted chemical shifts, particularly for the (15)N, (13)Calpha, and (13)Cbeta nuclei, improve substantially with enhanced conformational space sampling up to an optimal acceleration level. Significant improvement in the predicted chemical shift data coincides with those regions of the protein that exhibit backbone dynamics on longer time scales. Interestingly, the optimal acceleration level for reproduction of the chemical shift data has previously been shown to best reproduce the experimental residual dipolar coupling (RDC) data for this system, as both chemical shift data and RDCs report on an ensemble and time average in the millisecond range

Direct observation of hierarchical protein dynamics

One of the fundamental challenges of physical biology is to understand the relationship between protein dynamics and function. At physiological temperatures, functional motions arise from the complex interplay of thermal motions of proteins and their environments. Here, we determine the hierarchy in the protein conformational energy landscape that underlies these motions, based on a series of temperature-dependent magic-angle spinning multinuclear nuclear-magnetic-resonance relaxation measurements in a hydrated nanocrystalline protein. The results support strong coupling between protein and solvent dynamics above 160 kelvin, with fast solvent motions, slow protein side-chain motions, and fast protein backbone motions being activated consecutively. Low activation energy, small-amplitude local motions dominate at low temperatures, with larger-amplitude, anisotropic, and functionally relevant motions involving entire peptide units becoming dominant at temperatures above 220 kelvin

Functional trade-offs in cribellate silk mediated by spinning behavior

Web-building spiders are an extremely diverse predatory group due to their use of physiologically differentiated silk types in webs. Major shifts in silk functional properties are classically attributed to innovations in silk genes and protein expression. Here, we disentangle the effects of spinning behavior on silk performance of the earliest types of capture threads in spider webs for the first time. Progradungula otwayensis produces two variations of cribellate silk in webs: ladder lines are stereotypically combed with the calamistrum while supporting rail lines contain silk that is naturally uncombed, spun without the intervention of the legs. Combed cribellate silk is highly extensible and adhesive suggesting that the reserve warp and cribellate fibrils brings them into tension only near or after the underlying axial fibers are broken. In contrast, these three fiber components are largely aligned in the uncombed threads and deform as a single composite unit that is 5–10x stronger, but significantly less adhesive, allowing them to act as structural elements in the web. Our study reveals that cribellate silk can occupy a surprisingly diverse performance space, accessible through simple changes in spider behavior, which may have facilitated the impressive diversification of web architectures utilizing this ancient silk.Fil: Michalik, Peter. ERNST MORITZ ARNDT UNIVERSITÄT GREIFSWALD (UG);Fil: Piorkowski, Dakota. Tunghai University; ChinaFil: Blackledge, Todd A.. University of Akron; Estados UnidosFil: Ramirez, Martin Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentin

Distinct ubiquitin binding modes exhibited by SH3 domains: Molecular determinants and functional implications

SH3 domains constitute a new type of ubiquitin-binding domains. We previously showed that the third SH3 domain (SH3-C) of CD2AP binds ubiquitin in an alternative orientation. We have determined the structure of the complex between first CD2AP SH3 domain and ubiquitin and performed a structural and mutational analysis to decipher the determinants of the SH3-C binding mode to ubiquitin. We found that the Phe-to-Tyr mutation in CD2AP and in the homologous CIN85 SH3-C domain does not abrogate ubiquitin binding, in contrast to previous hypothesis and our findings for the first two CD2AP SH3 domains. The similar alternative binding mode of the SH3-C domains of these related adaptor proteins is characterised by a higher affinity to C-terminal extended ubiquitin molecules. We conclude that CD2AP/CIN85 SH3-C domain interaction with ubiquitin constitutes a new ubiquitin-binding mode involved in a different cellular function and thus changes the previously established mechanism of EGF-dependent CD2AP/CIN85 mono-ubiquitination. © 2013 Ortega Roldan et al

Bilingual poetry: expanding the cognitive and cultural dimensions of children’s learning

Stories and poetry have long been considered a resource for the language and literacy development of bilingual children, particularly if they can work with texts in both mother tongue and English. This paper demonstrates that bilingual learning is also beneficial for second and third generation children whose English is often stronger than their mother tongue. Presenting data from an action research project in East London primary schools, we show how children investigated metaphor and cultural content in a Bengali lullaby, clarifying concepts through dialogue with their parents. Comparison with a lullaby in English from North America generated additional ideas concerning different cultural values. The learning process enabled children to use their bilingual skills and draw on different aspects of their bicultural identities. Finally, we explain how bilingual poetry can be used to stimulate learning in a multilingual classroom context, through the example of a whole-class lesson based around Bengali and English lullabies

Conformational and thermodynamic changes of the repressor/DNA operator complex upon monomerization shed new light on regulation mechanisms of bacterial resistance against β-lactam antibiotics

In absence of β-lactam antibiotics, BlaI and MecI homodimeric repressors negatively control the expression of genes involved in β-lactam resistance in Bacillus licheniformis and in Staphylococcus aureus. Subsequently to β-lactam presence, BlaI/MecI is inactivated by a single-point proteolysis that separates its N-terminal DNA-binding domain to its C-terminal domain responsible for its dimerization. Concomitantly to this proteolysis, the truncated repressor acquires a low affinity for its DNA target that explains the expression of the structural gene for resistance. To understand the loss of the high DNA affinity of the truncated repressor, we have determined the different dissociation constants of the system and solved the solution structure of the B. licheniformis monomeric repressor complexed to the semi-operating sequence OP1 of blaP (1/2OP1blaP) by using a de novo docking approach based on inter-molecular nuclear Overhauser effects and chemical-shift differences measured on each macromolecular partner. Although the N-terminal domain of the repressor is not subject to internal structural rearrangements upon DNA binding, the molecules adopt a tertiary conformation different from the crystallographic operator–repressor dimer complex, leading to a 30° rotation of the monomer with respect to a central axis extended across the DNA

Accurate characterization of weak macromolecular interactions by titration of NMR residual dipolar couplings: application to the CD2AP SH3-C:ubiquitin complex

The description of the interactome represents one of key challenges remaining for structural biology. Physiologically important weak interactions, with dissociation constants above 100 μM, are remarkably common, but remain beyond the reach of most of structural biology. NMR spectroscopy, and in particular, residual dipolar couplings (RDCs) provide crucial conformational constraints on intermolecular orientation in molecular complexes, but the combination of free and bound contributions to the measured RDC seriously complicates their exploitation for weakly interacting partners. We develop a robust approach for the determination of weak complexes based on: (i) differential isotopic labeling of the partner proteins facilitating RDC measurement in both partners; (ii) measurement of RDC changes upon titration into different equilibrium mixtures of partially aligned free and complex forms of the proteins; (iii) novel analytical approaches to determine the effective alignment in all equilibrium mixtures; and (iv) extraction of precise RDCs for bound forms of both partner proteins. The approach is demonstrated for the determination of the three-dimensional structure of the weakly interacting CD2AP SH3-C:Ubiquitin complex (Kd = 132 ± 13 μM) and is shown, using cross-validation, to be highly precise. We expect this methodology to extend the remarkable and unique ability of NMR to study weak protein–protein complexes