Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information

Background The majority of peptide bonds in proteins are found to occur in the trans conformation. However, for proline residues, a considerable fraction of Prolyl peptide bonds adopt the cis form. Proline cis/trans isomerization is known to play a critical role in protein folding, splicing, cell signaling and transmembrane active transport. Accurate prediction of proline cis/trans isomerization in proteins would have many important applications towards the understanding of protein structure and function. Results In this paper, we propose a new approach to predict the proline cis/trans isomerization in proteins using support vector machine (SVM). The preliminary results indicated that using Radial Basis Function (RBF) kernels could lead to better prediction performance than that of polynomial and linear kernel functions. We used single sequence information of different local window sizes, amino acid compositions of different local sequences, multiple sequence alignment obtained from PSI-BLAST and the secondary structure information predicted by PSIPRED. We explored these different sequence encoding schemes in order to investigate their effects on the prediction performance. The training and testing of this approach was performed on a newly enlarged dataset of 2424 non-homologous proteins determined by X-Ray diffraction method using 5-fold cross-validation. Selecting the window size 11 provided the best performance for determining the proline cis/trans isomerization based on the single amino acid sequence. It was found that using multiple sequence alignments in the form of PSI-BLAST profiles could significantly improve the prediction performance, the prediction accuracy increased from 62.8% with single sequence to 69.8% and Matthews Correlation Coefficient (MCC) improved from 0.26 with single local sequence to 0.40. Furthermore, if coupled with the predicted secondary structure information by PSIPRED, our method yielded a prediction accuracy of 71.5% and MCC of 0.43, 9% and 0.17 higher than the accuracy achieved based on the singe sequence information, respectively. Conclusion A new method has been developed to predict the proline cis/trans isomerization in proteins based on support vector machine, which used the single amino acid sequence with different local window sizes, the amino acid compositions of local sequence flanking centered proline residues, the position-specific scoring matrices (PSSMs) extracted by PSI-BLAST and the predicted secondary structures generated by PSIPRED. The successful application of SVM approach in this study reinforced that SVM is a powerful tool in predicting proline cis/trans isomerization in proteins and biological sequence analysis.

Identifying optimal lipid raft characteristics required to promote nanoscale protein-protein interactions on the plasma membrane

The dynamic lateral segregation of signaling proteins into microdomains is proposed to facilitate signal transduction, but the constraints on microdomain size, mobility, and diffusion that might realize this function are undefined. Here we interrogate a stochastic spatial model of the plasma membrane to determine how microdomains affect protein dynamics. Taking lipid rafts as representative microdomains, we show that reduced protein mobility in rafts segregates dynamically partitioning proteins, but the equilibrium concentration is largely independent of raft size and mobility. Rafts weakly impede small-scale protein diffusion but more strongly impede long-range protein mobility. The long-range mobility of raft-partitioning and raft-excluded proteins, however, is reduced to a similar extent. Dynamic partitioning into rafts increases specific interprotein collision rates, but to maximize this critical, biologically relevant function, rafts must be small (diameter, 6 to 14 nm) and mobile. Intermolecular collisions can also be favored by the selective capture and exclusion of proteins by rafts, although this mechanism is generally less efficient than simple dynamic partitioning. Generalizing these results, we conclude that microdomains can readily operate as protein concentrators or isolators but there appear to be significant constraints on size and mobility if microdomains are also required to function as reaction chambers that facilitate nanoscale protein-protein interactions. These results may have significant implications for the many signaling cascades that are scaffolded or assembled in plasma membrane microdomains.

Refining animal models in fracture research: Seeking consensus in optimising both animal welfare and scientific validity for appropriate biomedical use

Background In an attempt to establish some consensus on the proper use and design of experimental animal models in musculoskeletal research, AOVET (the veterinary specialty group of the AO Foundation) in concert with the AO Research Institute (ARI), and the European Academy for the Study of Scientific and Technological Advance, convened a group of musculoskeletal researchers, veterinarians, legal experts, and ethicists to discuss, in a frank and open forum, the use of animals in musculoskeletal research. Methods The group narrowed the field to fracture research. The consensus opinion resulting from this workshop can be summarized as follows: Results & Conclusion Anaesthesia and pain management protocols for research animals should follow standard protocols applied in clinical work for the species involved. This will improve morbidity and mortality outcomes. A database should be established to facilitate selection of anaesthesia and pain management protocols for specific experimental surgical procedures and adopted as an International Standard (IS) according to animal species selected. A list of 10 golden rules and requirements for conduction of animal experiments in musculoskeletal research was drawn up comprising 1) Intelligent study designs to receive appropriate answers; 2) Minimal complication rates (5 to max. 10%); 3) Defined end-points for both welfare and scientific outputs analogous to quality assessment (QA) audit of protocols in GLP studies; 4) Sufficient details for materials and methods applied; 5) Potentially confounding variables (genetic background, seasonal, hormonal, size, histological, and biomechanical differences); 6) Post-operative management with emphasis on analgesia and follow-up examinations; 7) Study protocols to satisfy criteria established for a "justified animal study"; 8) Surgical expertise to conduct surgery on animals; 9) Pilot studies as a critical part of model validation and powering of the definitive study design; 10) Criteria for funding agencies to include requirements related to animal experiments as part of the overall scientific proposal review protocols. Such agencies are also encouraged to seriously consider and adopt the recommendations described here when awarding funds for specific projects. Specific new requirements and mandates related both to improving the welfare and scientific rigour of animal-based research models are urgently needed as part of international harmonization of standards.

Engineering sustainable solutions program : critical literacies for engineers portfolio

Purpose While a number of universities in Australia have embraced concepts such as project/problem‐based learning and design of innovative learning environments for engineering education, there has been a lack of national guidance on including sustainability as a “critical literacy” into all engineering streams. This paper was presented at the 2004 International Conference on Engineering Education in Sustainable Development (EESD) in Barcelona, Spain, outlining a current initiative that is seeking to address the “critical literacy” dilemma. Design/methodology/approach The paper presents the positive steps taken by Australia's peak engineering body, the Institution of Engineers Australia (EA), in considering accreditation requirements for university engineering courses and its responsibility to ensure the inclusion of sustainability education material. It then describes a current initiative called the “Engineering Sustainable Solutions Program – Critical Literacies for Engineers Portfolio” (ESSP‐CL), which is being developed by The Natural Edge Project (TNEP) in partnership with EA and Unesco. Findings Content for the module was gathered from around the world, drawing on research from the publication The Natural Advantage of Nations: Business Opportunities, Innovation, and Governance in the Twenty‐first Century. Parts of the first draft of the ESSP‐CL have been trialled at Griffith University, Queensland, Australia with first year environmental engineering students, in May 2004. Further trials are now proceeding with a number of other universities and organisations nationally and internationally. Practical implications It is intended that ESSP‐CL will be a valuable resource to universities, professional development activities or other education facilities nationally and internationally. Originality/value This paper fulfils an identified information/resources need.

Asphalt concrete surfaces macrotexture determination from still images

Road surface macrotexture is identified as one of the factors contributing to the surface's skid resistance. Existing methods of quantifying the surface macrotexture, such as the sand patch test and the laser profilometer test, are either expensive or intrusive, requiring traffic control. High-resolution cameras have made it possible to acquire good quality images from roads for the automated analysis of texture depth. In this paper, a granulometric method based on image processing is proposed to estimate road surface texture coarseness distribution from their edge profiles. More than 1300 images were acquired from two different sites, extending to a total of 2.96 km. The images were acquired using camera orientations of 60 and 90 degrees. The road surface is modeled as a texture of particles, and the size distribution of these particles is obtained from chord lengths across edge boundaries. The mean size from each distribution is compared with the sensor measured texture depth obtained using a laser profilometer. By tuning the edge detector parameters, a coefficient of determination of up to R2 = 0.94 between the proposed method and the laser profilometer method was obtained. The high correlation is also confirmed by robust calibration parameters that enable the method to be used for unseen data after the method has been calibrated over road surface data with similar surface characteristics and under similar imaging conditions.