Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach

Metal-binding proteins play important roles in structural stability, signaling, regulation, transport, immune response, metabolism control, and metal homeostasis. Because of their functional and sequence diversity, it is desirable to explore additional methods for predicting metal-binding proteins irrespective of sequence similarity. This work explores support vector machines (SVM) as such a method. SVM prediction systems were developed by using 53,333 metal-binding and 147,347 non-metal-binding proteins, and evaluated by an independent set of 31,448 metal-binding and 79,051 non-metal-binding proteins. The computed prediction accuracy is 86.3%, 81.6%, 83.5%, 94.0%, 81.2%, 85.4%, 77.6%, 90.4%, 90.9%, 74.9% and 78.1% for calcium-binding, cobalt-binding, copper-binding, iron-binding, magnesium-binding, manganese-binding, nickel-binding, potassium-binding, sodium-binding, zinc-binding, and all metal-binding proteins respectively. The accuracy for the non-member proteins of each class is 88.2%, 99.9%, 98.1%, 91.4%, 87.9%, 94.5%, 99.2%, 99.9%, 99.9%, 98.0%, and 88.0% respectively. Comparable accuracies were obtained by using a different SVM kernel function. Our method predicts 67% of the 87 metal-binding proteins non-homologous to any protein in the Swissprot database and 85.3% of the 333 proteins of known metal-binding domains as metal-binding. These suggest the usefulness of SVM for facilitating the prediction of metal-binding proteins. Our software can be accessed at the SVMProt server

Approaching the ideal elastic limit of metallic glasses

The ideal elastic limit is the upper bound to the stress and elastic strain a material can withstand. This intrinsic property has been widely studied for crystalline metals, both theoretically and experimentally. For metallic glasses, however, the ideal elastic limit remains poorly characterized and understood. Here we show that the elastic strain limit and the corresponding strength of submicron-sized metallic glass specimens are about twice as high as the already impressive elastic limit observed in bulk metallic glass samples, in line with model predictions of the ideal elastic limit of metallic glasses. We achieve this by employing an in situ transmission electron microscope tensile deformation technique. Furthermore, we propose an alternative mechanism for the apparent 'work hardening' behaviour observed in the tensile stress–strain curves

Unusual synergistic effect in layered Ruddlesden-Popper oxide enables ultrafast hydrogen evolution

Efficient electrocatalysts for hydrogen evolution reaction are key to realize clean hydrogen production through water splitting. As an important family of functional materials, transition metal oxides are generally believed inactive towards hydrogen evolution reaction, although many of them show high activity for oxygen evolution reaction. Here we report the remarkable electrocatalytic activity for hydrogen evolution reaction of a layered metal oxide, Ruddlesden-Popper-type Sr2RuO4 with alternative perovskite layer and rock-salt SrO layer, in an alkaline solution, which is comparable to those of the best electrocatalysts ever reported. By theoretical calculations, such excellent activity is attributed mainly to an unusual synergistic effect in the layered structure, whereby the (001) SrO-terminated surface cleaved in rock-salt layer facilitates a barrier-free water dissociation while the active apical oxygen site in perovskite layer promotes favorable hydrogen adsorption and evolution. Moreover, the activity of such layered oxide can be further improved by electrochemistry-induced activation

Influence of reaction time and synthesis temperature on the physical properties of ZnO nanoparticles synthesized by the hydrothermal method

Influence of synthesis temperature and reaction time on the structural and optical properties of ZnO nanoparticles synthesized by the hydrothermal method was investigated using X-ray diffraction (XRD), high resolution transmission electron microscopy (HR-TEM), energy-dispersive X-ray, Fourier transform infra-red spectroscopy, and UV–visible and fluorescence spectroscopy. The XRD pattern and HR-TEM images confirmed the presence of crystalline hexagonal wurtzite ZnO nanoparticles with average crystallite size in the range 30–40 nm. Their energy gap determined by fluorescence was found to depend on the synthesis temperature and reaction time with values in the range 2.90–3.78 eV. Thermal analysis, thermogravimetric and the differential scanning calorimetry were used to study the thermal reactions and weight loss with heat of the prepared ZnO nanoparticles

DR*W201/P65 Tetramer Visualization of Epitope-Specific CD4 T-Cell during M. tuberculosis Infection and Its Resting Memory Pool after BCG Vaccination

In vivo kinetics and frequencies of epitope-specific CD4 T cells in lymphoid compartments during M. tuberculosis infection and their resting memory pool after BCG vaccination remain unknown.Macaque DR*W201 tetramer loaded with Ag85B peptide 65 was developed to directly measure epitope-specific CD4 T cells in blood and tissues form macaques after M. tuberculosis infection or BCG vaccination via direct staining and tetramer-enriched approach. The tetramer-based enrichment approach showed that P65 epitope-specific CD4 T cells emerged at mean frequencies of approximately 500 and approximately 4500 per 10(7) PBL at days 28 and 42, respectively, and at day 63 increased further to approximately 22,000/10(7) PBL after M. tuberculosis infection. Direct tetramer staining showed that the tetramer-bound P65-specific T cells constituted about 0.2-0.3% of CD4 T cells in PBL, lymph nodes, spleens, and lungs at day 63 post-infection. 10-fold expansion of these tetramer-bound epitope-specific CD4 T cells was seen after the P65 peptide stimulation of PBL and tissue lymphocytes. The tetramer-based enrichment approach detected BCG-elicited resting memory P65-specific CD4 T cells at a mean frequency of 2,700 per 10(7) PBL.Our work represents the first elucidation of in vivo kinetics and frequencies for tetramer-bound epitope-specific CD4 T cells in the blood, lymphoid tissues and lungs over times after M. tuberculosis infection, and BCG immunization