Sequence‐based prediction of protein–peptide binding sites using support vector machine

Protein–peptide interactions are essential for all cellular processes including DNA repair, replication, gene‐expression, and metabolism. As most protein – peptide interactions are uncharacterized, it is cost effective to investigate them computationally as the first step. All existing approaches for predicting protein – peptide binding sites, however, are based on protein structures despite the fact that the structures for most proteins are not yet solved. This article proposes the first machine‐learning method called SPRINT to make Sequence‐based prediction of Protein – peptide Residue‐level Interactions. SPRINT yields a robust and consistent performance for 10‐fold cross validations and independent test. The most important feature is evolution‐generated sequence profiles. For the test set (1056 binding and non‐binding residues), it yields a Matthews’ Correlation Coefficient of 0.326 with a sensitivity of 64% and a specificity of 68%. This sequence‐based technique shows comparable or more accurate than structure‐based methods for peptide‐binding site prediction. SPRINT is available as an online server at: http://sparks-lab.org/ . © 2016 Wiley Periodicals, Inc.     

Synthesis and characterization of a new ternary imide-Li2Ca(NH)2

The ternary imide Li(2)Ca(NH)2 was successfully synthesized by dehydrogenating a mixture of LiNH(2) and CaH(2) at a molar ratio of 2:1 in a stream of purified argon at 300 degrees C. A powder X-ray diffraction measurement revealed that Li(2)Ca(NH)2 was of the trigonal anti-La(2)O(3) structure (space group Pm1) with lattice constants of a = 3.5664(3)A and c = 5.9540(8) A. Ca occupied the 1b site (0, 0, 1/2), Li occupied the 2d site (1/3, 2/3, 0.8841(22)), and N occupied the 2d site (1/3, 2/3, 0.2565(15)). Nuclear magnetic resonance and X-ray absorption fine structure analyses demonstrated that each Li ion was coordinated with four imide ions and each Ca ion was coordinated with six imide ions.     

Ultrafast electron transfer from oligo(p-phenylene-ethynylene)thiol to gold

The electron transfer dynamics of oligo(p-phenylene-ethynylene) (OPE) SAM on Au(111) was studied by resonant photoemission spectroscopy. The ultrafast electron transfer from OPE molecules to Au substrate was clearly observed. The time scale for this charge transfer is much less than 6 fs, the core-hole lifetime for C 1s. This strongly suggests that there is an intense interfacial electronic coupling between OPE molecules and the Au substrate.     

Configuration-dependent interface charge transfer at a molecule-metal junction

The role of the molecule-metal interface is a key issue in molecular electronics. Interface charge transfer processes for 4-fluorobenzenethiol monolayers with different molecular orientations on Au(111) were studied by resonant photoemission spectroscopy. The electrons excited into the LUMO or LUMO+1 are strongly localized for the molecules standing up on Au(111). In contrast, an ultrafast charge transfer process was observed for the molecules lying down on Au(111). This configuration-dependent ultrafast electron transfer is dominated by an adiabatic mechanism and directly reflects the delocalization of the molecular orbitals for molecules lying down on Au(111). Theoretical calculations confirm that the molecular orbitals indeed experience a localization-delocalization transition resulting from hybridization between the molecular orbitals and metal surface. Such an orientation-dependent transition could be harnessed in molecular devices that switch via charge transfer when the molecular orientation is made to change.     

Reactivity of [CpCr(CO)3]2 towards thione (CS) moieties in some sulfur-containing substrates

The reaction of [CpCr(CO)₃]₂ (Cp = η⁵-C₅H₅) (1) with 1 mol equivalent of 2,5-dimercapto-1,3,4-thiadiazole (DMcTH₂) at ambient temperature led to the isolation of a reddish-brown crystalline solid of CpCr(CO)₃(η¹-DMcTH) (5) and a green solid of CpCr(CO)₃H (2) in yields of ca. 28% and 30%, respectively, along with some [CpCr(CO)₂]₂ (3) and [CpCr(CO)₂]₂S (4). The reaction of 1 with 1 mol equivalent of vinylene trithiocarbonate (SCS(CH)₂S) (VTTC) at 90 °C led to the isolation of a red crystalline solid of CpCr(CO)₂(η²-SCHSC₂H₂) (6) in ca. 15% yield while the reaction of 1 with isopropylxanthic disulfide ((CH₃)₂CHOCS₂)₂ resulted in the formation of CpCr(CO)₂(η²-S₂COCH(CH₃)₂) (8) in ca. 80% yield. The complexes 5, 6 and 8 have been determined by single crystal X-ray diffraction analysis.     

Fabrication of size-tunable gold nanoparticles array with nanosphere lithography, reactive ion etching, and thermal annealing

Two-dimensional ordered arrays of gold (Au) nanoparticles were fabricated using two different variants of the nanosphere lithography technique. First, ordered arrays of polystyrene nanospheres on Si substrate were used as deposition masks through which gold films were deposited by electron beam evaporation. After the removal of the nanospheres, an array of triangular Au nanodisks was left on the Si substrate. After thermal annealing at increasing temperature, systematic shape transition of the nanostructures from original triangular Au nanodisks to rounded nanoparticles was observed. This approach allows us to systematically vary the size and morphology of the particles. In the second and novel technique, we made use of reactive ion etching to simultaneously reduce the dimension of the masking nanospheres and create arrays of nanopores on the substrate prior to the deposition of the Au films. These samples were subsequently annealed, which resulted in size-tunable and ordered Au nanoparticle arrays with the nanoparticles nested in the nanopores of the templated substrate. With the nanoparticles anchored in the nanopores, the substrate could be useful as a template for growth of other nanomaterials.     

Convenient synthesis of Cu3(BTC)2 encapsulated Keggin heteropolyacid nanomaterial for application in catalysis

Nanomaterial of Cu(3)(BTC)(2) (BTC = benzene tricarboxylic acid) incorporating Keggin heteropolyacid conveniently prepared at room temperature and recovered by freeze drying outperforms ultrastable Y zeolite in acid catalysed esterification reaction.     

Symmetrical transition of an atomic arrangement for 2D Bi films on Rh(111)

The atomic arrangement of submonolayer Bi films on Rh(111) surface was examined using low-energy electron diffraction (LEED) and scanning tunneling microscopy (STM). With low coverage, the LEED patterns showed incommensurate (IC) spots. The unit cell of IC was close to c(2 × 4) and had twofold symmetry. As the coverage increased, the unit cell shrank continuously along the [$\overline{1}10$] direction, and the commensurate c(2 × 4) was formed at a coverage of 0.5 ML. At the coverage above 0.5 ML, two different structures of c(2 × 4) and (4 × 4) were observed by STM. When the surface is fully saturated by monolayer Bi atoms, Bi atoms formed the uniform (4 × 4) structure with sixfold symmetry. This is due to a strong Bi–Rh attractive interaction resulting in the two-dimensional localization of Bi adsorbates on the surface. As a result, a symmetrical transition of Bi films from twofold to sixfold symmetry occurred on Rh(111).     

Ferromagnetic resonance study of interface anisotropies in exchange-biased Fe(0 0 1)/KNiF3 bilayers

Magnetic anisotropies at epitaxial Fe/KNiF₃ interfaces were probed by ferromagnetic resonance. Fe(0 0 1) films coupled to single crystal KNiF₃ exhibit four-fold in-plane anisotropy and a unidirectional bias upon field-cooling. In Fe(0 0 1) with polycrystalline KNiF₃, the bias direction deviates from the field-cooling direction. Lattice mismatch strain due to polycrystalline KNiF₃ also induces uniaxial anisotropy in Fe.