Tyrosine Kinase Ligand-Receptor Pair Prediction by Using Support Vector Machine

Receptor tyrosine kinases are essential proteins involved in cellular differentiation and proliferation in vivo and are heavily involved in allergic diseases, diabetes, and onset/proliferation of cancerous cells. Identifying the interacting partner of this protein, a growth factor ligand, will provide a deeper understanding of cellular proliferation/differentiation and other cell processes. In this study, we developed a method for predicting tyrosine kinase ligand-receptor pairs from their amino acid sequences. We collected tyrosine kinase ligand-receptor pairs from the Database of Interacting Proteins (DIP) and UniProtKB, filtered them by removing sequence redundancy, and used them as a dataset for machine learning and assessment of predictive performance. Our prediction method is based on support vector machines (SVMs), and we evaluated several input features suitable for tyrosine kinase for machine learning and compared and analyzed the results. Using sequence pattern information and domain information extracted from sequences as input features, we obtained 0.996 of the area under the receiver operating characteristic curve. This accuracy is higher than that obtained from general protein-protein interaction pair predictions

Dioxygen Reactivity of Copper(I) Complexes with Tetradentate Tripodal Ligands Having Aliphatic Nitrogen Donors: Synthesis, Structures, and Properties of Peroxo and Superoxo Complexes

Oxygenation of copper(I) with tetradentate tripodal ligands (L) comprised of a tris(aminoethyl)amine (tren) skeleton having sterically bulky substituent(s) on the terminal nitrogens has been investigated, where L = tris(N-benzylaminoethyl)amine (LH,Bn), tris(N-benzyl-N-methylaminoethyl)amine (LMe,Bn), or tris(N,N-dimethylaminoethyl)amine (LMe,Me). All the copper(I) complexes reacted with dioxygen at low temperatures to produce superoxocopper(II) and/or trans-(μ-1,2-peroxo)-dicopper(II) complexes depending on the steric bulkiness of the terminal nitrogens and the reaction conditions. The reaction of a copper(I) complex [Cu(LH,Bn)]+ at −90 °C in acetone resulted in the formation of a superoxo complex [Cu(LH,Bn)(O2)]+ as a less stable species and a peroxo complex [{Cu(LH,Bn)}2(O2)]2+ as a stable species. The structures of [Cu(LH,Bn)]ClO4 and [{Cu(LH,Bn)}2(O2)](BPh4)2·8(CH3)2CO were determined by X-ray crystallography. [{Cu(LH,Bn)}2(O2)]2+ has a trans-(μ-1,2-peroxo)-dicopper(II) core with a trigonal bipyramidal structure. The O–O bond distance is 1.450(5) Å with an intermetallic Cu···Cu separation of 4.476(2) Å. The resonance Raman spectrum of [{Cu(LH,Bn)}2(O2)]2+ measured at −90 °C in acetone-d6 showed a broad ν(O–O) band at 837–834 cm−1 (788 cm−1 for an 18O labeled sample) and two ν(Cu–O) bands at 556 and 539 cm−1, suggesting the presence of two peroxo species in solution. [Cu(LMe,Bn)]+ also produced both superoxo and trans-μ-1,2-peroxo species, [Cu(LMe,Bn)(O2)]+ and [{Cu(LMe,Bn)}2(O2)]2+. At a lower concentration of [Cu(LMe,Bn)]+ (∼0.24 mM) and higher dioxygen concentration (P(O2) = ∼1 atm), the superoxo species is predominantly formed, whereas at a higher concentration of [Cu(LMe,Bn)]+ (∼1 mM) and lower dioxygen concentration (P(O2) = ∼0.02 atm) the formation of the peroxo species is observed. The resonance Raman spectrum of [Cu(LMe,Bn)(O2)]+ (∼1 mM) in acetone-d6 at ∼−95 °C exhibited a ν(O–O) band at 1120 cm−1 (1059 cm−1 for an 18O labeled sample) and that of [{Cu(LMe,Bn)}2(O2)]2+ (∼3 mM) in acetone-d6 at ∼−90 °C showed two ν(O–O) bands at 812 and 797 cm−1 (767 and 753 cm−1 for an 18O labeled sample), respectively. A similar observation was also made for [{Cu(LMe,Me)}2(O2)]2+. Relationships between the energies of the LMCT and d–d transitions and those of the ν(O–O) and ν(Cu–O) stretching vibrations and the steric constraints in the Cu(II)–(O22−)–Cu(II) core are discussed

Binary Nanoparticles Coassembly in Bioinspired Block Copolymer Films: A Stepwise Synthesis Approach Using Multifunctional Catechol Groups and Magneto-Optical Properties

The development of hybrid films containing binary nanoparticles is one of the current key objectives in nanotechnology. Different nanoparticles dispersed in a polymer matrix exhibit diverse functions, and their properties are influenced by the interplay between the nanoparticles. The poly­(vinyl catechol)-<i>block</i>-polystyrene (PVCa-<i>b</i>-PSt) block copolymer containing a catechol group, which is inspired by the adhesive protein found in the mussel foot, is an attractive platform for the coassembly of binary nanoparticles because the catechol group has various desirable properties, including the ability to coordinate metal oxides and reduce metal ions. In the fabrication of hybrid materials based on PVCa-<i>b</i>-PSt thin films, it is challenging to control the microdomain morphologies and the nanoparticle assembly process. In this work, we investigate the impact of solvent vapor annealing on microphase-separated nanostructures in lamellae-forming PVCa-<i>b</i>-PSt. We show that a fast solvent vapor annealing in a tetrahydrofuran atmosphere for 10 min induces the formation of perpendicularly oriented lamellar structures within PVCa-<i>b</i>-PSt thin films. We also propose a stepwise approach to create binary nanoparticles coassemblies in PVCa-<i>b</i>-PSt thin films. In the first step of this process, we exploit the metal–coordination properties of PVCa-<i>b</i>-PSt catechol groups to drive the directed self-assembly of magnetite (Fe₃O₄) nanoparticles for the preparation of magnetic hybrid thin films. The Fe₃O₄ nanoparticles are dispersed and localized mainly within PVCa microdomains of the lamellar PVCa-<i>b</i>-PSt thin films. In the second step, the catechol group reduces the Ag⁺ ion in the magnetic hybrid thin films, which leads to the formation of hybrid thin films containing Ag nanoparticles. Plasmonic Ag nanoparticles and magnetic Fe₃O₄ nanoparticles coassemble in the PVCa microdomains. The resulting plasmonic/magnetic hybrid thin films exhibit an enhanced magneto-optical Kerr effect because of the localized surface plasmon resonance of the Ag nanoparticles near Fe₃O₄ nanoparticles within the PVCa microdomains. Such magneto-optical (MO) properties make the hybrid thin films interesting for imaging of magnetic fields and MO devices. Our results indicate that PVCa-<i>b</i>-PSt is a promising platform for developing well-ordered hybrid thin films containing different nanoparticles