Modes of conformational changes of proteins adsorbed on a planar hydrophobic polymer surface reflecting their adsorption behaviors

Infrared spectra of hen egg white lysozyme and bovine serum albumin (BSA) adsorbed on a solid poly tris(trimethylsiloxy)silylstyrene (pTSS) surface in D2O solution were measured using attenuated total reflection (ATR) Fourier transform infrared spectroscopy. From the area and shape of the amide I' band of each spectrum, the adsorption amount and the secondary structure were determined simultaneously, as a function of adsorption time. We could show that the average conformation for all the adsorbed lysozyme molecules was solely determined by the adsorption time, and independent of the bulk concentration, while the adsorption amount increased with the bulk concentration as well as the adsorption time. These results suggest that lysozyme molecules form discrete assemblies on the surface, and that the surface assemblies grow over several hours to have a definite architecture independent of the adsorption amount. As for BSA, the extent of the conformational change was solely determined by the adsorption amount, regardless of the bulk concentration and the adsorption time. These differences in the adsorption properties of lysozyme and BSA may reflect differences in their conformational stabilities.     

Magnetic/Conducting Hybrid Compound Composed of 1-D Chain [Mn2Cl5(EtOH)]∞ and BEDT-TTF Stacking Layer

An assembled compound (BEDT-TTF)₂[Mn₂Cl₅(EtOH)] (1) consisting of two structural lattices of Mn(II)-Cl one-dimensional (1-D) chains and bis(ethylenedithio)tetrathiafulvalene (BEDT-TTF) stacking layers was synthesized by electrochemical crystallization. Compound 1 crystallized in triclinic space group P-1 (#2) with a=13.1628(5) Å, b=20.3985(9) Å, c=7.4966(3) Å, α=98.3498(8)°, β=104.980(1)°, γ=74.602(2)°, V=1868.3(1) ų, and Z=2. The 1-D chains and the stacking layers are aligned along the c-axis of the unit cell. The 1-D chain is described as [Mn₂Cl₅(EtOH)]_∞⁻ in which two Mn(II) ions and four Cl⁻ ions form a ladder-like chain with Kagomé (cuboidal) sublattices, and the remaining Cl⁻ ion and an ethanol molecule cap the edge-positioned Mn(II) ions of the chains. The BEDT-TTF molecules are packed between the Mn-Cl chains (ac-plane), the intermolecular S·S contacts of which are approximately found in the range 3.440(2)-3.599(2) Å. The packing feature of BEDT-TTF molecules is very similar to that of (BEDT-TTF)₂ClO₄(TCE)_0.5 (TCE=1,1,2-trichloroethane) (J. Am. Chem. Soc., 105, 297 (1983)). Regarding the electronic state of each BEDT-TTF molecule, Raman spectroscopic analysis and ESR study revealed the presence of half-valence BEDT-TTF molecules (charge delocalization) in 1. Magnetic measurements clearly demonstrated that the paramagnetic spins on the 1-D chain [Mn₂Cl₅(EtOH)]_∞⁻ arrange antiferromagnetically in the low-temperature region. Additionally, 1 exhibits metallic conductivity in the temperature range 2.0-300 K (σ=21 S cm⁻¹ at 300 K and 1719 S cm⁻¹ at 2.0 K), due to the contribution of the stacked BEDT-TTFs. Consequently, these peculiarities that correspond to antiferromagnetic/metallic conductivity demonstrate the “bi-functionality” of 1.     

Asymmetric Hydroformylation of Vinylfurans Catalyzed by {(11bS)‐4‐{[(1R)‐2′‐Phosphino[1,1′‐binaphthalen]‐2‐yl]oxy}dinaphtho[2,1‐d:1′,2′‐f]‐ [1,3,2]dioxaphosphepin}rhodium(I) [RhI{(R,S)‐binaphos}] Derivatives

The asymmetric hydroformylation of 2‐ and 3‐vinylfurans ( 2a and 2b , resp.) was investigated by using [Rh{(R,S)‐binaphos}] complexes as catalysts ((R,S)‐binaphos = (11bS)‐4‐{[1R)‐2′‐phosphino[1,1′‐binaphthalen]‐2‐yl]oxy}dinaphtho[2,1‐d:1′,2′‐f][1,3,2]dioxaphosphepin; 1 ). Hydroformylation of 2 gave isoaldehydes 3 in high regio‐ and enantioselectivities (Scheme 2 and Table). Reduction of the aldehydes 3 with NaBH₄ successfully afforded the corresponding alcohols 5 without loss of enantiomeric purity (Scheme 3).     

Cloning, sequencing, and functional analysis of the biosynthetic gene cluster of macrolactam antibiotic vicenistatin in Streptomyces halstedii

Vicenistatin, an antitumor antibiotic isolated from Streptomyces halstedii, is a unique 20-membered macrocyclic lactam with a novel aminosugar vicenisamine. The vicenistatin biosynthetic gene cluster (vin) spanning approximately 64 kbp was cloned and sequenced. The cluster contains putative genes for the aglycon biosynthesis including four modular polyketide synthases (PKSs), glutamate mutase, acyl CoA-ligase, and AMP-ligase. Also found in the cluster are genes of NDP-hexose 4,6-dehydratase and aminotransferase for vicenisamine biosynthesis. For the functional confirmation of the cluster, a putative glycosyltransferase gene product, VinC, was heterologously expressed, and the vicenisamine transfer reaction to the aglycon was chemically proved. A unique feature of the vicenistatin PKS is that the loading module contains only an acyl carrier protein domain, in contrast to other known PKS-loading modules containing certain activation domains. Activation of the starter acyl group by separate polypeptides is postulated as well.     

Energy transfer reaction of cationic porphyrin complexes on the clay surface: effect of sample preparation method

Photochemical energy transfer of non-aggregated cationic porphyrins on an anionic-type clay (Smecton SA) surface was investigated. The efficiency of energy transfer and excited-state quenching in the absence of energy transfer were evaluated at various loading levels of porphyrin on the clay surface and were found to be significantly affected by the loading level. As the latter increased, both energy transfer efficiency and excited-state quenching increased. Judging from the dependency of energy-transfer efficiency on the porphyrin loading level, a partially clustered structure, but without aggregation, of porphyrins on the clay surface is proposed.     

Basic peptides as functional components of non-viral gene transfer vehicles

Improving the performance of non-viral gene-delivery vehicles that consist of synthetic compounds and nucleic acids is a key to successful gene therapy. Supplementing synthetic vehicles with various biological functions by using natural or artificial peptides is a promising approach with which to achieve this goal. One of the obstacles hindering this effort is that some of the potentially useful peptides, especially those with many basic amino acid residues, interfere with the formation of the complex owing to strong electrostatic interactions with the nucleic acid. In this review, we describe our recent work in examining the potential of these peptides in gene delivery, using a recombinant lambda phage particle as the model for the gene-delivery complex. Lambda phage encapsulates large duplex DNA in a rigid polyplex-like shell with a diameter of 55 nm, and can display various peptides on this capsid, independently of particle formation. By examining the expression of marker genes encapsulated in the phage capsid, we have demonstrated that the protein transduction domain of HIV Tat protein and the nuclear localization signal derived from SV40 T antigen can remarkably facilitate the delivery of these marker genes across the two major barriers, the cell membrane and the nuclear membrane, respectively. Our results indicate that these basic peptides can constitute effective components of synthetic gene-transfer complexes, as long as sufficient copies are displayed on the outer surface of the complex.     

Design of a tripartite network for the prediction of drug targets

Drug-target networks have aided in many target prediction studies aiming at drug repurposing or the analysis of side effects. Conventional drug-target networks are bipartite. They contain two different types of nodes representing drugs and targets, respectively, and edges indicating pairwise drug-target interactions. In this work, we introduce a tripartite network consisting of drugs, other bioactive compounds, and targets from different sources. On the basis of analog relationships captured in the network and so-called neighbor targets of drugs, new drug targets can be inferred. The tripartite network was found to have a stable structure and simulated network growth was accompanied by a steady increase in assortativity, reflecting increasing correlation between degrees of connected nodes leading to even network connectivity. Local drug environments in the tripartite network typically contained neighbor targets and revealed interesting drug-compound-target relationships for further analysis. Candidate targets were prioritized. The tripartite network design extends standard drug-target networks and provides additional opportunities for drug target prediction.     

Single-Round DNA Aptamer Selection by Combined Use of Capillary Electrophoresis and Next Generation Sequencing: An Aptaomics Approach for Identifying Unique Functional Protein-Binding DNA Aptamers

In DNA aptamer selection, existing methods do not discriminate aptamer sequences based on their binding affinity and function and the reproducibility of the selection is often poor, even for the selection of well-known aptamers like those that bind the commonly used model protein thrombin. In the present study, a novel single-round selection method (SR-CE selection) was developed by combining capillary electrophoresis (CE) with next generation sequencing. Using SR-CE selection, a successful semi-quantitative and semi-comprehensive aptamer selection for thrombin was demonstrated with high reproducibility for the first time. Selection rules based on dissociation equilibria and kinetics were devised to obtain families of analogous sequences. Selected sequences of the same family were shown to bind thrombin with high affinity. Furthermore, data acquired from SR-CE selection was mined by creating sub-libraries that were categorized by the functionality of the aptamers (e. g., pre-organized aptamers versus structure-induced aptamers). Using this approach, a novel fluorescent molecular recognition sensor for thrombin with nanomolar detection limits was discovered. Thus, in this proof-of-concept report, we have demonstrated the potential of a “DNA Aptaomics” approach to systematically design functional aptamers as well as to obtain high affinity aptamers.