Kinetics of polymer translocation through a pore

We theoretically study kinetics of a polymer threading through a pore embedded in a flat membrane. We numerically solve three coupled kinetic equations for the number n(1) of polymer segments in one side of the membrane and expansion factors of the polymer chain in each side of the membrane. We find the time evolution n(1) proportional to t(1/(1+nu)) at late stages and the translocation time tau(t) is scaled as tau(t) proportional to 1+nu) for large number n of the polymer segments, where nu is the effective size exponent of the radius of gyration of the polymer. When the polymer is translocated into a region with a good solvent condition (nu=3/5), we obtain n(1) proportional to t(5/8) and tau(t) proportional to n(8/5).     

Chemical structure of iodine-doped polyisoprene

A nonconjugated conducting polymer (1,4-rans-polyisoprene) at different iodine doping levels has been studied with the 27.7-keV Mössbauer resonance of¹²⁹I. At the light doping level, almost all iodines are covalently bonding to the carbon atoms, breaking the double bonds of the main chain. At the medium doping level, other iodine species are found, which are idendified as anion species, l^?, l ₃ ^? and l ₃ ^? .At the heavy doping level, polyiodide anions, l ₃ ^? and l ₅ ^? , increase as compared to the covalently bonding iodine atoms and addtionally molecular iodine l₂ exists.     

Pattern enrichment analysis for phage selection of stapled peptide ligands

Phage display is the most widely used technique to discover de novo peptides that bind to target proteins. However, it is associated with some challenges such as compositional bias. In this study, to overcome these difficulties, we devised a ‘pattern enrichment analysis.’ In this method, two samples (one obtained by affinity selection, the other simply amplified without selection) are prepared, and the two sequence datasets read on next-generation sequencer are compared to find the three-residue pattern most enriched in the selected sample. This allows us to compare two sequence datasets with high coverage and facilitates the identification of peptide sequences and the key residues for binding. We also demonstrated that this approach in the combination with structured peptide libraries allowed spatial mapping of the enriched sequence patterns. Here, we prepared a phage library displaying chemically stapled helical peptides with the X₁C₂X₃X₄X₅X₆X₇X₈C₉X₁₀ sequence, where X is any amino acid. To validate our method, we performed screening against the HDM2 protein. The results showed that the hydrophobic residues (Phe, Tyr, Trp and Leu) that are key to interactions with HDM2 were clearly identified by the pattern enrichment analysis. We also performed selection targeting the SARS-CoV-2 spike RBD in the same manner. The results showed that similar patterns were enriched among the hit peptides that inhibited the protein–protein interaction.

To effectively identify helical peptide binders from a phage library, we developed “pattern enrichment analysis,” which finds the enriched three-residue patterns by comparison with a control sample.     

Molecular Design of Polyoxometalate-Based Compounds for Environmentally-Friendly Functional Group Transformations: From Molecular Catalysts to Heterogeneous Catalysts

This review article summarizes our recent researches for molecular design of polyoxometalates (POMs) and their related compounds for environmentally-friendly functional group transformations. The divacant POM [γ-SiW₁₀O₃₄(H₂O)₂]⁴⁻ exhibits high catalytic performance for mono-oxygenation-type reactions including epoxidation of olefins and allylic alcohols, sulfoxidation, and hydroxylation of organosilanes with H₂O₂. We have successfully synthesized several POM-based molecular catalysts (metal-substituted POMs) with controlled active sites by the introduction of metal species into the divacant POM as a “structural motif”. These molecular catalysts can efficiently activate H₂O₂ (vanadium-substituted POM for epoxidation) and alkynes (copper-substituted POM for click reaction and oxidative homocoupling of alkynes). The aluminum-substituted POM exhibits Lewis acidic catalysis for diastereoselective cyclization of (+)-citronellal to (−)-isopulegol. In addition, we have developed POM-based “molecular heterogeneous catalysts” by the “solidification” and “immobilization” of catalytically active POMs.     

Chiral Ammonium Betaine‐Catalyzed Highly Stereoselective Aza‐Henry Reaction of α‐Aryl Nitromethanes with Aromatic N‐Boc Imines

A highly stereoselective aza‐Henry reaction of α‐aryl nitromethanes with aromatic N‐Boc imines was established by using C₁‐symmetric chiral ammonium betaine as a bifunctional organic base catalyst. Various substituted aryl groups for both imines and nitromethanes were tolerated in the reaction, and a series of precursors for the synthesis of unsymmetrical anti‐1,2‐diaryl ethylenediamines was provided.     

Selective permeation of CO2 through poly 2-(N,N-dimethyl)aminoethyl methacrylate membrane prepared by plasma-graft polymerization technique

A membrane having an amine moiety was prepared by plasma-grafting 2-(N,N-dimethyl)aminoethyl methacrylate (DAMA) onto a microporous polyethylene substrate. Permselectivity of the membrane for CO₂ over N₂ was achieved in both dry and water swollen conditions. When the CO₂ partial pressure in the feed gas was 0.047 atm, the selectivity of CO₂ over N₂ reached 130 for the highly swollen water containing membrane. This value was found to agree with that obtained with a mobile carrier membrane (supported liquid membrane) using DAMA as the carrier. The effects of several experimental conditions such as degree of grafting, feed partial pressure and temperature on the membrane performance were studied. It was suggested that the membrane acted as a fixed carrier membrane for CO₂ facilitated transport in under the dry condition and acted as a fixed reaction site membrane in the water swollen condition. The carrier transport mechanism is discussed for dry and aqueous membranes.     

Atomic electron-pair distances and subshell radii in position and momentum space

For the 53 neutral atoms from He to Xe in their ground states, the average distances < u> _{n l , n ′ l ′} in position space and < v> _{n l , n ′ l ′} in momentum space between an electron in a subshell nl and another electron in a subshell n ^′ l ^′ are studied, where n and l are the principal and azimuthal quantum numbers of an atomic subshell, respectively. Analysis of 1700 subshell pairs shows that the electron-pair distances < u> _{n l , n ′ l ′} in position space have an empirical but very accurate linear correlation with a one-electron quantity U _{n l , n ′ l ′}≡L _r +S _r ²/(3L _r ), where L _r and S _r are the larger and smaller of subshell radii < r> _{n l} and < r> _{n ′ l ′}, respectively. The correlation coefficients are never smaller than 0.999 for the 66 different combinations of two subshells appearing in the 53 atoms. The same is also true in momentum space, and the electron-pair momentum distances < > _{n l , n ′ l ′} have an accurate linear correlation with a one-electron momentum quantity V _{n l , n ′ l ′}≡L _p +S _p ²/(3L _p ), where L _p and S _p are the larger and smaller of average subshell momenta < p> _{n l} and < p> _{n ′ l ′}, respectively. Trends in the proportionality constants between < u> _{n l , n ′ l ′} and U _{n l , n ′ l ′} and between < > _{n l , n ′ l ′} and V _{n l , n ′ l ′} are discussed based on a hydrogenic model for the subshell radial functions. Received: 8 April 1998 / Accepted: 6 July 1998 / Published online: 18 September 1998     

TYROSINE-SENSITIZED PHOTODIMERIZATION OF THYMINE IN AQUEOUS SOLUTION

Abstract. Photodimerization of thymine in aqueous solution in the presence of tyrosine was studied with monochromatic UV irradiation. The total dimer formation was sensitized in the presence of tyrosine. The action spectrum of sensitized total dimer formation has a peak near 280 nm corresponding to the absorption maximum of tyrosine. Triplet quenchers reduced the sensitization substantially. It seems probable that tyrosine-sensitized photodimerization of thymine occurred via triplet-triplet energy transfer from tyrosine to thymine.     

Systematic study of protein detection mechanism of self-assembling 19F NMR/MRI nanoprobes toward rational design and improved sensitivity

(19)F NMR/MRI probe is expected to be a powerful tool for selective sensing of biologically active agents owing to its high sensitivity and no background signals in live bodies. We have recently reported a unique supramolecular strategy for specific protein detection using a protein ligand-tethered self-assembling (19)F probe. This method is based on a recognition-driven disassembly of the nanoprobes, which induced a clear turn-on signal of (19)F NMR/MRI. In the present study, we conducted a systematic investigation of the relationship between structure and properties of the probe to elucidate the mechanism of this turn-on (19)F NMR sensing in detail. Newly synthesized (19)F probes showed three distinct behaviors in response to the target protein: off/on, always-on, and always-off modes. We clearly demonstrated that these differences in protein response could be explained by differences in the stability of the probe aggregates and that "moderate stability" of the aggregates produced an ideal turn-on response in protein detection. We also successfully controlled the aggregate stability by changing the hydrophobicity/hydrophilicity balance of the probes. The detailed understanding of the detection mechanism allowed us to rationally design a turn-on (19)F NMR probe with improved sensitivity, giving a higher image intensity for the target protein in (19)F MRI.     

Total synthesis of (+)-tubelactomicin A. 2. Synthesis of the upper-half segment and completion of the total synthesis

[reaction: see text]. We have completed the total synthesis of natural (+)-tubelactomicin A (1), a 16-membered macrolide antibiotic. This Letter presents a highly efficient synthesis of the upper-half segment (C14-C24) and the completion of the total synthesis featuring a high-yielding Stille coupling for the connection of the upper-half and lower-half segments and Mukaiyama macrolactonization for the construction of the entire structure of 1.