Amino acid residues in GRK1/GRK7 responsible for interaction with S-modulin/recoverin

GRK1 is a visual pigment kinase in rods and is essential for inactivation of light-activated rhodopsin. The GRK1 activity is inhibited by binding of the Ca(2+)-bound form of S-modulin/recoverin. We previously identified the S-modulin/recoverin site to interact with GRK1. In the present study, we identified its counterpart in GRK1. We synthesized 29 of GRK1 or GRK7 partial peptides that cover the entire sequence of GRK1/GRK7, and examined whether these peptides inhibit S-modulin/recoverin activity most probably by preoccupying the binding site for GRK1. The inhibition was the greatest with the N-terminal peptide (p1, aa 3-23 in GRK7). On mutation of each of eight amino acid residues highly conserved in the p1 region of more than 10 orthologs, the inhibition was significantly reduced in the mutation of Leu(6), Asn(12) and Tyr(15). We further examined the binding of the peptides, including mutated ones, to S-modulin/recoverin with a resonance mirror biosensor. The binding correlated well with the degree of the inhibition by a peptide. The inhibition, therefore, seemed to be due to a direct binding of the kinase peptide to the binding site of active S-modulin/recoverin. A GRK1 region close to its C-terminus also seemed to be the binding site for S-modulin/recoverin.     

Ab initio protein structure prediction with force field parameters derived from water-phase quantum chemical calculation

Molecular dynamics (MD) simulations are extensively used in the study of the structures and functions of proteins. Ab initio protein structure prediction is one of the most important subjects in computational biology, and many trials have been performed using MD simulation so far. Since the results of MD simulations largely depend on the force field, reliable force field parameters are indispensable for the success of MD simulation. In this work, we have modified atom charges in a standard force field on the basis of water-phase quantum chemical calculations. The modified force field turned out appropriate for ab initio protein structure prediction by the MD simulation with the generalized Born method. Detailed analysis was performed in terms of the conformational stability of amino acid residues, the stability of secondary structure of proteins, and the accuracy for prediction of protein tertiary structure, comparing the modified force field with a standard one. The energy balance between alpha-helix and beta-sheet structures was significantly improved by the modification of charge parameters.     

Nuclear spin conversion of methane in solid parahydrogen

The nuclear spin conversion of CH(4) and CD(4) isolated in solid parahydrogen was investigated by high resolution Fourier transform infrared spectroscopy. From the analysis of the temporal changes of rovibrational absorption spectra, the nuclear spin conversion rates associated with the rotational relaxation from the J=1 state to the J=0 state for both species were determined at temperatures between 1 and 6 K. The conversion rate of CD(4) was found to be 2-100 times faster than that of CH(4) in this temperature range. The faster conversion in CD(4) is attributed to the quadrupole interaction of D atoms in CD(4), while the conversion in CH(4) takes place mainly through the nuclear spin-nuclear spin interaction. The conversion rates depend on crystal temperature strongly above 3.5 K for CH(4) and above 2 K for CD(4), while the rates were almost constant below these temperatures. The temperature dependence indicates that the one-phonon process is dominant at low temperatures, while two-phonon processes become important at higher temperatures as a cause of the nuclear spin conversion.     

A new interpretation of the reaction pathway of deprotonative metalation with TMP-Zn-ate/TMEDA Complex [TMEDA.Na(micro-tBu)(micro-TMP)Zn(tBu)

Density functional theory (DFT) calculations of possible reaction pathways and mechanisms for the deprotonation of benzene with Mulvey's reagent, TMEDA.Na(micro-R)(micro-TMP)Zn(R) (TMEDA=N,N,N',N'-tetramethylethylenediamine, R = alkyl, TMP = 2,2,6,6-tetramethylpiperidide) indicate that the deprotonation of benzene with Mulvey's reagent proceeds through a stepwise mechanism, not a one-step mechanism. In the first step, deprotonation involving the TMP ligand on the reagent is kinetically more favorable than that involving the alkyl ligand.     

Dynamic interaction between oppositely charged vesicles: aggregation, lipid mixing, and disaggregation

We investigated dynamic interactions between oppositely charged small unilamellar vesicles using positively charged vesicles containing 1,2-dioleoyl-3-trimethylammonium-propane or 3beta-[N-(N('),N(')-dimethylaminoethane)-carbamoyl] cholesterol and negatively charged vesicles containing L-alpha-phosphatidyl-DL-glycerol. Aggregation, lipid bilayer mixing, contents mixing and contents leakage were systematically examined using optical density measurements, fluorescence resonance energy transfer assays, fluorescence quenching assays, light-scattering analyses, and freeze-fracture transmission electron microscopy. The oppositely charged vesicles aggregated immediately. Lipid mixing was observed, but there was no mixing of the contents. The vesicle aggregates disaggregated spontaneously after several minutes. The surface potential of the disaggregated vesicles was neutralized. From these results, we infer that the lipids in the external monolayers were exchanged between the oppositely charged vesicles while the internal monolayers remained intact. The two types of cationic lipids used exhibited different speeds of disaggregation.     

Tuning the chiral cavity of macrocyclic receptor for chiral recognition and discrimination

The size and shape of the chiral cavity of a macrocyclic receptor were tuned by the alteration of the binaphthyl moiety to improve the chiral recognition/discrimination ability. For example, host 3 with the 3,5-bis(trifluoromethyl)phenyl group at the 3,3'-positions showed improved enantioselectivity for small molecules such as 2-chloropropionic acid and methyl lactate as evaluated by the binding constants. This host 3 also had an excellent ability as an NMR chiral solvating agent.     

Dynamic Lone Pair Expression as Chemical Bonding Origin of Giant Phonon Anharmonicity in Thermoelectric InTe

Loosely bonded (“rattling”) atoms with s² lone pair electrons are usually associated with strong anharmonicity and unexpectedly low thermal conductivity, yet their detailed correlation remains largely unknown. Here we resolve this correlation in thermoelectric InTe by combining chemical bonding analysis, inelastic X-ray and neutron scattering, and first principles phonon calculations. We successfully probe soft low-lying transverse phonons dominated by large In¹⁺ z-axis motions, and their giant anharmonicity. We show that the highly anharmonic phonons arise from the dynamic lone pair expression with unstable occupied antibonding states induced by the covalency between delocalized In¹⁺ 5s² lone pair electrons and Te 5p states. This work pinpoints the microscopic origin of strong anharmonicity driven by rattling atoms with stereochemical lone pair activity, important for designing efficient materials for thermoelectric energy conversion.     

Tin(II)-Based Metal–Organic Frameworks Enabling Efficient,Selective Reduction of CO2 to Formate under Visible Light

Certain metal complexes are known as high-performance CO₂ reduction photocatalysts driven by visible light. However, most of them rely on rare, precious metals as principal components, and integrating the functions of light absorption and catalysis into a single molecular unit based on abundant metals remains a challenge. Metal-organic frameworks (MOFs), which can be regarded as intermediate compounds between molecules and inorganic solids, are potential platforms for the construction of a simple photocatalytic system composed only of Earth-abundant nontoxic elements. In this work, we report that a tin-based MOF enables the conversion of CO₂ into formic acid with a record high apparent quantum yield (9.8 % at 400 nm) and >99 % selectivity without the need for any additional photosensitizer or catalyst. This work highlights a new MOF with strong potential for photocatalytic CO₂ reduction driven by solar energy.     

A Dicyanomethyl Radical Conjugated with a Pyridylamino Group: Combining Radical-based Dynamic Covalent Chemistry and Coordination Chemistry

In this work, we aimed to develop a dicyanomethyl radical that undergoes both reversible C−C bond formation/dissociation and metal-ligand coordination reactions to combine dynamic covalent chemistry (DCC) based on organic radicals with coordination chemistry. We have previously reported a dicyanomethyl radical conjugated with a triphenylamine ( 1 ⋅) that exhibits a monomer/dimer equilibrium between the σ-bonded dimer ( 1₂ ). We designed and synthesized a novel dicyanomethyl radical with a pyridyl group as a coordination point ( 2 ⋅) by replacing the phenyl group of 1 ⋅ with a 3-pyridyl group. We showed that 2 ⋅ is also in an equilibrium with the σ-bonded dimer ( 2₂ ) in solution and has suitable thermodynamic parameters for application in DCC. 2₂ coordinates to PdCl₂ in a 2 : 2 ratio to selectively form a metallamacrocycle ( 2₂ )₂(PdCl₂)₂, and its structure was clarified by single crystal X-ray analysis. Variable-temperature NMR, ESR, and electronic absorption measurements revealed that ( 2₂ )₂(PdCl₂)₂ also undergoes the reversible C−C bond formation/dissociation reaction. Ligand-exchange experiment showed that 2₂ was liberated from ( 2₂ )₂(PdCl₂)₂ by the addition of another ligand with a higher affinity for Pd^II. This work demonstrated that DCC based on dicyanomethyl radicals works orthogonally to metal-ligand coordination reactions.     

Nuclease tolerant FRET probe based on DNA-quantum dot conjugation.

We have developed a fluorescence resonance energy transfer (FRET) probe based on the conjugation of a quantum dot (QD) with dye (YOYO-3) intercalated DNA. The FRET-inducing electrostatic coupling of DNA and the QD made structural changes to the QD-DNA conjugates, which significantly prevented an enzymatic reaction between the DNA and a conventional restriction endonuclease (EcoRI).