Structural aspects for the recognition of ATP by ribonucleopeptide receptors

A modular structure of ribonucleopeptide (RNP) affords a framework to construct macromolecular receptors and fluorescent sensors. We have isolated ATP-binding RNP with the minimum of nucleotides for ATP binding, in which the RNA consensus sequence is different from those reported for RNA aptamers against the ATP analogues. The three-dimensional structure of the substrate-binding complex of RNP was studied to understand the ATP-binding mechanism of RNP. A combination of NMR measurements, enzymatic and chemical mapping, and nucleotide mutation studies of the RNP-adenosine complex show that RNP interacts with the adenine ring of adenosine by forming a U:A:U triple with two invariant U nucleotides. The observed recognition mode for the adenine ring is different from those of RNA aptamers for ATP derivatives reported previously. The RNP-adenosine complex is folded into a particular structure by formation of the U:A:U triple and a Hoogsteen type A:U base pair. This recognition mechanism was successfully utilized to convert the substrate-binding specificity of RNP from ATP- to GTP-binding with a C(+):G:C triple recognition mode.     

Measurement-based quantum computer in the gapped ground state of a two-body Hamiltonian

We propose a scheme for a ground-code measurement-based quantum computer, which enjoys two major advantages. First, every logical qubit is encoded in the gapped degenerate ground subspace of a spin-1 chain with nearest-neighbor two-body interactions, so that it equips built-in robustness against noise. Second, computation is processed by single-spin measurements along multiple chains dynamically coupled on demand, so as to keep teleporting only logical information into a gap-protected ground state of the residual chains after the interactions with spins to be measured are turned off. We describe implementations using trapped atoms or polar molecules in an optical lattice, where the gap is expected to be as large as 0.2 or 4.8 kHz, respectively.     

Polycyclic N-hetero compounds. XX. Synthesis of 11,13,15-triazasteroid with an alkyl group in the d-ring and an investigation of its antidepressive activity

11,13,15-Triazasteroidal skeleton with an alkyl group in the D-ring was synthesized and it was screened for antidepressive activity. Compounds VIIId and XIIa exhibited antireserpine action.     

Photoreaction generating active oxygens of In(3+)-tetrakis(4-methylpyridyl)-porphine in the presence of albumins

The complex formation of In(3+)-tetrakis(4-N-methylpyridyl)-porphine (In-TMPyP) with albumin was studied by resonance Raman spectroscopy. Albumin coordinated to In(3+) through the -S(-) group(s). The photoreaction was investigated using the visible spectral change and In-TMPyP-thiourea complex was used as a model. It was demonstrated that the complex in a weak basic solution (pH 8.5) is excited by light and the excited complex converts oxygen to superoxide anion, which finally cleavages the porphine ring of In-TMPyP.     

An Engineered Aryl Acid Adenylation Domain with an Enlarged Substrate Binding Pocket

Adenylation (A) domains act as the gatekeepers of non‐ribosomal peptide synthetases (NRPSs), ensuring the activation and thioesterification of the correct amino acid/aryl acid building blocks. Aryl acid building blocks are most commonly observed in iron‐chelating siderophores, but are not limited to them. Very little is known about the reprogramming of aryl acid A‐domains. We show that a single asparagine‐to‐glycine mutation in an aryl acid A‐domain leads to an enzyme that tolerates a wide range of non‐native aryl acids. The engineered catalyst is capable of activating non‐native aryl acids functionalized with nitro, cyano, bromo, and iodo groups, even though no enzymatic activity of wild‐type enzyme was observed toward these substrates. Co‐crystal structures with non‐hydrolysable aryl‐AMP analogues revealed the origins of this expansion of substrate promiscuity, highlighting an enlargement of the substrate binding pocket of the enzyme. Our findings may be exploited to produce diversified aryl acid containing natural products and serve as a template for further directed evolution in combinatorial biosynthesis.     

Reversed-phase HPLC determination of chlorophyll a' and naphthoquinones in photosystem I of red algae: existence of two menaquinone-4 molecules in photosystem I of Cyanidium caldarium.

Chlorophyll (Chl) a', the C13(2)-epimer of Chl a, is one of the two Chl molecules constituting the primary electron donor (P700) of photosystem (PS) I of a thermophilic cyanobacterium Synechococcus elongatus. To examine whether PS I of other oxygenic photosynthetic organisms in general contain one Chl a' molecule in P700, the pigment composition of thylakoid membranes and PS I preparations isolated from red algae Porphyridium purpureum and Cyanidium caldarium was examined by reversed-phase HPLC with particular attention to Chl a' and phylloquinone (PhQ), the secondary electron acceptor of PS I. The two red algae contained one Chl a' molecule at the core part of PS I. In PS I of C. caldarium, two menaquinone-4 (MQ-4) molecules were detected in place of PhQ used by higher plants and cyanobacteria. The 1:2:1 stoichiometry among Chl a', PhQ (MQ-4) and P700 in PS I of the red algae indicates that one Chl a' molecule universally exists in PS I of oxygenic photosynthetic organisms, and two MQ-4 molecules are associated with PS I of C. caldarium.     

Auger-free luminescence due to interatomic p–d transition and self-trapped exciton luminescence in Rb2ZnCl4 crystals

It is reported that Auger-free (AF) luminescence appears with two bands at 4.5 and 6.3 eV in Rb₂ZnCl₄. This luminescence originates from a radiative transition of the Cl 3p valence electrons into the Zn 3d outermost-core holes. The present work is the first observation of AF luminescence due to interatomic p–d transitions in halide crystals. The appearance of two AF luminescence bands suggests the existence of two types of AF transitions following core hole creation. A largely Stokes-shifted luminescence band is also found to appear at 1.9 eV. This band has an excitation threshold at the fundamental absorption edge, and is ascribed to the radiative decay of a self-trapped exciton.     

Quantum computational capability of a 2D valence bond solid phase

Quantum phases of naturally-occurring systems exhibit distinctive collective phenomena as manifestation of their many-body correlations, in contrast to our persistent technological challenge to engineer at will such strong correlations artificially. Here we show theoretically that quantum correlations exhibited in the 2D valence bond solid phase of a quantum antiferromagnet, modeled by Affleck, Kennedy, Lieb, and Tasaki (AKLT) as a precursor of spin liquids and topological orders, are sufficiently complex yet structured enough to simulate universal quantum computation when every single spin can be measured individually. This unveils that an intrinsic complexity of naturally-occurring 2D quantum systems—which has been a long-standing challenge for traditional computers—could be tamed as a computationally valuable resource, even if we are limited not to create newly entanglement during computation. Our constructive protocol leverages a novel way to herald the correlations suitable for deterministic quantum computation through a random sampling, and may be extensible to other ground states of various 2D valence bond phases beyond the AKLT state.     

Metallic film formation using direct micropatterning with photoreactive metal complexes

Palladium, cobalt, and nickel in complex with photoacid-generating ligands, 4-(2-nitrobenzyloxycarbonyl)catechol and 4-(6-nitroveratryloxycarbonyl)catechol, were prepared in solution. Films formed from the metal complex solutions perform as positive-tone, directly photopatternable palladium, cobalt, nickel oxide, or composite film precursors. After exposure, acid-bearing selectively soluble complexes could be removed to give patterned films upon developing in aqueous base, which were transformable to the corresponding pattern-preserving metal/metal oxide film. The photodynamics of photoinduced solubility and direct micropatterning of palladium, cobalt, nickel, and palladium/nickel oxide composite films were investigated. Employing palladium as the initiator for autocatalytic chemical plating, selective direct copper plating on palladium film on polyethylene naphthalate and palladium/nickel oxide composite film on glass was accomplished.