Yoichi Iitaka

A preliminary investigation on the molecular structure of rice dwarf virus ribonucleic acid

X-Ray diffraction and infrared absorption measurements have been made of a ribonucleic acid obtained from rice dwarf virus which was isolated from the infected rice leaves. On a fibre diagram obtained at 75% relative humidity, 52 independent reflections were observed. All of them are indexed on a hexagonal lattice with a = 40·0 A and c = 30·5 A. It was found that the unit cell contains three molecules, each of which is displaced along the c-axis direction by c /3 from the neighbours. Intensities of the reflections were used to calculate the cylindrically symmetrical Patterson function. From this Patterson function it was concluded that the ribose-phosphate chains form two intertwined helices one of which is displaced along the helix axis by 13·0 A from the other. Each helix has its axis parallel to the c -axis, a pitch of 30·5 A, and ten nucleotide residues per turn. On the basis of the infrared dichroism observed for the 1225 cm −1 and 1084 cm −1 bands, the orientation of the PO 2 − group has been determined. The O…..O line makes an angle of about 70° and the bisector of 2 − group in the A and B forms of DNA.

Crystal structure of a bacterial protein proteinase inhibitor (Streptomyces subtilisin inhibitor) at 2·6 Å resolution

The crystal structure of a bacterial protein proteinase inhibitor (Streptomyces subtilisin inhibitor) was solved at 2·6 A resolution. Each subunit of the dimeric inhibitor has a five-stranded antiparallel β-sheet and two short α-helices. The subunit-subunit interface formed by a stack of two β-sheets provided by the two subunits resembles the dimer-dimer interface of concanavalin A. Conformation of the reactive site around the scissible bond Met73-Val74 seems very rigid. Between bovine pancreatic trypsin inhibitor (Kunitz) and the Streptomyces inhibitor, the reactive site conformations are almost identical with each other from the P2 to P2′ residues, while between the soybean trypsin inhibitor (Kunitz) and the Streptomyces inhibitor they are similar from the P2 to P1′ residues. There are overall similarities in conformation extending from the P3 to P2′ residues between the Streptomyces inhibitor and a hypothetical substrate presumed (Robertus et al., 1972b) to be bound to subtilisin BPN′ in a productive binding mode. Apart from the reactive site, there seems to be no structural relationship among the Streptomyces, bovine pancreatic and soybean inhibitors, suggesting their convergent evolution from separate ancestral proteins.

Squalene derivatives from Eurycoma longifolia

Abstract Three novel cytotoxic squalene-type triterpenes, eurylene, 14-deacetyl eurylene and longilene peroxide, together with teurilene were isolated from the

Triterpenes fromMaytenus ilicifolia

Two new friedelane-type triterpenes, D:A-friedoolean-24-al-3-en-3-ol-2-on-29-oic acid and D:A-friedoolean-1-en-29-ol-3-one, named as cangoronine and ilicifoline respectively, in addition to seven known friedelane-, pristimerin- and tingenone-type triterpenes have been isolated fromMaytenus ilicifolia. The structures were established by spectroscopic and X-ray analyses. The cytotoxic activities of these compounds are also reported.

Inclusion complex formation in a particular geometry by a water-soluble paracyclophane in aqueous solution — NMR Studies —

NMR studies (1H and 13C) demonstrating an inclusion complex formation in a particular geometry between a water-soluble paracyclophane, CP44, and hydrophobic substrates in acidic aqueous solution are described.

Side-chain interaction between the α-helices of poly-γ-benzyl-l- and d-glutamates☆

Abstract X-Ray diffraction and infrared absorption measurements have been made of a number of fibers obtained from mixtures of poly-γ-benzyl- l - and d -glutamates. An extensive examination has been made especially of the structural difference previously found between a fiber of an equimolar mixture of PBLG + PBDG and a fiber of pure PBLG. It has been found that the arrangement of the benzyl group at the end of the side-chain is much more regular in the equimolar mixture than that in pure PBLG. The X-ray data obtained are explained by considering that, in the fiber of PBLG + PBDG, the main-chain forms an α-helix which has 3.58 residues per turn, and that some of the benzyl groups are arranged along a helix with a different screw symmetry from the main-chain helix. Such an arrangement of the benzyl groups is considered to be caused by a side-chain-side-chain interaction and to give rise to three intense “extra” layer lines observed at 10.9, 5.0 and 3.6 A.

Conformational analysis of antitumor cyclic hexapeptides, RA series

Abstract Conformational analysis of an antitumor cyclic hexapeptide, RA and its analogues isolated from Rubia akane and R.cordifolia was conducted by the spectroscopic and computational chemical methods. A combination of different homo- and heteronuclear two-dimentional NMR techniques at 500MHz have enabled us to perform complete assignment of the 1H and 13C signals of the two conformers A and B of RA-VII in CDCl3. The structures of the three conformers (A, B and C) in DMSO-d6 were also determined by 2D-NMR techniques, temperature effects on NH protons and NOE experiments. Distances deduced from the NMR measurements were used for the refinements by the restrained molecular dynamics calculations using AMBER program. These conformational analysis showed that these conformers were caused by geometrical isomerization and that the predominant conformer A exhibits a typical type II β-turn structure, which is similar to the crystal structure analyzed by the X-ray diffractions. The reduced biological activity of the N-methyl derivative of RA-VII in comparison to RA-VII may be responsible for the more weakly populated conformer A in solution. Further, the presence of a highly strained 14-membered ring was necessary to maintain the typical type II β-turn structure of conformer A, and the ring system and turn structure were considered to play an important role in its antitumor activity.

Isolation and structure determination of a new marine toxin, neosurugatoxin, from the Japanese Ivory Shell, .

A new toxin, named neosurugatoxin, was isolated from the toxic Japanese Ivory Shell and its structure was determined by X-ray crystallographic analysis.

Studies on AI-77s, microbial products with gastroprotective activity. Structures and the chemical nature of AI-77s

Abstract The structures and the chemical nature of a novel gastroprotective substance AI-77-B (1) and its analogues AI-77-C (2), D (3), F (4) and G (5), which are produced by Bacillus pumilus AI-77, are described. The structure of 1 was confirmed to be 6-[[1(S)-(3(S), 4-dihydro-8-hydroxy-1-oxo-1H-2-benzopyran-3-yl)-3-methylbutyl]amino]-4(S),5(S)-dihydroxy-6-oxo-3(S)-aminohexanoic acid by X-ray in combination with chemical studies and the structures of 2, 3, 4 and 5 were determined by chemical syntheses from 1 and spectral analyses.

Horizontal‐type four‐circle diffractometer station of the vertical wiggler beamline at the Photon Factory

An experimental station with a four‐circle diffractometer combined with tunable and focusing optics was designed and constructed for x‐ray crystallography using synchrotron radiation from the vertical wiggler at the Photon Factory. The optics implemented into beamline 14A comprises a double‐crystal monochromator and a double‐focusing mirror so as to yield high photon flux x rays tunable over wide wavelength regions. The diffractometer with its equatorial plane in the horizontal was specially fabricated for rapid and accurate measurements of x‐ray diffraction intensities from macromolecular crystals, and was provided with an alignment carriage as well as computer control and measuring systems. The station has proved to be particularly useful for such applications as anomalous scattering studies of protein crystals and also EXAFS studies at high photon energies.