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Biomedical subjects

F Takusagawa

Publications and source records attributed to F Takusagawa.

31 records · Page 2Linked to original sources
PubMed1992

Crystal structure of the 2:1 complex between d(GAAGCTTC) and the anticancer drug actinomycin D.

The crystal structures of the 2:1 complex of the self-complementary DNA octamer d(GAAGCTTC) with actinomycin D has been determined at 3.0 A resolution. This is the first example of a crystal structure of a DNA-drug complex in which the drug intercalates into the middle of a relatively long DNA segment. The results finally confirmed the DNA-actinomycin intercalation model proposed by Sobell & co-workers in 1971. The DNA molecule adopts a severely distorted and slightly kinked B-DNA-like structure with an actinomycin D molecule intercalated in the middle sequence, GC. The two cyclic depsipeptides, which differ from each other in overall conformation, lie in the minor groove. The complex is further stabilized by forming base-peptide and chromophore-backbone hydrogen bonds. The DNA helix appears to be unwound by rotating one of the base-pairs at the intercalation site. This single base-pair unwinding motion generates a unique asymmetrically wound helix at the binding site of the drug, i.e. the helix is loosened at one end of the intercalation site and tightened at the other end. The large unwinding of the DNA by the drug intercalation is absorbed mostly in a few residues adjacent to the intercalation site. The asymmetrical twist of the DNA helix, the overall conformation of the two cyclic depsipeptides and their interaction mode with DNA are correlated to each other and rationally explained.

Base Composition↗
PubMed1991

Structures of two conformationally defined phenylethanolamines: exo-1,4-epoxy-2-formamido-1,2,3,4-tetrahydro-8-trifluoromethylnaphthale ne and exo-1,4-epoxy-2-formamido-1,2,3,4-tetrahydro-6-trifluoromethylnaphthale ne.

(+/-)-exo-1,4-Epoxy-2-formamido-1,2,3,4-tetrahydro-8- trifluoromethylnaphthalene (1), C12H10F3NO2, Mr = 257.21, Pccn, a = 8.895 (1), b = 19.968 (5), c = 12.656 (3) A, V = 2247.9 (8) A3, Z = 8, Dx = 1.520 g cm-3, lambda(Mo K alpha) = 0.71069 A, mu = 1.49 cm-1, F(000) = 1056, T = 297 K, R = 0.0466 for 1481 independent reflections collected. The torsion angle for N(10)-C(2)-C(1)-C(8a) is 167.4 (2) degrees. (+/-)-exo-1,4-Epoxy-2-formamido-1,2,3,4-tetrahydro-6- trifluoromethylnaphthalene, (2), C12H10F3NO2, Mr = 257.21, P2(1)2(1)2(1), a = 8.52 (2), b = 26.15 (2), c = 5.06 (5) A, V = 1127 (11) A3, Z = 4, Dx = 1.516 g cm-3, lambda(Mo K alpha) = 0.71069 A, mu = 1.29 cm-1, F(000) = 528, T = 297 K, R = 0.108 for 932 independent reflections collected. The torsion angle N(10)-C(2)-C(1)-C(8a) is 172.5 (6) degrees; the formamido group in both (1) and (2) is exo. X-ray studies on (1) suggest a hydrogen bond between N(10) and O(12) and similarly for (2).

Chemical Phenomena↗
PubMed1990

The crystal structure of d(GTACGTAC) at 2.25 A resolution: are the A-DNA's always unwound approximately 10 degrees at the C-G steps?

The structure of the self-complementary octamer d(GTACGTAC) has been analyzed by a single crystal X-ray diffraction method at 2.25 A resolution. The crystallographic R factor was 0.184 for all 1233 reflections at this resolution. In spite of the alternating purine-pyrimidine sequence, d(GTACGTAC) adopts the A-form conformation rather than the left-handed Z-form. The average helix twist and the mean rise per base pair are 32.1 degrees and 3.18 A, respectively. The d(GTACGTAC) helix is characterized by a wide open major groove and small base-pair tilt (9.7 degrees). The partial unwinding of the helix is observed only at the central pyrimidine-purine C-G step, but not at the other pyrimidine-purine T-A steps. Based on this study and six other X-ray studies, we propose a hypothesis that the A-DNA's are always unwound approximately 10 degrees at the C-G steps. Significant differences in base-pair stacking modes are seen between the purine-pyrimidine step and the pyrimidine-purine step. All deoxyribose rings adopt the C3'-endo conformation. All backbone torsion angles fall into the range expected for the A-DNA form, except for the nucleotide G5, whose alpha and gamma torsion angles adopt the trans, trans conformation instead of the common gauche-, gauche+ conformation.

Base Sequence↗
PubMed1989

Structure of [N,N'-propylenebis(2-pyrrolylmethyleneaminato)]nickel(II).

[Ni(C13H14N4)], Mr = 284.98, monoclinic, P2(1)/c, a = 10.096 (2), b = 9.360 (2), c = 30.565 (4) A, beta = 119.45 (2) degrees, V = 2515.1 (9) A3, Z = 8, Dx = 1.505 g cm-3, Cu K alpha, lambda = 1.5418 A, mu = 20.22 cm-1, F(000) = 1168, T = 298 (2) K, 437 parameters refined, final R = 0.038 for all 2587 reflections. The complex takes a square-planar geometry around the Ni atom. Although the coordination geometries of the two crystallographically independent complexes are quite similar to each other, significant differences in planarity and Ni-N distances are observed.

Crystallization↗
PubMed1985

The role of the cyclic depsipeptide rings in antibiotics.

The physical and biological roles of the cyclic depsipeptides of actinomycin, quinomycin and triostin antibiotic families are proposed by examining the crystal structures of d(GC)-actinomycin D and d(CGTACG)-triostin A. The analyses suggest that not only are DNA-amino acid hydrogen-bonding and chromophore-base pair stacking crucially important for DNA-antibiotic interaction, but also that the unique structure of the cyclic depsipeptides (the perfect hydrophobic character of the inner surface) is equally necessary to insure that these interactions are directed, unambiguous and screened from interference by solvent. Beyond this, the characteristic nature of the outer surfaces suggests a further hypothesis for the biological role of the cyclic depsipeptide rings; when the antibiotics bind in the region around the pause or rho-dependent termination sites on the DNA, the drugs actually terminate transcription by RNA polymerase and cause release of a premature RNA transcript. Termination is likely because the antibiotics carry five to six consecutive apparent A/T sequences on the surface of the cyclic depsipeptide rings, thus presenting a deceptive termination signal to the polymerase.

Anti-Bacterial Agents↗
PubMed1984

Crystallization and preliminary X-ray study of a complex between d(ATGCAT) and actinomycin D.

Crystals of a 2:1 complex between the self-complementary DNA hexamer d(ATGCAT) and the antitumor drug actinomycin D have been grown from solutions of polyethylene glycol 400. The crystals are orthorhombic with space group P2(1)2(1)2(1) and a = 95.6, b = 42.7, and c = 40.8 A. A Patterson map calculated from preliminary diffractometer data as well as packing considerations suggest a model in which the actinomycin D is intercalated into a double-stranded DNA hexamer. There are four such complexes in the asymmetric unit.

Crystallization↗
PubMedDate not supplied

Crystallization and preliminary X-ray diffraction studies of glycine methyltransferase from rat liver.

Glycine methyltransferase from rat liver is a tetrameric enzyme with 292 amino acid residues in each identical subunit and catalyzes the AdoMet-dependent methylation of glycine to form sarcosine. The enzyme was crystallized by the hanging drop vapor diffusion method, using polyethylene glycol 4000 as a precipitant. The crystal belongs to the orthorhombic space group P2(1)2(1)2, with unit cell dimensions of a = 86.4, b = 175.7, c = 45.5 A and with two subunits in the asymmetric unit. The crystals diffract beyond 2.4 A resolution, and a set of 2.4 A resolution data were measured.

Animals↗