Browsing by Author "Alexopoulos, E."

The formation of the complex of 7-amino-actinomycin D with potentially single-stranded DNA has been studied by X-ray crystallography in the solid state, by NMR in solution and by molecular modelling. The crystal structures of the complex with 5'-TTAG[(BrU)-U-5]T-3' provide interesting examples of MAD phasing in which the dispersive component of the MAD signal was almost certainly enhanced by radiation damage. The trigonal and orthorhombic crystal modifications both contain antibiotic molecules and DNA strands in the form of a 2:4 complex: in the orthorhombic form there is one such complex in the asymmetric unit, while in the trigonal structure there are four. In both structures the phenoxazone ring of the first drug intercalates between a BrU-G (analogous to T-G) wobble pair and a G-T pair where the T is part of a symmetry-related molecule. The chromophore of the second actinomycin intercalates between the BrU-G and G-BrU wobble pairs of the partially paired third and fourth strands. The base stacking also involves (A T) T triplets and Watson-Crick A-T pairs and leads to similar complex three-dimensional networks in both structures, with looping-out of unpaired bases. Although the available NOE constraints of a solution containing the antibiotic and d(TTTAGTTT) strands in the ratio 1:1 are insufficient to determine the structure of the complex from the NMR data alone, they are consistent with the intercalation geometry observed in the crystal structure. Molecular-dynamics (MD) trajectories starting from the 1:2 complexes observed in the crystal showed that although the thymines flanking the d(AGT) core are rather flexible and the G-T pairing is not permanently preserved, both strands remain bound to the actinomycin by strong interactions between it and the guanines between which it is sandwiched. Similar strong binding (hemi-intercalation) of the actinomycin to a single guanine was observed in the MD trajectories of a 1:1 complex. The dominant interaction is between the antibiotic and guanine, but the complexes are stabilized further by promiscuous base-pairing.

The crystal structure of H-(L-Tyr-d-Tyr)(4)-L-Lys-OH has been determined to 1.3 Angstrom resolution. The D, L-alternating peptide crystallizes in the tetragonal system, space group P4(3)2(1)2, with unit-cell parameters a = b = 27.99 (3), c = 78.93 (8) Angstrom. The crystals contain two molecules in the asymmetric unit that form a double-stranded right-handed antiparallel beta-helix. The structure has been solved by SIRAS using a crystal soaked in an iodide-containing solution for 1 min. The programs SHELXD and SHELXE were used to determine the iodide substructure and also the experimental electron-density map. Using the coordinates of known D,L-peptides deposited in the PDB, several attempts were made to solve the structure by molecular-replacement techniques. Although the backbone of the MR model selected shows great similarity and was used to trace the actual peptide structure in the map, it was not possible to obtain the correct solution before the experimental phases became available. The correct fragment orientations are easily determined, but the same does not apply to the translation search. Nevertheless, insights into fragment search and expansion were gained from the tests described in this paper. The correlation coefficient calculated with the resolution shell of data around 2.4 Angstrom, a distance corresponding to most 1-3 interatomic vectors, is a particularly good discriminator of correct orientations in the rotation search of small fragments.

The reaction of the lithium beta-diketoiminate complex (dipp)NacNacLi.OEt2 {(dipp)NacNac = 2-[(2,6-diisopropylphenyl) amino]-4-[(2,6-diisopropylphenyl)imino]pent-2-enyl} with ZnCl2 yielded the corresponding (dipp)NacNacZnCl (1) and (dipp)NacNacZn(mu-Cl)(2)Li(OEt2)(2) (1a). Treatment of 1 with LiCdropCPh and NaBH4 in diethyl ether gave (dipp)NacNacZnCdropCPh (2) and (dipp)NacNacZn(mu-H)(2)BH2 (3). The core element of compounds 1a-3 is a six-membered ZnN2C3 ring. The structure of la shows the beta-diketoiminate backbone in a boat conformation with the tetrahedrally coordinated metal centre in la at the prow and the opposing carbon atom at the stem. The zinc atoms in 2 and 3 show a planar arrangement to the beta-diketoiminate plane. The zinc atom in 2 is three-coordinated and that in 3 four-coordinated. Treatment of (dipp)NacNacLi.OEt2 with CuI in diethyl ether yielded {[Li(OEt2)][(dipp)NacNacCuI}](2) (4). In contrast to 1a-3, compound 4 contains a dimetallic system. The core of compound 4 consists of two six-membered LiN2C3 rings and one four-membered Cu2I2 ring. In addition to bonds to the two iodine atoms, the three-coordinated copper atom has a further bond to the gamma-carbon atom of the six-membered LiN2C3 ring, (C) Wiley-VCH Verlag GmbH, 69451 Weinheim, Germany, 2002.

The monomeric zinc compounds with three-coordinated zinc (dipp)NacNacZnCl (1), (dipp)NacNacZnMe (2), (dipp)NacNacZntBu (3), and (dipp)NacNacZnPh (4) were prepared under mild conditions in strong coordinating donor solvents. Compounds 2-4 have been structurally characterized. The beta -diketoiminate ligand (2-((2,6-diisopropylphenyl)amino)-4-((2,6-diisopropylphenyl)imino)pent-2-ene) ((dipp)NacNac) acts as a chelating ligand through its two N atoms, forming a six-membered ring with the zinc atom.

The reaction of the beta -diketoiminate lithium complex (dipp)NacNacLi . OEt2 ((dipp)NacNac = 2-((2,6-diisopropylphenyl)amino) -4- ((2,6-diisopropylphenyl)imino) -pent-2-enyl) with iPrMgCl and MgI2 yield the corresponding (dipp)NacNacMgiPr degrees OEt2 (1) and (dipp)NacNacMgI . OEt2 (2). The reaction of 2 with NaBH4 in diethylether gives (dipp)NacNacMg(mu -H)(3)BH . OEt2 (3). The core element of compounds 1-3 is a six-membered ring formed by N(1)-C(1)-C(2)-C(3)-N(2) and magnesium. The structures of 1 and 2 show the beta -diketoiminate backbone in a boat-conformation with the tetrahedrally coordinated metal center at the prow and the opposing carbon atom at the stern. The magnesium atom in 3 is octahedrally coordinated and out of the beta -diketoiminate plane.