Showing papers by "George M. Sheldrick published in 2005"

Improving Radiation-Damage Substructures for Rip.

Abstract: Specific radiation damage can be used to solve macromolecular structures using the radiation-damage-induced phasing (RIP) method. The method has been investigated for six disulfide-containing test structures (elastase, insulin, lysozyme, ribonuclease A, trypsin and thaumatin) using data sets that were collected on a third-generation synchrotron undulator beamline with a highly attenuated beam. Each crystal was exposed to the unattenuated X-ray beam between the collection of a `before' and an `after' data set. The X-ray `burn'-induced intensity differences ranged from 5 to 15%, depending on the protein investigated. X-ray-susceptible substructures were determined using the integrated direct and Patterson methods in SHELXD. The best substructures were found by downscaling the `after' data set in SHELXC by a scale factor K, with optimal values ranging from 0.96 to 0.99. The initial substructures were improved through iteration with SHELXE by the addition of negatively occupied sites as well as a large number of relatively weak sites. The final substructures ranged from 40 to more than 300 sites, with strongest peaks as high as 57σ. All structures except one could be solved: it was not possible to find the initial substructure for ribonuclease A, however, SHELXE iteration starting with the known five most susceptible sites gave excellent maps. Downscaling proved to be necessary for the solution of elastase, lysozyme and thaumatin and reduced the number of SHELXE iterations in the other cases. The combination of downscaling and substructure iteration provides important benefits for the phasing of macromolecular structures using radiation damage.

Structure of Ecballium Elaterium Trypsin Inhibitor II (Eeti-II): A Rigid Molecular Scaffold

Abstract: The Ecballium elaterium trypsin inhibitor II (EETI-II) belongs to the family of squash inhibitors and is one of the strongest inhibitors known for trypsin. The eight independent molecules of EETI-II in the crystal structure reported here provide a good opportunity to test the hypothesis that this small cystine-knot protein (knottin) is sufficiently rigid to be used as a molecular scaffold for protein-engineering purposes. To extend this test, the structures of two complexes of EETI-II with trypsin have also been determined, one carrying a four-amino-acid mutation of EETI-II. The remarkable similarity of these structures confirms the rigidity of the molecular framework and hence its suitability as a molecular scaffold.

Structures of Complexes between Echinomycin and Duplex DNA.

Abstract: The structure of the bis-intercalation complex of the depsipeptide antibiotic echinomycin with (CGTACG)2 has been redetermined at a higher resolution (1.4 A) and new high-resolution structures (1.1–1.5 A) are reported for the complexes of echinomycin with (GCGTACGC)2 (at both low and high ionic strengths) and (ACGTACGT)2. The structures show the expected Hoogsteen pairing for the base pairs flanking the intercalating chromophores on the outside and Watson–Crick pairing for both base pairs enclosed by the echinomycin. In the octamer complexes but not the hexamer complex, the echinomycin molecule, which would possess a molecular twofold axis were it not for the thioacetal bridge, shows twofold disorder. In all the structures the stacking of the base pairs and chromophores is extended by intermolecular stacking. The structures provide more precise details of the hydrogen bonding and other interactions between the bis-intercalating antibiotics and the duplex DNA than were previously available.

Structure of the lipopeptide antibiotic tsushimycin.

Abstract: The amphomycin derivative tsushimycin has been crystallized and its structure determined at 1.0 A resolution. The asymmetric unit contains 12 molecules and with 1300 independent atoms this structure is one of the largest solved using ab initio direct methods. The antibiotic is comprised of a cyclodecapeptide core, an exocyclic amino acid and a fatty-acid residue. Its backbone adopts a saddle-like conformation that is stabilized by a Ca2+ ion bound within the peptide ring and accounts for the Ca2+-dependence of this antibiotic class. Additional Ca2+ ions link the antibiotic molecules to dimers that enclose an empty space resembling a binding cleft. The dimers possess a large hydrophobic surface capable of interacting with the bacterial cell membrane. The antibiotic daptomycin may exhibit a similar conformation, as the amino-acid sequence is conserved at positions involved in Ca2+ binding.

Sesquiterpene Lactones from Elephantopus scaber

Abstract: The ethanolic and acetone extracts of the whole plant of Elephantopus scaber were found to contain ethyl hexadecanoate, ethyl-9,12-octadecadienoate, ethyl-(Z)-9-octadecenoate, ethyl octadecanoate, lupeol, stigmasterol, stigmasterol glucoside, deoxyelephantopin (1) and two new germacranolide sesquiterpene lactones named 17,19-dihydrodeoxyelephantopin (2) and iso-17,19- dihydrodeoxyelephantopin (3) whose stereostructures were determined by spectroscopic methods, comparison with reported data and single-crystal X-ray analysis.

Crystal and Solution Structures of 7-Amino-Actinomycin D Complexes with D(Ttagbrut), D(Ttagtt) and D(Tttagttt)

Abstract: 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[Br5U]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.

Sesquiterpene Lactones from Elephantopus scaber.

Abstract: The ethanolic and acetone extracts of the whole plant of Elephantopus scaber were found to contain ethyl hexadecanoate, ethyl-9,12-octadecadienoate, ethyl-(Z)-9-octadecenoate, ethyl octadecanoate, lupeol, stigmasterol, stigmasterol glucoside, deoxyelephantopin (1) and two new germacranolide sesquiterpene lactones named 17,19-dihydrodeoxyelephantopin (2) and iso-17,19- dihydrodeoxyelephantopin (3) whose stereostructures were determined by spectroscopic methods, comparison with reported data and single-crystal X-ray analysis.