Kristallographische sowie Modeling Studien von intermolekularen Wechselwirkungen von biologischem Interesse

Die vorliegende Doktorarbeit beinhaltet drei Projekte. Im ersten Teil wurden die Bindungsverhaeltnisse im Komplex des Antikrebsantibiotikums 7-Aminoactinomycin-D mit der nicht-komplementaeren DNA 5'-TTAGBrUT-3' mit roentgenstrukturanalytischen Methoden untersucht. Es wurden 2 Kristallformen erhalten, eine hexagonale und eine orthorhombische. Die Strukturloesung zeigt in beiden Faellen das Vorliegen einer antiparallelen doppelstraengigen DNA in Komplex mit 7-AAMD ueber eine Interkalation des Phenoxazonrings des Antibiotikums zwischen falsch gepaarten G-BrU oder G-T Basen.Im zweiten Projekt wird die Kristallisation und Strukturloesung des alternierenden d,l-Peptids H-(L-Tyr-D-Tyr)4-Lys-OH beschrieben. In der Kristallstruktur liegt das Peptid als doppelstraengige antiparallele beta-helix vor.Im dritten Projekt wurden theoretische Bindungsstudien durchgefuehrt bezueglich der Wechselwirkung von organischen Liganden mit der Ligandebindedomaene des humanen Estrogen Rezeptors Alpha

Solution and structure of an alternating D,L-peptide

The crystal structure of H-(L-Tyr-D-Tyr)4-L-Lys-OH has been determined to 1.3 Å resolution. The D,L-alternating peptide crystallizes in the tetragonal system, space group P43212, with unit-cell parameters a = b = 27.99 (3), c = 78.93 (8) Å. The crystals contain two molecules in the asymmetric unit that form a double-stranded right-handed antiparallel β-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 Å, a distance corresponding to most 1-3 interatomic vectors, is a particularly good discriminator of correct orientations in the rotation search of small fragments. © 2004 International Union of Crystallography.We are thankful to the European Community (Access to Research Infrastructure Action of the Improving Human Potential Programme to the EMBL Hamburg Outstation, contract No. HPRI-1999-CT-00017), to the Fonds der Chemischen Industrie and to the DFG (SFB416) and European Union Integrated Project BIOXHIT for supportPeer Reviewe

Crystallization and preliminary X-ray analysis of the inducible lysine decarboxylase from Escherichia coli

The structure of the decameric inducible lysine decarboxylase from E. coli was determined by SIRAS using a hexatantalum dodecabromide (Ta6Br12 2+) derivative. Model building and refinement are under way

Crystal and solution structures of 7-amino-actinomycin D complexes with d(TTAGBrUT), d(TTAGTT) and d(TTTAGTTT)

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. © 2005 International Union of Crystallography - all rights reserved.We are grateful to the Fonds der Chemischen Industrie, the Deutsche Forschungsgemeinschaft (SFB416) and the European Community (Access to Research Infrastructure Action of the Improving Human Potential Programme to the EMBL Hamburg Outstation, contract No. HPRI-1999-CT-000017) for support and to EMBL/DESY, Hamburg for a generous allocation of beamtime. EAJE thanks the Volkswagen Stiftung, Fundación Antorchas, ANPCyT, CONICET and UBA for financial supportPeer Reviewe

Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase

The inducible lysine decarboxylase, LdcI, has a protective role during acid stress in bacteria. An inhibitory interaction between LdcI and the stringent response effector ppGpp is required for modulating LdcI activity during acid stress under starvation conditions