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  • Articles: DFG German National Licenses  (18)
  • 1
    Electronic Resource
    Electronic Resource
    Human milk lactoferrin is a serine protease that cleaves Haemophilus surface proteins at arginine-rich sites (2003)
    Oxford, UK : Blackwell Science Ltd
    Molecular microbiology 47 (2003), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: Lactoferrin is a member of the lactotransferrin family of non-haem, iron-binding glycoproteins and is found at high concentrations in all human secretions, where it plays a major role in mucosal defence. In recent work, we observed that lactoferrin has proteolytic activity and attenuates the pathogenic potential of Haemophilus influenzae by cleaving and removing two putative colonization factors, namely the IgA1 protease protein and the Hap adhesin. Experiments with protease inhibitors further suggested that lactoferrin may belong to a serine protease family. In the present study we explored the mechanism of lactoferrin protease activity and discovered that mutation of either Ser259 or Lys73 results in a dramatic decrease in proteolysis. Examination of the crystal structure revealed that these two residues are located in the N-terminal lobe of the protein, adjacent to a 12–15 Å cleft that separates the N-lobe and the C-lobe and that can readily accommodate large polypeptide substrates. In additional work, we found that lactoferrin cleaves IgA1 protease at an arginine-rich region defined by amino acids 1379–1386 (RRSRRSVR) and digests Hap at an arginine-rich sequence between amino acids 1016 and 1023 (VRSRRAAR). Based on our results, we conclude that lactoferrin is a serine protease capable of cleaving arginine-rich sequences. We speculate that Ser259 and Lys73 form a catalytic dyad, reminiscent of a number of bacterial serine proteases. In addition, we speculate that lactoferrin may cleave arginine-rich sequences in a variety of microbial virulence proteins, contributing to its long-recognized antimicrobial properties.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2958.2003.03327.x
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  • 2
    Electronic Resource
    Electronic Resource
    Structure of Rhombohedral 2 Zinc Insulin Crystals (1969)
    [s.l.] : Nature Publishing Group
    Nature 224 (1969), S. 491-495 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] An electron density map has been calculated at a resolution of 2.8 Å which shows many details of the arrangement of the atoms in rhombohedral crystals of ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/224491a0
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  • 3
    Electronic Resource
    Electronic Resource
    Structure of copper- and oxalate-substituted human lactoferrin at 2.0 Å resolution (1994)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 50 (1994), S. 302-316 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The three-dimensional structure of human dicupric monooxalate lactoferrin, Cu2oxLf, has been determined to 2.0 Å resolution, using X-ray diffraction data collected by diffractometry to 2.5 Å resolution, and oscillation photography on a synchrotron source to 2.0 Å resolution. Difference electron-density maps calculated between Cu2oxLf and both dicupric lactoferrin, Cu2Lf, and diferric lactoferrin, Fe2Lf, showed that the oxalate had replaced a carbonate in the C-terminal binding site, and that, relative to Cu2Lf, there were no significant differences in the N-terminal site. The structure was then refined crystallographically by restrained least-squares methods. The final model, in which the r.m.s. deviation in bond distances is 0.017 Å, contains 5314 protein atoms (691 residues), two Cu2+ ions, one bicarbonate ion, one oxalate ion, 325 solvent molecules and one sugar residue. The crystallographic R factor of 0.193 is for 46 134 reflections in the range 8.0 to 2.0 Å resolution. The oxalate ion is coordinated to copper in a 1,2-bidentate fashion, and the added bulk of the anion results in the rearrangement of the side chains of nearby arginine and tyrosine residues. No other major alterations in the molecule can be observed, the overall protein structure being the same as that for Cu2Lf and Fe2Lf.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444994000491
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  • 4
    Electronic Resource
    Electronic Resource
    Search designs for protein crystallization based on orthogonal arrays (1994)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 50 (1994), S. 429-440 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: In protein crystallography, the initial experimental problem is the identification of physical and chemical conditions that will support nucleation and crystal growth. Ideally, experiments to search for such conditions would be based on a full-factorial structure, with variation in the temperature and solution composition. However, consideration of even a moderate number of possibilities for the composition of the system will result in factorial experiments which may be prohibitively large. In this paper it is proposed that search experiments for protein crystallization might be based on orthogonal arrays. These are subsets of full-factorial experiments which possess a great deal of symmetry, such that a uniform distribution of points throughout the experimental region is preserved. Such experiments have reasonable size, explore the proposed experimental region in a systematic fashion, and form a logical basis for a sequential approach to the search for crystallization conditions. Examples of such initial search experiments are given, and their application to some recent protein crystallization problems in this laboratory is described briefly. The relationship of this approach to other protein crystallization search procedures is also discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444993014374
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  • 5
    Electronic Resource
    Electronic Resource
    Use of iron anomalous scattering with multiple models and data sets to identify and refine a weak molecular replacement solution: structure analysis of cytochrome c' from two bacterial species (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 282-289 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of cytochrome c′ from two bacterial species, Alcaligenes sp and Alcaligenes denitrificans, have been determined from X-ray diffraction data to 3.0 Å resolution using the anomalous scattering of the single Fe atom in each to identify and refine a weak molecular-replacement solution. Molecular-replacement studies, with the program AMORE, used two isomorphous data sets (from the two species), two independent search models (the cytochromes c′ from Rhodospirillum molischianum and Rhodospirillum rubrum), both with and without side chains, and two different resolution ranges (10.0–4.0 and 15.0–3.5Å) to generate a large number of potential solutions. No single solution stood out and none appeared consistently. The Fe-atom position in each structure was then determined from its anomalous-scattering contribution and all molecular- replacement solutions were discarded which did not (i) place the Fe atom correctly and (ii) orient the molecule such that a crystallographic twofold axis generated a dimer like those of the two search models. Finally, electron-density maps phased solely by the Fe-atom anomalous scattering were calculated. As these were combined and subjected to solvent flattening and histogram matching (with the program SQUASH), correlation with the remaining molecular-replacement solutions identified one as correct and enabled it to be improved and subjected to preliminary refinement. The correctness of the solution is confirmed by parallel isomorphous-replacement studies.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444994012874
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  • 6
    Electronic Resource
    Electronic Resource
    Crystallization and preliminary X-ray diffraction studies of a cobalt-substituted derivative of the iron-dependent alcohol dehydrogenase from Zymomonas mobilis (1996)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 218-220 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The iron-dependent alcohol dehydrogenase from Zymomonas mobilis has been crystallized in a form suitable for X-ray diffraction studies. The crystals grew in hanging drops by vapor diffusion, equilibrating with a solution comprising 25–27% methoxypolyethylene glycol 5000 and 1 mM Co2+ in a 0.2 M succinic acid/potassium hydroxide buffer at pH 5.5–5.7 at 281 K. Crystals are tetragonal, P4122 (or P4322), with unit-cell dimensions a = b = 125.7, c = 248.1 Å. Four molecules comprise the asymmetric unit, and a self-rotation function indicates twofold local symmetry perpendicular to the unique axis and 15° from a crystallographic twofold axis. Diffraction data to 3.0 Å have been collected.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444995009103
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  • 7
    Electronic Resource
    Electronic Resource
    Three-Dimensional Structure of Cytochrome c' from Two Alcaligenes Species and the Implications for Four-Helix Bundle Structures (1996)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 356-368 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The three-dimensional structures of two cytochromes c′ have been determined in order to analyse the common features of proteins of this family and their relationship with other four-helix bundle structures. The structure of cytochrome c′ from Alcaligenes sp was determined by molecular replacement supplemented with the iron anomalous scattering and the use of a single isomorphous heavy-atom derivative, and was refined using synchrotron data to 1.8 Å resolution. The final model, comprising 956 protein atoms (one monomer) and 89 water molecules, has a final R value of 0.188 for all data in the range 20.0–1.8 Å resolution (14 673 reflections). The structure of the cytochrome c′ from Alcaligenes denitrificans is isomorphous and essentially identical (r.m.s. deviation for all atoms 0.36 Å). Although its amino-acid sequence has not been determined chemically, only four differences from that of Alcaligenes sp cytochrome c′ were identified by the X-ray analysis. The final model for Alcaligenes denitrificans cytochrome c', comprising 953 protein atoms and 75 water molecules, gave a final R factor of 0.167 for all data in the range 20.0–2.15 Å (8220 reflections). The cytochrome c′ monomer forms a classic four-helix bundle, determined by the packing of hydrophobic side chains around the enclosed haem group. There are very few cross-linking hydrogen bonds between the helices, the principal side-chain hydrogen bonding involving one of the haem propionates and a conserved Arg residue. The cytochrome c′ dimer is created by a crystallographic twofold axis. Monomer–monomer contacts primarily involve the two A helices, with size complementarity of side chains in a central solvent-excluded portion of the interface and hydrogen bonding at the periphery. Both species have a pyroglutamic acid N-terminal residue. The haem iron is five-coordinate, 0.32 Å out of the haem plane towards the fifth ligand, His120. The unusual magnetic properties of the Fe atom may be linked to a conserved basic residue, Arg124, adjacent to His120.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444995008328
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  • 8
    Electronic Resource
    Electronic Resource
    Deposition of macromolecular data (1996)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 609-609 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444996000388
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  • 9
    Electronic Resource
    Electronic Resource
    Structure of apo-azurin from Alcaligenes denitrificans at 1.8 Å resolution (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 331-343 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of apo-azurin from Alcaligenes denitrificans has been determined at high resolution by X-ray crystallography. Two separate structure analyses have been carried out, (i) on crystals obtained from solutions of apo-azurin and (ii) on crystals obtained by removal of copper from previously formed crystals of holo-azurin. Data to 1.8 Å resolution were collected from the apo-azurin crystals, by Weissenberg photography (with image plates) using synchrotron radiation and by diffractometry, and the structure was refined by restrained least-squares methods to a final R value of 0.160 for all data in the range 10.0–1.8 Å. The final model of 1954 protein atoms, 246 water molecules (66 half-weighted), four SO42− ions, and two low-occupancy (0.13 and 0.15) Cu atoms has r.m.s. deviations of 0.012, 0.045 and 0.013 Å from standard bond lengths, angle distances and planar groups. For copper-removed azurin, data to 2.2 Å were collected by diffractometry and the structure refined by restrained least squares to a final R value of 0.158 for all data in the range 10.0–2.2 Å. The final model of 1954 protein atoms, 264 water molecules, two SO42− ions, two low occupancy (0.18 and 0.22) metal atoms and one unidentified atom (modelled as S) has r.m.s. deviations of 0.013, 0.047 and 0.012 Å from standard bond lengths, angle distances and planar groups. The two structures are essentially identical to each other and show no significant differences from the oxidized and reduced holo-azurin structures. The ligand side chains move slightly closer together following the removal of copper, with the radius of the cavity between the three strongly binding ligands, His 46, His 117 and Cys 112, shrinking from 1.31 Å in reduced azurin to 1.24 Å in oxidized azurin and 1.16 Å in apo-azurin. There is a suggestion of increased flexibility in one of the copper-binding loops but the structure supports the view that the copper site found in holo-azurin is a stable structure, defined by the constraints of the polypeptide structure even in the absence of a bound metal ion.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444992013544
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  • 10
    Electronic Resource
    Electronic Resource
    Metal substitution in a blue-copper protein: the crystal structure of cadmium-azurin at 1.8 Å resolution (1994)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 50 (1994), S. 263-270 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of cadmium-substituted azurin have been prepared by diffusing CdII into crystals of apo-azurin grown previously and their structure has been determined at high resolution by X-ray crystallography. Data to 1.8 Å resolution were collected by Weissenberg photography (with image plates) using synchrotron radiation. These data were combined with a 2.2 Å diffractometer data set to give 90% coverage to 1.8 Å. An initial model was derived from the isomorphous CuII-azurin structure, and the cadmium and ligand positions added from `omit' maps. Refinement was by restrained least squares (program PROLSQ), to a final R value of 0.168 for all data in the range 10.0–1.8 Å (23 349 reflections). The final model of 1954 protein atoms, two CdII ions (occupancy 0.75), four SO{_4^{2-}} ions and 239 water molecules has r.m.s. deviations of 0.015, 0.045 and 0.013 Å from standard bond lengths, angle distances and planar groups. The protein structure is essentially the same as that of CuII-azurin, with an r.m.s. deviation of 0.18 Å for 97% of main-chain atoms after superposition of the two structures. The Cd atom is within 0.2 Å of the equivalent copper position, displaced slightly away from the axial Met ligand towards the carbonyl O atom of Gly45. The latter has also moved slightly towards the metal, by a rotation of the peptide unit, to give a Cd—O bond of 2.76 Å. The Cd—S(Cys) bond is lengthened to 2.39 Å. The coordination geometry is slightly more tetrahedral than for CuII, and the cadmium–oxygen interaction is consistent with the presence of an oxygen ligand in the coordination sphere of stellacyanin.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444993014398
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