Gertraud Koellner

Calf spleen purine nucleoside phosphorylase: purification, sequence and crystal structure of its complex with an N(7)-acycloguanosine inhibitor

Calf spleen purine nucleoside phosphorylase was purified to homogeneity and its amino acid sequence was determined. The complex of the enzyme with an N(7)‐acycloguanosine inhibitor crystallized in the cubic space group P213, with unit cell dimension and one monomer in the asymmetric crystal unit. The biologically active trimer is formed by the crystallographic three‐fold axis. The structure was solved by molecular replacement methods, using the model of the human erythrocyte enzyme, and refined at a resolution of 2.9 Å to an R‐factor of 0.21. The orientation of the inhibitor at the active site is examined in relation to the catalytic activity of the enzyme in the phosphorolysis of nucleosides.

A Neutral Molecule in a Cation-binding Site: Specific Binding of a PEG-SH to Acetylcholinesterase from Torpedo californica

The crystal structure of acetylcholinesterase from Torpedo californica complexed with the uncharged inhibitor, PEG-SH-350 (containing mainly heptameric polyethylene glycol with a terminal thiol group) is determined at 2.3 A resolution. This is an untypical acetylcholinesterase inhibitor, since it lacks the cationic moiety typical of the substrate (acetylcholine). In the crystal structure, the elongated ligand extends along the whole of the deep and narrow active-site gorge, with the terminal thiol group bound near the bottom, close to the catalytic site. Unexpectedly, the cation-binding site (formed by the faces of aromatic side-chains) is occupied by CH(2) groups of the inhibitor, which are engaged in C-H...pi interactions that structurally mimic the cation-pi interactions made by the choline moiety of acetylcholine. In addition, the PEG-SH molecule makes numerous other weak but specific interactions of the C-H...O and C-H...pi types.

Cooperative hydrogen bond cycles involving OH⋯π and CH⋯O hydrogen bonds as found in a hydrated dialkyne

Abstract In the crystal structure of a di-aIkyne that contains a cocrystallized water molecule, an unprecedentedly rich system of interconnected OH⋯O, CH⋯ and OH⋯π hydrogen bonds is found. The pattern can be decomposed into cooperative rings and chains, in which the weak CH⋯O and OH⋯π bonds participate not as bystanders, but as full members.

A vibrating flexible chain in a molecular cage: Crystal structure of the complex cyclomaltoheptaose (β-cyclodextrin)-1,4-butanediol·6.25H2O☆

A single crystal X-ray diffraction study of the title complex carried out at room temperature revealed space group P2(1), a = 21.199(12), b = 9.973(3), c = 15.271(8) A, beta = 110.87(3) degrees, V = 3017(3) A3, 4681 unique reflections with Fo greater than 1 sigma (Fo). The structure was refined to R = 0.069, resolution lambda/2sin theta max = 0.89 A. The crystal packing is of the cage type and is isomorphous to that of beta-cyclodextrin (beta CD) dodecahydrate. One 1,4-butanediol and approximately 1.25 water molecules are enclosed in each beta CD cavity. The hydroxyl groups of the 1,4-butanediol molecule are located at each end of the cavity and form hydrogen bonds with neighboring water and beta CD molecules. The flexible (CH2)4 moiety vibrates extensively in the central part of the cavity. Water molecules and hydroxyl groups are chelated between O-6 and O-5 of at least five glucose residues.

Calf spleen purine-nucleoside phosphorylase: crystal structure of the binary complex with a potent multisubstrate analogue inhibitor

Purine-nucleoside phosphorylase (PNP) deficiency in humans leads to inhibition of the T-cell response. Potent membrane-permeable inhibitors of this enzyme are therefore considered to be potential immunosuppressive agents. The binary complex of the trimeric calf spleen phosphorylase, which is highly homologous to human PNP, with the potent ground-state analogue inhibitor 9-(5,5-difluoro-5-phosphonopentyl)guanine (DFPP-G) was crystallized in the cubic space group P2(1)3, with unit-cell parameter a = 93.183 A and one monomer per asymmetric unit. High-resolution X-ray diffraction data were collected using synchrotron radiation (EMBL Outstation, DESY, Hamburg, station X13). The crystal structure was refined to a resolution of 2.2 A and R and Rfree values of 19.1 and 24.2%, respectively. The crystal structure confirms that DFPP-G acts as a multisubstrate analogue inhibitor as it binds to both nucleoside- and phosphate-binding sites. The structure also provides the answers to some questions regarding the substrate specificity and molecular mechanism of trimeric PNPs. The wide access to the active-site pocket that was observed in the reported structure as a result of the flexibility or disorder of two loops (residues 60-65 and 251-266) strongly supports the random binding of substrates. The putative hydrogen bonds identified in the base-binding site indicate that N1-H and not O6 of the purine base defines the specificity of trimeric PNPs. This is confirmed by the fact that the contact of guanine O6 with Asn243 Odelta1 is not a direct contact but is mediated by a water molecule. Participation of Arg84 in the binding of the phosphonate group experimentally verifies the previous suggestion [Blackburn & Kent (1986), J. Chem. Soc. Perkin Trans. I, pp. 913-917; Halazy et al. (1991), J. Am. Chem. Soc. 113, 315-317] that fluorination of alkylphosphonates yields compounds with properties that suitably resemble those of phosphate esters and in turn leads to optimized interactions of such analogues with the phosphate-binding site residues. DFPP-G shows a Ki(app) in the nanomolar range towards calf and human PNPs. To date, no high-resolution X-ray structures of these enzymes with such potent ground-state analogue inhibitors have been available in the Protein Data Bank. The present structure may thus be used in the rational structure-based design of new PNP inhibitors with potential medical applications.

Crystalline β-cyclodextrin · 12 H2O reversibly dehydrates to β-cyclodextrin · 10.5 H2O under ambient conditions☆

Abstract In contact with mother liquor, crystalline β-cyclodextrin (β-CD) hydrate has composition ∼ β-CD · 12 H2O. If crystals are dried at ambient conditions (18°C, · 50 % humidity), the unit cell volume diminishes ∼ 30 to 50 A3. X-ray structure analysis of a dry crystal (0.89 A resolution, 4617 data, R = 0.059) showed the composition β-CD · 10.5 H2O, with ∼ 5.5 water molecules in the β-CD cavity (7 partially and 2 fully occupied sites) and ∼ 5.0 between the β-CD molecules. The positions of the β-CD host and of most of the hydration waters are conserved during dehydration, but the occupancies of the waters in the β-CD cavity diminish. Dry crystals put into solvent re-hydrate to the original form. The mechanism of de- and re-hydration is not evident.

Isostructural replacement of an N–H ⋯ O by a C–H ⋯ O hydrogen bond in complex stabilisation: crystal structures of β-cyclodextrin complexed with diethanolamine and with pentane-1,5-diol

In the isomorphous crystal structures of the inclusion complexes β-cyclodextrin–diethanolamine and β-cyclodextrin–pentane-1,5-diol, the flexible guest molecules have identical conformations; they form the same intermolecular contacts, with a structure-stabilizing N–H ⋯ O hydrogen bond in the former being replAccd by a C–H ⋯ O interaction in the latter.

Crystal structures of cyclomaltoheptaose (β-cyclodextrin) complexed with ethylene glycol·8.0H2O and glycerol·7.2H2O☆

Single-crystal X-ray diffraction studies were carried out for the title compounds at room temperature. The crystal packings are of the cage-type and isomorphous to that of beta-cyclodextrin (beta CD) hydrate. In both crystal structures, disorder and extensive thermal vibrations of the complexed guest molecules are observed. In beta CD-ethylene glycol.8H2O, one ethylene glycol molecule (disordered over two discrete sites) and three water molecules (four discrete sites) are included in the beta CD cavity. Within the beta CD cavity, all oxygen sites (ordered and disordered) are in positions occupied by water molecules in beta CD.12H2O; this is only possible because the ethylene glycol molecule adopts the low-energy conformation with the O-C-C-O torsion angle approximately 60 degrees and an O...O separation of 2.9 A, in which its hydroxyl groups can directly substitute for two hydrogen-bonding water molecules. In beta CD-glycerol.7.2H2O, one glycerol molecule (disordered over two discrete sites) and two water molecules (two fully occupied sites) are included in the beta CD cavity. The general situation in both compounds parallels that found earlier in beta CD-ethanol.8H2O. It is assumed that the disorder is dynamic, i.e., associated with jumps between the partially occupied molecular sites.

Interactions of trimeric purine nucleoside phosphorylases with ground state analogues--calorimetric and fluorimetric studies.

Abstract Binding enthalpies, dissociation constants and stoichiometry of binding for interaction of trimeric calf spleen and Cellulomonas sp. purine nucleoside phosphorylases with their ground state analogues (substrates and inhibitors) were studied by calorimetric and spectrofluorimetric methods. Data for all ligands, with possible exception of hypoxanthine, are consistent with three identical non-interacting binding sites.

Crystallization and preliminary X-ray studies of purine nucleoside phosphorylase from Cellulomonas sp.

The commercially available enzyme purine nucleoside phosphorylase (PNP) from Cellulomonas sp. was purified by ion--exchange chromatography, partially sequenced and crystallized in two different crystal forms using the hanging-drop vapour-diffusion technique. Crystal form A grows as polyeders and/or cubes in the cubic space group P4232 with unit-cell dimension a = 162.5 A. Crystal form B appears as thick plates in the space group P212121 with unit-cell dimensions a = 63.2, b = 108.3 and c = 117.4 A. Both crystal forms contain three monomers (one trimer) in the asymmetric unit.