Amy K. Katz

Metal Ion Roles and the Movement of Hydrogen during Reaction Catalyzed by D-Xylose Isomerase: A Joint X-Ray and Neutron Diffraction Study

Conversion of aldo to keto sugars by the metalloenzyme D-xylose isomerase (XI) is a multistep reaction that involves hydrogen transfer. We have determined the structure of this enzyme by neutron diffraction in order to locate H atoms (or their isotope D). Two studies are presented, one of XI containing cadmium and cyclic D-glucose (before sugar ring opening has occurred), and the other containing nickel and linear D-glucose (after ring opening has occurred but before isomerization). Previously we reported the neutron structures of ligand-free enzyme and enzyme with bound product. The data show that His54 is doubly protonated on the ring N in all four structures. Lys289 is neutral before ring opening and gains a proton after this; the catalytic metal-bound water is deprotonated to hydroxyl during isomerization and O5 is deprotonated. These results lead to new suggestions as to how changes might take place over the course of the reaction.

Hydrogen location in stages of an enzyme-catalyzed reaction: time-of-flight neutron structure of D-xylose isomerase with bound D-xylulose

The time-of-flight neutron Laue technique has been used to determine the location of hydrogen atoms in the enzyme d-xylose isomerase (XI). The neutron structure of crystalline XI with bound product, d-xylulose, shows, unexpectedly, that O5 of d-xylulose is not protonated but is hydrogen-bonded to doubly protonated His54. Also, Lys289, which is neutral in native XI, is protonated (positively charged), while the catalytic water in native XI has become activated to a hydroxyl anion which is in the proximity of C1 and C2, the molecular site of isomerization of xylose. These findings impact our understanding of the reaction mechanism.

A preliminary time-of-flight neutron diffraction study of Streptomyces rubiginosus D-xylose isomerase.

The metalloenzyme D-xylose isomerase forms well ordered crystals that diffract X-rays to ultrahigh resolution (<1 A). However, structural analysis using X-ray diffraction data has as yet been unable to differentiate between several postulated mechanisms that describe the catalytic activity of this enzyme. Neutrons, with their greater scattering sensitivity to H atoms, could help to resolve this by determining the protonation states within the active site of the enzyme. As the first step in the process of investigating the mechanism of action of D-xylose isomerase from Streptomyces rubiginosus using neutron diffraction, data to better than 2.0 A were measured from the unliganded protein at the Los Alamos Neutron Science Center Protein Crystallography Station. Measurement of these neutron diffraction data represents several milestones: this is one of the largest biological molecules (a tetramer, MW approximately 160 000 Da, with unit-cell lengths around 100 A) ever studied at high resolution using neutron diffraction. It is also one of the first proteins to be studied using time-of-flight techniques. The success of the initial diffraction experiments with D-xylose isomerase demonstrate the power of spallation neutrons for protein crystallography and should provide further impetus for neutron diffraction studies of biologically active and significant proteins. Further data will be measured from the enzyme with bound substrates and inhibitors in order to provide the specific information needed to clarify the catalytic mechanism of this enzyme.

Two-Metal Binding Motifs in Protein Crystal Structures

The binding of two metal ions that are in close proximity in proteins is examined using a combination of (1) crystallographic structural database analyses and (2) density functional theory calculations on model complexes. Divalent magnesium and manganese ions are the focus of the present study. It is found that in all proteins in the Protein Databank that have two closely positioned magnesium or manganese ions, these metal ions are generally bridged by at least one negatively charged oxygen-containing group—carboxylate, phosphate, or sulfate. This group transfers (negative) electron density to the metal ions and this helps to reduce electrostatic repulsion in the region. The geometry of the two-metal complex appears to depend on the nature of the negatively charged group between them. When a single oxygen atom is also in a bridging position, the two metal ions are found to be closer together than when only a carboxylate group binds them together. This suggests that this bridging oxygen atom may be negatively charged, e.g., a hydroxide ion rather than a water molecule. Details of the geometry of such bridges and the relevant motifs that are found in crystal structures are described.

C-H···O hydrogen bonds in molecular complexes of 1,3,5-trinitrobenzene with some N-heterocycles

The crystal structures of the molecular complexes of sym-trinitrobenzene (TNB) with acridine, 1,10-phenanthroline and phenazine are discussed. In all three cases, the structures are held together by C–H⋯O and π⋯π interactions, and TNB forms hydrogen bonded dimers and tapes that are not found in its native crystal structure. Acridine and 1,10-phenanthroline yield 1 ∶ 1 complexes that have very similar structures. The related molecule phenazine, however, gives a different 2 ∶ 3 complex in which guest exchange, as seen in other recently reported examples, is not observed. A case is made for the reporting of such ‘low yield’ supramolecular reactions because they still provide valuable information about the packing characteristics of organic molecules.

Evidence for the characterisation of the C–H···π interaction as a weak hydrogen bond: toluene and chlorobenzene solvates of 2,3,7,8-tetraphenyl-1,9,10-anthyridine

The crystal structures of the toluene and chlorobenzene solvates of 2,3,7,8-tetraphenyl-1,9,10-anthyridine are nearly identical save for differences in the mode of solvent inclusion; these differences have an important bearing on the nature of the C–H···π interactions in these structures.

Matching of molecular and supramolecular symmetry. An exercise in crystal engineering

With the aim of understanding the transfer of molecular threefold symmetry into supramolecular systems, the crystal structures of 2,4,6-tris(5-chloro-3-pyridyloxy)-1,3,5-triazine, 1,3,5-tris(3-methylphenyl)benzene and 1,3,5-tripyrrolylbenzene are described. In all three cases, C3 molecular symmetry is carried over into hexagonal crystal packing. This is rationalized in terms of the supramolecular or void symmetry and the relevant intermolecular interactions.

Melting-points of the meta- and para-isomers of anisylpinacolone

The generally higher melting-point of a para-disubstituted benzene relative to the corresponding meta-isomer has been ascribed to the fact that, being more symmetrical, it can pack more tightly. Exceptionally, it was observed that whereas m-anisylpinacolone melts at 58.0 °C, the para-isomer melts lower at 39.5 °C. In this work we have attempted to understand this apparent anomaly. The crystal structures of both isomers were determined and the packing analysed. Energy calculations of the static structures and molecular dynamics (MD) simulations at temperatures just below the respective melting-points were performed. The structure analyses indicate that the intermolecular contacts are comparably weak in the two cases, and do not appear to be the direct cause of the melting-point difference. Thermal motion analysis, packing energies and MD simulations on minicrystals indicate the importance of both enthalpic and entropic factors in the melting behaviour of the two isomers. The higher melting point of the meta-isomer could originate from both a smaller ΔSf and higher ΔHf relative to the para-isomer. Copyright

Unusually long cooperative chain of seven hydrogen bonds. An alternative packing type for symmetrical phenols

Conformational flexibility in a symmetrical tris-phenol leads to close packed structures that are also characterised by an extended though finite cooperative chain of hydrogen bonds.

4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone, a Nicotine-derived Carcinogenic Nitrosaminoketone (NNK): Three-dimensional Structure

The three-dimensional structure of the carcinogenic nicotine-derived nitrosaminoketone, 4-(methyl-nitrosamino)-l-(3-pyridyl)-l-butanone, has been determined by X-ray crystallographic techniques. The molecule is essentially planar except for the methylnitrosamine group which is oriented at a dihedral angle of 68.7° to the pyridine ring. Molecules pack by way of —H⋯O interactions that involve the —NNO group.