Structure of the Bacterial Cellulose Ribbon and Its Assembly-Guiding Cytoskeleton by Electron Cryotomography.

Cellulose is a widespread component of bacterial biofilms, where its properties of exceptional water retention, high tensile strength, and stiffness prevent dehydration and mechanical disruption of the biofilm. Bacteria in the genus Gluconacetobacter secrete crystalline cellulose, with a structure very similar to that found in plant cell walls. How this higher-order structure is produced is poorly understood. We used cryo-electron tomography and focused-ion-beam milling of native bacterial biofilms to image cellulose-synthesizing Gluconacetobacter hansenii and Gluconacetobacter xylinus bacteria in a frozen-hydrated, near-native state. We confirm previous results suggesting that cellulose crystallization occurs serially following its secretion along one side of the cell, leading to a cellulose ribbon that can reach several micrometers in length and combine with ribbons from other cells to form a robust biofilm matrix. We were able to take direct measurements in a near-native state of the cellulose sheets. Our results also reveal a novel cytoskeletal structure, which we have named the cortical belt, adjacent to the inner membrane and underlying the sites where cellulose is seen emerging from the cell. We found that this structure is not present in other cellulose-synthesizing bacterial species, Agrobacterium tumefaciens and Escherichia coli 1094, which do not produce organized cellulose ribbons. We therefore propose that the cortical belt holds the cellulose synthase complexes in a line to form higher-order cellulose structures, such as sheets and ribbons.IMPORTANCE This work's relevance for the microbiology community is twofold. It delivers for the first time high-resolution near-native snapshots of Gluconacetobacter spp. (previously Komagataeibacter spp.) in the process of cellulose ribbon synthesis, in their native biofilm environment. It puts forward a noncharacterized cytoskeleton element associated with the side of the cell where the cellulose synthesis occurs. This represents a step forward in the understanding of the cell-guided process of crystalline cellulose synthesis, studied specifically in the Gluconacetobacter genus and still not fully understood. Additionally, our successful attempt to use cryo-focused-ion-beam milling through biofilms to image the cells in their native environment will drive the community to use this tool for the morphological characterization of other studied biofilms.

Double differential cross sections for proton induced electron emission from molecular analogues of DNA constituents for energies in the Bragg peak region.

For track structure simulations in the Bragg peak region, measured electron emission cross sections of DNA constituents are required as input for developing parameterized model functions representing the scattering probabilities. In the present work, double differential cross sections were measured for the electron emission from vapor-phase pyrimidine, tetrahydrofuran, and trimethyl phosphate that are structural analogues to the base, the sugar, and the phosphate residue of the DNA, respectively. The range of proton energies was from 75 keV to 135 keV, the angles ranged from 15° to 135°, and the electron energies were measured from 10 eV to 200 eV. Single differential and total electron emission cross sections are derived by integration over angle and electron energy and compared to the semi-empirical Hansen-Kocbach-Stolterfoht (HKS) model and a quantum mechanical calculation employing the first Born approximation with corrected boundary conditions (CB1). The CB1 provides the best prediction of double and single differential cross section, while total cross sections can be fitted with semi-empirical models. The cross sections of the three samples are proportional to their total number of valence electrons.

Solid-state tautomeric structure and invariom refinement of a novel and potent HIV integrase inhibitor.

The conformation and tautomeric structure of (Z)-4-[5-(2,6-difluorobenzyl)-1-(2-fluorobenzyl)-2-oxo-1,2-dihydropyridin-3-yl]-4-hydroxy-2-oxo-N-(2-oxopyrrolidin-1-yl)but-3-enamide, C27H22F3N3O5, in the solid state has been resolved by single-crystal X-ray crystallography. The electron distribution in the molecule was evaluated by refinements with invarioms, aspherical scattering factors by the method of Dittrich et al. [Acta Cryst. (2005), A61, 314-320] that are based on the Hansen-Coppens multipole model [Hansen & Coppens (1978). Acta Cryst. A34, 909-921]. The ß-diketo portion of the molecule exists in the enol form. The enol -OH hydrogen forms a strong asymmetric hydrogen bond with the carbonyl O atom on the ß-C atom of the chain. Weak intramolecular hydrogen bonds exist between the weakly acidic α-CH hydrogen of the keto-enol group and the pyridinone carbonyl O atom, and also between the hydrazine N-H group and the carbonyl group in the ß-position from the hydrazine N-H group. The electrostatic properties of the molecule were derived from the molecular charge density. The molecule is in a lengthened conformation and the rings of the two benzyl groups are nearly orthogonal. Results from a high-field (1)H and (13)C NMR correlation spectroscopy study confirm that the same tautomer exists in solution as in the solid state.

Experimental and database-transferred electron-density analysis and evaluation of electrostatic forces in coumarin-102 dye.

The electron-density distribution of a new crystal form of coumarin-102, a laser dye, has been investigated using the Hansen-Coppens multipolar atom model. The charge density was refined versus high-resolution X-ray diffraction data collected at 100 K and was also constructed by transferring the charge density from the Experimental Library of Multipolar Atom Model (ELMAM2). The topology of the refined charge density has been analysed within the Bader `Atoms In Molecules' theory framework. Deformation electron-density peak heights and topological features indicate that the chromen-2-one ring system has a delocalized π-electron cloud in resonance with the N (amino) atom. The molecular electrostatic potential was estimated from both experimental and transferred multipolar models; it reveals an asymmetric character of the charge distribution across the molecule. This polarization effect is due to a substantial charge delocalization within the molecule. The molecular dipole moments derived from the experimental and transferred multipolar models are also compared with the liquid and gas-phase dipole moments. The substantial molecular dipole moment enhancements observed in the crystal environment originate from the crystal field and from intermolecular charge transfer induced and controlled by C-H···O and C-H···N intermolecular hydrogen bonds. The atomic forces were integrated over the atomic basins and compared for the two electron-density models.

Is it possible to derive quantitative information on polarization of electron density from the multipolar model?

The accuracy of electrostatic properties estimated from the Hansen-Coppens multipolar model was verified. Tests were carried out to determine whether the multipolar model is accurate enough to study changes of electrostatic properties under the influence of a crystal field. Perturbed and unperturbed electron densities of individual molecules of amino acids and dipeptides were obtained from cluster and perturbation theory calculations. This enabled the changes in electrostatic properties values caused by polarization of the electron density to be characterized. Multipolar models were then fitted to the subsequent theoretical electron densities. The study revealed that electrostatic properties obtained from the multipolar models are significantly different from those obtained directly from the theoretical densities. The electrostatic properties of isolated molecules are reproduced better by multipolar models than the electrostatic properties of molecules in a crystal. Changes of electrostatic properties caused by perturbation of electron density due to the crystal environment are barely described by the multipolar model. As a consequence, the electrostatic properties obtained from multipolar models fitted to the perturbed theoretical densities derived either from cluster or periodic calculations do not differ much from those estimated from multipolar models fitted to densities of isolated molecules. The main reason for this seems to be related to an inadequate description of electron-density polarization in the vicinity of the nuclei by the multipolar model.

Experimental and theoretical charge density distribution in a host-guest system: synthetic terephthaloyl receptor complexed to adipic acid.

The experimental charge density distributions in a host-guest complex have been determined. The host, 1,4-bis[[(6-methylpyrid-2-yl)amino]carbonyl]benzene (1) and guest, adipic acid (2). The molecular geometries of 1 and 2 are controlled by the presence in the complex of intermolecular hydrogen bonding interactions and the presence in the host 1 of intramolecular hydrogen bonding motifs. This system therefore serves as an excellent model for studying noncovalent interactions and their effects on structure and electron density, and the transferability of electron distribution properties between closely related molecules. For the complex, high resolution X-ray diffraction data created the basis for a charge density refinement using a pseudoatomic multipolar expansion (Hansen-Coppens formalism) against extensive low-temperature (T = 100 K) single-crystal X-ray diffraction data and compared with a selection of theoretical DFT calculations on the same complex. The molecules crystallize in the noncentrosymmetric space group P2(1)2(1)2(1) with two independent molecules in the asymmetric unit. A topological analysis of the resulting density distribution using the atoms in molecules methodology is presented along with multipole populations, showing that the host and guest structures are relatively unaltered by the geometry changes on complexation. Three separate refinement protocols were adopted to determine the effects of the inclusion of calculated hydrogen atom anisotropic displacement parameters on hydrogen bond strengths. For the isotropic model, the total hydrogen bond energy differs from the DFT calculated value by ca. 70 kJ mol(-1), whereas the inclusion of higher multipole expansion levels on anisotropic hydrogen atoms this difference is reduced to ca. 20 kJ mol(-l), highlighting the usefulness of this protocol when describing H-bond energetics.

The crystal structures of yeast Get3 suggest a mechanism for tail-anchored protein membrane insertion.

Tail-anchored (TA) proteins represent a unique class of membrane proteins that contain a single C-terminal transmembrane helix. The post-translational insertion of the yeast TA proteins into the ER membrane requires the Golgi ER trafficking (GET) complex which contains Get1, Get2 and Get3. Get3 is an ATPase that recognizes and binds the C-terminal transmembrane domain (TMD) of the TA proteins. We have determined the crystal structures of Get3 from two yeast species, S. cerevisiae and D. hansenii, respectively. These high resolution crystal structures show that Get3 contains a nucleotide-binding domain and a "finger" domain for binding the TA protein TMD. A large hydrophobic groove on the finger domain of S. cerevisiae Get3 structure might represent the binding site for TMD of TA proteins. A hydrophobic helix from a symmetry-related Get3 molecule sits in the TMD-binding groove and mimics the TA binding scenario. Interestingly, the crystal structures of the Get3 dimers from S. cerevisiae and D. hansenii exhibit distinct conformations. The S. cerevisiae Get3 dimer structure does not contain nucleotides and maintains an "open" conformation, while the D. hansenii Get3 dimer structure binds ADP and stays in a "closed" conformation. We propose that the conformational changes to switch the Get3 between the open and closed conformations may facilitate the membrane insertions for TA proteins.

Topological features of both electron density and electrostatic potential in the bis(thiosemicarbazide)zinc(II) dinitrate complex.

The experimental electron density of the bis(thiosemicarbazide)zinc(II) dinitrate complex, [Zn(CH5N3S)2](NO3)2,was studied. The Hansen-Coppens multipole model was used to extract the electron density from high-resolution X-ray diffraction data collected at 100 K. Careful strategies were designed for the electron density refinements regarding the charge transfer between the anionic and the cationic parts of the complex. Particular attention was also paid to the treatment of the electron density of the zinc atom interacting with two thiosemicarbazide ligands in a tetrahedral coordination. Nevertheless, the filled 3d valence shell of Zn was found unperturbed, and only the 4s shell was engaged in the metal-ligand interaction. Topological properties of both electron density and electrostatic potential, including kinetic and potential energy densities, and atomic charges were reported to quantify a metal-ligand complex with particular Zn-S and Zn-N bonds and hydrogen-bonding features. Chemical activities were screened through the molecular surface on which the three-dimensional electrostatic potential function was projected. The experimental results were compared to those obtained from gas-phase quantum calculations, and a good agreement was reached between these two approaches. Finally, among other electrostatic potential critical points, the values at the maxima corresponding to the nuclear sites were used as indices of the hydrogen-bonding capacity of the thiosemicarbazide ligand.

Binding of genistein to the estrogen receptor based on an experimental electron density study.

In a continuing effort to determine a relationship between the biological function and the electronic properties of steroidal and nonsteroidal estrogens by analysis of the submolecular properties, an experimental charge density study has been pursued on the nonsteroidal phytoestrogen, genistein. X-ray diffraction data were obtained using a Rigaku R-Axis Rapid high-power rotating anode diffractometer with a curved image plate detector at 20(1) K. The total electron density was modeled using the Hansen-Coppens multipole model. Genistein packs in puckered sheets characterized by intra- and intermolecular hydrogen bonds while weaker intermolecular hydrogen bonds (O...H-C) exist between the sheets. A topological analysis of the electron density of genistein was then completed to characterize all covalent bonds, three O...H-O and four O...H-C intermolecular hydrogen bonds. Two O...H-O hydrogen bonds are incipient (partially covalent) type bonds, while the other O...H-O hydrogen bond and O...H-C hydrogen bonds are of the pure closed-shell interaction type. In addition, two intermolecular H...H interactions have also been characterized from the topology of the electron density. The binding of genistein to the estrogen receptor is discussed in terms of the electrostatic potential derived from the electron density distribution.

Experimental evidence for the existence of non-nuclear maxima in the electron-density distribution of metallic beryllium. A comparative study of the maximum entropy method and the multipole refinement method.

The electron-density distribution (EDD) of metallic beryllium has been derived from the structure factors of Larsen & Hansen [(1984). Acta Cryst. B40, 169-179] using the maximum entropy method (MEM). Subsequent topological analysis reveals non-nuclear maxima (NNM) in the EDD. Plots of the gradient field of the electron density illustrates this finding. A possible critical-point network for the hexagonal close-packed (h.c.p.) structure of beryllium is suggested. It is thus demonstrated that it is possible to obtain detailed topological information about the electron density in metallic beryllium without the use of a structural model. In order to test the findings of the MEM, the same set of structure factors were analysed using the multipole refinement method (MRM). Use of the MRM also reveals NNM. The results of the two different approaches to electron-density analysis are contrasted and discussed. Expressed within the framework of the theory of atoms in molecules, our results suggest that the h.c.p. structure of beryllium has no Be atoms directly bonded to other Be atoms. The structure is held together through a three-dimensional network of bonds between the NNM and Be atoms as well as between different NNM. The topological analysis thus reveals that the beryllium structure has important interactions connecting Be atoms of different basal plane layers. The breaking of these interactions when forming a surface may explain the abnormally large expansion of the inter-layer distance in the beryllium surface structure.