Comparison of Spatial Structures and Packaging of Phosphorybosil Pyrophosphate Synthetase 2 from Thermus thermophilus HB27 in Rhombohedral and Tetragonal Crystals

We report the spatial structure of phosphoribosyl pyrophosphate synthetase 2 from the thermophilic bacterium Thermus thermophilus HB27 (TthPRPPS2) obtained at a 1.85 Å resolution using a diffraction set collected from rhombohedral crystals (space group R32-h), grown with lithium sulfate as a precipitant. This crystal structure was compared with the structure of TthPRPPS2, previously obtained at a 2.2 Å resolution using diffraction sets from the tetragonal crystals (space group P41212), grown with ammonium sulfate as a precipitant. The comparison of these structures allows the study of the differences between protein molecules in both crystalline structures, as well as the packaging of enzyme molecules in crystals of both spatial groups. Our results may contribute to the research of the structural basis of catalytic activity and substrate specificity of this enzyme.

Coherent crystal branches: the impact of tetragonal symmetry on the 2D confined polymer nanostructure

The symmetry of polymer crystals greatly affects the optical, thermal conductivity and mechanical properties of the materials. Past studies have shown that the two-dimensional (2D) confined crystallization of polymer nanorods could produce anisotropic structures. However, few researchers have focused on understanding confined nanostructures from the perspective of crystal symmetry. In this research, we demonstrate the molecular chain self-assembly of tetragonal crystals under cylindrical confinement. We specifically selected poly(4-methyl-1-pentene) (P4MP1) with a 41 or 72 helical conformation (usually crystallizing with a tetragonal lattice) as the model polymer. We found a coherent crystal branching of the tetragonal crystal in the P4MP1 nanorods. The unusual 45°- and 135°-{200} diffractions and the meridional 220 diffraction (from 45°-tilted crystals) have shown a uniform crystal branching between the a 1-axis crystals and the 45°-tilted crystals in the rod long axis, which originates from a structural defect associated with tetragonal symmetry. Surprisingly, this chain packing defect in the tetragonal cell can be controlled to develop along the rod long axis in 2D confinement.

Wave propagation in micromorphic anisotropic continua with an application to tetragonal crystals

We study the coupled macroscopic and lattice wave propagation in anisotropic crystals seen as continua with affine microstructure (or micromorphic). In the general case, we obtain qualitative information on the frequencies and the dispersion relations. These results are then specialized to crystals of the tetragonal point group for various propagation directions: exact representation for the acoustic and optic frequencies and for the coupled vibrations modes are obtained for propagation directions along the tetragonal c-axis.

Lysozyme crystals dyed with bromophenol blue: where has the dye gone?

Protein crystals can easily be coloured by adding dyes to their mother liquor, but most structures of these protein–dye complexes remain unsolved. Here, structures of lysozyme in complex with bromophenol blue obtained by soaking orthorhombic and tetragonal crystals in a saturated solution of the dye at different pH values from 5.0 to 7.5 are reported. Two different binding sites can be found in the lysozyme–bromophenol blue crystals: binding site I is located near the amino- and carboxyl-termini, while binding site II is located adjacent to helices α1 (residues 4–15) and α3 (residues 88–100). In the orthorhombic crystals soaked at pH 7.0, binding of the dye takes place in both sites without significant changes in the unit cell. However, soaking tetragonal crystals with bromophenol blue results in two different complexes. Crystals soaked at pH 5.5 (HEWL-T1) show a single dye molecule bound to site II, and the crystals belong to space group P43212 without significant changes in the unit cell (a = b = 78.50, c = 37.34 Å). On the other hand, crystals soaked at pH 6.5 in the presence of imidazole (HEWL-T2) show up to eight molecules of the dye bound to site II, and display changes in space group (P212121) and unit cell (a = 38.00, b = 76.65, c = 84.86 Å). In all of the structures, the dye molecules are placed at the surface of the protein near to positively charged residues accessible through the main solvent channels of the crystal. Differences in the arrangement of the dye molecules at the surface of the protein suggest that the binding is not specific and is mainly driven by electrostatic interactions.

Nematicity with a twist: Rotational symmetry breaking in a moiré superlattice

Motivated by recent reports of nematic order in twisted bilayer graphene (TBG), we investigate the impact of the triangular moiré superlattice degrees of freedom on nematicity. In TBG, the nematic order parameter is not Ising like, as in tetragonal crystals, but has a three-state Potts character related to the threefold rotational symmetry (C3z) of the moiré superlattice. We find that, even in the presence of static strain that explicitly breaks the C3z symmetry, the system can still undergo a nematic-flop phase transition that spontaneously breaks in-plane twofold rotations. Moreover, elastic fluctuations, manifested as acoustic phonons, mediate a nemato-orbital coupling that ties the nematic director orientation to certain soft directions in momentum space, rendering the Potts-nematic transition mean field and first order. In contrast to the case of rigid crystals, the Fermi surface hot spots associated with these soft directions are maximally coupled to low-energy nematic fluctuations in the moiré superlattice case.

The structure of an iron-containing alcohol dehydrogenase from a hyperthermophilic archaeon in two chemical states

An iron-containing alcohol dehydrogenase (FeADH) from the hyperthermophilic archaeonThermococcus thioreducenswas crystallized in unit cells belonging to space groupsP21,P212121andP43212, and the crystal structures were solved at 2.4, 2.1 and 1.9 Å resolution, respectively, by molecular replacement using the FeADH fromThermotoga maritima(Schwarzenbacheret al., 2004) as a model. In the monoclinic and orthorhombic crystals the dehydrogenase (molecular mass 41.5 kDa) existed as a dimer containing a twofold noncrystallographic symmetry axis, which was crystallographic in the tetragonal crystals. In the monoclinic and orthorhombic asymmetric units one molecule contained iron and an NADP molecule, while the other did not. The tetragonal crystals lacked both iron and NADP. The structure is very similar to that of the FeADH fromT. maritima(average r.m.s. difference for Cαatoms of 1.8 Å for 341 aligned atoms). The iron, which is internally sequestered, is bound entirely by amino acids from one domain: three histidines and one aspartic acid. The coenzyme is in an extended conformation, a feature that is common to the large superfamily of NADH-dependent dehydrogenases that share a classical nucleotide-binding domain. A long broad tunnel passes entirely through the enzyme between the two domains, completely encapsulating the coenzyme.