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PubMed1994

Crystal structure of beta-D-cellotetraose hemihydrate with implications for the structure of cellulose II.

The crystal structure of beta-D-cellotetraose shows the same molecule packing as cellulose II, with two antiparallel molecules in the unit cell: For cellulose II, the orientation of the C6-O6 bonds has been described as gauche-trans and trans-gauche, respectively, for the two antiparallel molecules, which otherwise have identical conformations. In contrast, in beta-D-cellotetraose all C6-O6 bonds are gauche-trans, but the conformations of the two antiparallel molecules are different. Energy minimization and molecular dynamics studies suggest that the structure of cellulose II should be reinvestigated in light of these findings.

Carbohydrate Conformation↗
PubMed2004

Preparation of acentric porous coordination frameworks from an interpenetrated diamondoid array through anion-exchange procedures: crystal structures and properties.

The formation, crystal structures, and properties of a series of three-dimensional (3-D) Cu(II) coordination polymers, [[Cu(L)2(H2O)2](PF6)2(H2O)(1.25)]n (1), [[CuL(N3)2](H2O)(1.5)]n (2), and [[CuL(H2O)(SO4)](H2O)2]n (3), with an angular bridging ligand 2,5-bis(4-pyridyl)-1,3,4-oxadiazole (L) are reported. Complex 1 crystallizes in the tetragonal I4(1)/a space group (a = b = 13.462(2) A, c = 46.47(1) A, Z = 8), complex 2 in the orthorhombic Pna2(1) space group (a = 6.379(2) A, b = 10.060(3) A, c = 27.232(9) A, Z = 4), and complex 3 in the orthorhombic P2(1)2(1)2(1) space group (a = 5.510(2) A, b = 10.576(4) A, c = 28.34(1) A, Z = 4). Different polymeric frameworks are obtained by only varying the counterions. These include the 2-fold interpenetrated diamondoid structure of 1, the acentric alpha-Po network of 2, and the chiral open framework of 3 with (6(3)).(6(9).8) topology. The interesting anion-exchange, porous, and magnetic properties of these coordination supramolecules have been investigated in detail.

Journal Article↗
PubMed2000

Structural analysis of the transcriptional activation region on Fis: crystal structures of six Fis mutants with different activation properties.

The Fis protein regulates gene expression in Escherichia coli by activating or repressing transcription of a variety of genes. Fis can activate transcription when bound to DNA upstream of the RNA-polymerase-binding site, such as in the rrnB P1 promoter, or when bound to a site overlapping the -35 RNA polymerase binding site, such as in the proP P2 promoter. It has been suggested that transcriptional activation in both promoters results from interactions between specific amino acids within a turn connecting the B and C helices (the BC turn) in Fis and the C-terminal domain of the alpha-subunit of RNA polymerase (alphaCTD of RNAP). Here, crystal structures of six Fis BC turn mutants with different transcriptional activation properties, Q68A, R71Y, R71L, G72A, G72D and Q74A, were determined at 1.9 to 2.8 A resolution. Two of these mutants, R71Y and R71L, crystallized in unit cells which are different from that of wild-type Fis, and the structure of R71L offers the most complete Fis model to date in that the extended structure of the N-terminal region is revealed. The BC turn in all of these mutant structures remains in a nearly identical gamma gamma beta-turn conformation as present in wild-type Fis. Analyses of the molecular surfaces of the transactivation region of the mutants suggest that several residues in or near the BC turn, including Gln68, Arg71, Gly72 and Gln74, form a ridge that could contact the alphaCTD of RNAP on one side. The structures and biochemical properties of the mutants suggest that Arg71 is the most critical residue for contacting RNAP within this ridge and that the glycine at position 72 helps to stabilize the structure.

Amino Acid Substitution↗
PubMed2005

Crystal structure and structural stability of acylphosphatase from hyperthermophilic archaeon Pyrococcus horikoshii OT3.

To elucidate the structural basis for the high stability of acylphosphatase (AcP) from Pyrococcus horikoshii OT3, we determined its crystal structure at 1.72 A resolution. P. horikoshii AcP possesses high stability despite its approximately 30% sequence identity with eukaryotic enzymes that have moderate thermostability. The overall fold of P. horikoshii AcP was very similar to the structures of eukaryotic counterparts. The crystal structure of P. horikoshii AcP shows the same fold betaalphabetabetaalphabeta topology and the conserved putative catalytic residues as observed in eukaryotic enzymes. Comparison with the crystal structure of bovine common-type AcP and that of D. melanogaster AcP (AcPDro2) as representative of eukaryotic AcP revealed some significant characteristics in P. horikoshii AcP that likely play important roles in structural stability: (1) shortening of the flexible N-terminal region and long loop; (2) an increased number of ion pairs on the protein surface; (3) stabilization of the loop structure by hydrogen bonds. In P. horikoshii AcP, two ion pair networks were observed one located in the loop structure positioned near the C-terminus, and other on the beta-sheet. The importance of ion pairs for structural stability was confirmed by site-directed mutation and denaturation induced by guanidium chloride.

Acid Anhydride Hydrolases↗
PubMed1985

Refined crystal structure of deoxyhemoglobin S. II. Molecular interactions in the crystal.

The refined crystal structure of deoxyhemoglobin S (Padlan, E. A., and Love, W. E. (1985) J. Biol. Chem. 260, 8272-8279) was used to analyze in detail the molecular interactions between hemoglobin tetramers in the crystal. The analysis confirms the close similarity and also the nonequivalence of the molecular interactions involving the two independent tetramers in the asymmetric unit of the crystal. The residue at the site of the hemoglobin S mutation, beta 6, is intimately involved in the lateral contacts between adjacent molecules. The molecular contacts in the crystals of deoxyhemoglobin S, deoxyhemoglobin A, and deoxyhemoglobin F were compared; some contacts involve the same regions of the molecule although the details of the interactions are very different. The effect of introducing an R state tetramer into the deoxyhemoglobin S strands was investigated using the known structure of carbon monoxyhemoglobin A. It was found that substituting a molecule of carbon monoxyhemoglobin A for one of the deoxyhemoglobin S tetramers results in extensive molecular interpenetration.

Carboxyhemoglobin↗
PubMed2004

Epitaxial growth of a colloidal hard-sphere hcp crystal and the effects of epitaxial mismatch on crystal structure.

We demonstrate the epitaxial growth of hard-sphere hcp and double hcp crystals using a surface pattern that directly dictates the stacking sequence. A detailed three-dimensional analysis based on real-space measurements is performed on crystal structure as a function of template-crystal mismatch, which demonstrates the possibilities of colloidal epitaxy as a model system for studying the effects of a patterned substrate on crystal structure. Perfect template-induced hcp-crystal growth occurs at an isotropically deformed template. At deformed lattices we observe growth of a non-close-packed superstructure and of a perfect (100)-aligned fcc crystal. Small mismatches lead to increased out-of-plane displacements followed by a structural breakup in "crystal" grains where particle positions in successive layers are strictly periodic and "defect" grains where these positions are displaced with respect to each other. Large mismatches prevent crystallization in the surface layers. The volume fraction was found to vary drastically (up to about 20% ) as a function of template deformation.

Journal Article↗
PubMed2006

Multiple solvent crystal structures: probing binding sites, plasticity and hydration.

Multiple solvent crystal structures (MSCS) of porcine pancreatic elastase were used to map the binding surface the enzyme. Crystal structures of elastase in neat acetonitrile, 95% acetone, 55% dimethylformamide, 80% 5-hexene-1,2-diol, 80% isopropanol, 80% ethanol and 40% trifluoroethanol showed that the organic solvent molecules clustered in the active site, were found mostly unclustered in crystal contacts and in general did not bind elsewhere on the surface of elastase. Mixtures of 40% benzene or 40% cyclohexane in 50% isopropanol and 10% water showed no bound benzene or cyclohexane molecules, but did reveal bound isopropanol. The clusters of organic solvent probe molecules coincide with pockets occupied by known inhibitors. MSCS also reveal the areas of plasticity within the elastase binding site and allow for the visualization of a nearly complete first hydration shell. The pattern of organic solvent clusters determined by MSCS for elastase is consistent with patterns for hot spots in protein-ligand interactions determined from database analysis in general. The MSCS method allows probing of hot spots, plasticity and hydration simultaneously, providing a powerful complementary strategy to guide computational methods currently in development for binding site determination, ligand docking and design.

Animals↗
PubMed2004

The 2.9A resolution crystal structure of malate dehydrogenase from Archaeoglobus fulgidus: mechanisms of oligomerisation and thermal stabilisation.

The crystal structure of malate dehydrogenase from the hyperthermophilic archaeon Archeoglobus fulgidus, in complex with its cofactor NAD, was solved at 2.9A resolution. The crystal structure shows a compact homodimer with one coenzyme bound per subunit. The substrate binding site is occupied by a sulphate ion. In order to gain insight into adaptation mechanisms, which allow the protein to be stable and active at high temperatures, the 3D structure was compared to those of several thermostable and hyperthermostable homologues, and to halophilic malate dehydrogenase. The hyperthermostable A. fulgidus MalDH protein displays a reduction of the solvent-exposed surface, an optimised compact hydrophobic core, a high number of hydrogen bonds, and includes a large number of ion pairs at the protein surface. These features occur concomitantly with a reduced number of residues in the protein subunit, due to several deletions in loop regions. The loops are further stiffened by ion pair links with secondary structure elements. A. fulgidus malate dehydrogenase is the only dimeric protein known to date that belongs to the [LDH-like] MalDH family. All the other known members of this family are homo-tetramers. The crystal structures revealed that the association of the dimers to form tetramers is prevented by several deletions, taking place at the level of two loops that are known to be essential for the tetramerisation process within the LDH and [LDH-like] MalDH enzymes.

Archaeoglobus fulgidus↗
PubMed2005

Ab initio crystal structure prediction-I. Rigid molecules.

A new methodology for the prediction of molecular crystal structures using only the atomic connectivity of the molecule under consideration is presented. The approach is based on the global minimization of the lattice enthalpy of the crystal. The modeling of the electrostatic interactions is accomplished through a set of distributed charges that are optimally and automatically selected and positioned based on results of quantum mechanical calculations. A four-step global optimization algorithm is used for the identification of the local minima of the lattice enthalpy surface. A parallelized implementation of the algorithm permits a much more extensive search of the solution space than has hitherto been possible, allowing the identification of crystal structures in less frequently occurring space groups and with more than one molecule in the asymmetric unit. The algorithm has been applied successfully to the prediction of the crystal structures of 3-aza-bicyclo(3.3.1)nonane-2,4-dione (P2(1)/a, Z' = 1), allopurinol (P2(1)/c, Z' = 1), 1,3,4,6,7,9-hexa-azacycl(3.3.3)azine (Pbca, Z' = 2), and triethylenediamine (P6(3)/m, Z' = 1). In all cases, the experimentally known structure is among the most stable predicted structures, but not necessarily the global minimum.

Journal Article↗
PubMed2005

Analysis of strategies to improve the directionality of square lattice band-edge photonic crystal structures.

Recently, photonic crystal band-edge structures have been analyzed in the literature. However, most devices that have been presented so far emit light in different directions. We present a modal analysis (no gain included) of a few schemes to improve the directionality of these devices, i.e., in such a way that light that exits from them will travel mainly in a certain direction, eventually coupling its energy to a wide waveguide.

Journal Article↗
PubMed1999

The structural basis of Rho effector recognition revealed by the crystal structure of human RhoA complexed with the effector domain of PKN/PRK1.

The small G protein Rho has emerged as a key regulator of cellular events involving cytoskeletal reorganization. Here we report the 2.2 A crystal structure of RhoA bound to an effector domain of protein kinase PKN/PRK1. The structure reveals the antiparallel coiled-coil finger (ACC finger) fold of the effector domain that binds to the Rho specificity-determining regions containing switch I, beta strands B2 and B3, and the C-terminal alpha helix A5, predominantly by specific hydrogen bonds. The ACC finger fold is distinct from those for other small G proteins and provides evidence for the diverse ways of effector recognition. Sequence analysis based on the structure suggests that the ACC finger fold is widespread in Rho effector proteins.

Amino Acid Motifs↗
PubMed1985

Nucleic acid binding drugs. Part XIII. Molecular motion in a drug-nucleic acid model system: thermal motion analysis of a proflavine-dinucleoside crystal structure.

The high-resolution crystal structure of the intercalation complex between proflavine and cytidylyl-3',5'-guanosine (CpG) has been studied by thermalmotion analysis. This has provided information on the translational and librational motions of individual groups in the complex. Many of these motions are similar to, though of larger magnitude than in uncomplexed dinucleosides. Pronounced librational effects were observed along the base pairs and in the plane of the drug chromophore.

Acridines↗
PubMed2006

Crystal structure of mammalian cysteine dioxygenase. A novel mononuclear iron center for cysteine thiol oxidation.

Cysteine dioxygenase is a mononuclear iron-dependent enzyme responsible for the oxidation of cysteine with molecular oxygen to form cysteine sulfinate. This reaction commits cysteine to either catabolism to sulfate and pyruvate or the taurine biosynthetic pathway. Cysteine dioxygenase is a member of the cupin superfamily of proteins. The crystal structure of recombinant rat cysteine dioxygenase has been determined to 1.5-A resolution, and these results confirm the canonical cupin beta-sandwich fold and the rare cysteinyltyrosine intramolecular cross-link (between Cys(93) and Tyr(157)) seen in the recently reported murine cysteine dioxygenase structure. In contrast to the catalytically inactive mononuclear Ni(II) metallocenter present in the murine structure, crystallization of a catalytically competent preparation of rat cysteine dioxygenase revealed a novel tetrahedrally coordinated mononuclear iron center involving three histidines (His(86), His(88), and His(140)) and a water molecule. Attempts to acquire a structure with bound ligand using either cocrystallization or soaking crystals with cysteine revealed the formation of a mixed disulfide involving Cys(164) near the active site, which may explain previously observed substrate inhibition. This work provides a framework for understanding the molecular mechanisms involved in thiol dioxygenation and sets the stage for exploration of the chemistry of both the novel mononuclear iron center and the catalytic role of the cysteinyl-tyrosine linkage.

Amino Acid Sequence↗
PubMed2001

Crystal structure of native and Cd/Cd-substituted Dioclea guianensis seed lectin. A novel manganese-binding site and structural basis of dimer-tetramer association.

Diocleinae legume lectins are a group of oligomeric proteins whose subunits display a high degree of primary structure and tertiary fold conservation but exhibit considerable diversity in their oligomerisation modes. To elucidate the structural determinants underlaying Diocleinae lectin oligomerisation, we have determined the crystal structures of native and cadmium-substituted Dioclea guianensis (Dguia) seed lectin. These structures have been solved by molecular replacement using concanavalin (ConA) coordinates as the starting model, and refined against data to 2.0 A resolution. In the native (Mn/Ca-Dguia) crystal form (P4(3)2(1)2), the asymmetric unit contains two monomers arranged into a canonical legume lectin dimer, and the tetramer is formed with a symmetry-related dimer. In the Cd/Cd-substituted form (I4(1)22), the asymmetric unit is occupied by a monomer. In both crystal forms, the tetrameric association is achieved by the corresponding symmetry operators. Like other legume lectins, native D. guianensis lectin contains manganese and calcium ions bound in the vicinity of the saccharide-combining site. The architecture of these metal-binding sites (S1 and S2) changed only slightly in the cadmium/cadmium-substituted form. A highly ordered calcium (native lectin) or cadmium (Cd/Cd-substituted lectin) ion is coordinated at the interface between dimers that are not tetrameric partners in a similar manner as the previously identified Cd(2+) in site S3 of a Cd/Ca-ConA. An additional Mn(2+) coordination site (called S5), whose presence has not been reported in crystal structures of any other homologous lectin, is present in both, the Mn/Ca and the Cd/Cd-substituted D. guianensis lectin forms. On the other hand, comparison of the primary and quaternary crystal structures of seed lectins from D. guianensis and Dioclea grandiflora (1DGL) indicates that the loop comprising residues 117-123 is ordered to make interdimer contacts in the D. grandiflora lectin structure, while this loop is disordered in the D. guianensis lectin structure. A single amino acid difference at position 131 (histidine in D. grandiflora and asparagine in D. guianensis) drastically reduces interdimer contacts, accounting for the disordered loop. Further, this amino acid change yields a conformation that may explain why a pH-dependent dimer-tetramer equilibrium exists for the D. guianensis lectin but not for the D. grandiflora lectin.

Binding Sites↗
PubMed1998

Crystal Structure, Electronic Structure, and Temperature-Dependent Raman Spectra of Tl[Ag(CN)(2)]: Evidence for Ligand-Unsupported Argentophilic Interactions.

The structure of thallium dicyanoargentate(I) has been determined crystallographically. The crystal structure shows an Ag-Ag distance of 3.11 Å. This is the shortest Ag-Ag distance reported for any silver dicyanide salt whose crystal structure has been determined. Raman spectra of the compound show four nu(C)(-)(N) peaks that are well-resolved in the 10-80 K temperature range. This result agrees well with group theory analysis. Extended Hückel calculations using relativistic wave functions have been carried out for two models which describe the interactions between the Ag(CN)(2)(-) ions within the crystal structure of Tl[Ag(CN)(2)]. The results of these calculations indicate the formation of potential wells at short Ag-Ag distances. The data in this study suggest the significance of ligand-unsupported silver-silver interactions (argentophilicity) in Tl[Ag(CN)(2)]. Tl-Ag interactions are determined to be insignificant in the compound. Tl[Ag(CN)(2)] crystallizes in the monoclinic space group P2(1)/c (No. 14), with a = 7.798(1) Å, b = 14.685(3) Å, c = 8.566(2) Å, beta = 91.66(2) degrees, Z = 8, R = 0.0643, and R(w) = 0.0899.

Journal Article↗
PubMed2006

Studying thermodynamic aspects of sublimation, solubility and solvation processes and crystal structure analysis of some sulfonamides.

Crystal structures of N-(2-chlorophenyl)-benzene-sulfonamide (I), N-(2,3-dichlorophenyl)-benzene-sulfonamide (II), N-(4-chlorophenyl)-benzene-sulfonamide (III) were solved by X-ray diffraction method. Temperature dependencies of saturated vapor pressure and thermodynamic functions of sublimation process were calculated (I: DeltaG(sub)(298)=50.4kJmol(-1); DeltaH(sub)(298)=114+/-1kJmol(-1); DeltaS(sub)(298)=213+/-3Jmol(-1)K(-1); II: DeltaG(sub)(298)=54.1kJmol(-1); DeltaH(sub)(298)=124.9+/-1.6kJmol(-1); DeltaS(sub)(298)=237+/-5Jmol(-1)K(-1); III: DeltaG(sub)(298)=49.9kJmol(-1); DeltaH(sub)(298)=98.6+/-1.9kJmol(-1); DeltaS(sub)(298)=163+/-5Jmol(-1)K(-1)). Thermochemical parameters of fusion process for the compounds were obtained. Enthalpies of evaporation were estimated from enthalpies of sublimation and fusion. Temperature dependencies of the solubility in water, n-octanol and n-hexane were measured. The thermodynamic functions of solubility and solvation processes were deduced. Specific and non-specific solvation terms were distinguished using the transfer from the "inert"n-hexane to the other solvents. The transfer processes of the molecules from water to n-octanol were analyzed and main driven forces were established.

1-Octanol↗
PubMed2005

Structural role of countertransport revealed in Ca(2+) pump crystal structure in the absence of Ca(2+).

Ca(2+)-ATPase of sarcoplasmic reticulum is an ATP-powered Ca(2+) pump but also a H(+) pump in the opposite direction with no demonstrated functional role. Here, we report a 2.4-A-resolution crystal structure of the Ca(2+)-ATPase in the absence of Ca(2+) stabilized by two inhibitors, dibutyldihydroxybenzene, which bridges two transmembrane helices, and thapsigargin, also bound in the membrane region. Now visualized are water and several phospholipid molecules, one of which occupies a cleft between two transmembrane helices. Atomic models of the Ca(2+) binding sites with explicit hydrogens derived by continuum electrostatic calculations show how water and protons fill the space and compensate charge imbalance created by Ca(2+)-release. They suggest that H(+) countertransport is a consequence of a requirement for maintaining structural integrity of the empty Ca(2+)-binding sites. For this reason, cation countertransport is probably mandatory for all P-type ATPases and possibly accompanies transport of water as well.

Animals↗