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PubMedDate not supplied

[Use of phase diagrams in crystallization of oligonucleotide duplexes. II. Setting of the crystallized samples].

Oligonucleotide crystallization technique based on the method of phase diagrams is described in detail with (pGpT)3.(pApC)3 hexamer as an example. The key point of the technique consists of dividing the multiparameter crystallization space into a set of regions, each of which corresponds to the precipitation of a duplex in complex with a certain number of counterions.

Crystallization↗
PubMed1989

Effect of crystal packing environment on conformation of the DNA duplex. Molecular structure of the A-DNA octamer d(G-T-G-T-A-C-A-C) in two crystal forms.

The structure of the octamer d(G-T-G-T-A-C-A-C) was determined in two different crystal forms, tetragonal P4(3)2(1)2 and hexagonal P6(1)22. Although in both forms the octamer adopts an A-DNA structure, there are significant conformational differences between them. In particular, the P-05' and the C5'-C4' bonds of the middle adenine (A5) residue exhibit a distorted trans-trans conformation in the tetragonal form, while they adopt the standard gauche-, gauche+ conformation in the hexagonal form. These differences can be correlated with certain features of the crystal packing interactions in the two forms. Furthermore, a comparison of the structures of various A-DNA octamers reveals that the A-form can be divided into two subclasses such that the hexagonal structures have helical and base pair parameters that fall closer to fiber A-DNA values, while in the tetragonal structures these parameters deviate more from fiber A-DNA. These results indicate that environment plays a major role in determining DNA conformation.

Base Composition↗
PubMed1988

Crystallization and preliminary analysis of crystals of apolipophorin III isolated from Locusta migratoria.

Crystals of apolipophorin III, isolated from the locust Locusta migratoria, have been reproducibly grown from ammonium sulfate solutions and are well suited for an x-ray crystallographic analysis. Locust apolipophorin III is a glycosylated protein with a molecular weight of 19,100 and interacts with lipophorin, the major lipoprotein complex in insects. The crystals belong to the space group P6122 or P6522 with unit cell dimensions of a = b = 67.5 A, c = 155.6 A and diffract to a nominal resolution of 2.5 A. They are physically robust and are stable in the x-ray beam for over a week. A complete native x-ray data set has been collected and processed to 3.0-A resolution.

Animals↗
PubMed1986

Crystallization and preliminary analysis of crystals of high potential iron-sulfur protein from Rhodospirillum tenue.

Large single crystals of the high potential iron-sulfur protein isolated from Rhodospirillum tenue strain 3761 have been obtained. They belong to the space group P2(1) with unit cell dimensions of a = 36.7 A, b = 52.6 A, c = 27.6 A, and beta = 90.8 degrees. There are two molecules in the asymmetric unit. Based on oscillation photographs, the crystals diffract to at least 1.6 A resolution. They are stable in the x-ray beam and appear suitable for a high resolution x-ray structure analysis.

Crystallization↗
PubMed1995

Influence of crystallization on strength and color of castable glass-ceramics containing two crystals.

The mechanical properties, color and transparency of glass-ceramics are highly dependent on the ceramming temperature and/or amount of the crystal phase in the glass matrix. In this study, the influence of crystallization on the strength and color, translucency of castable ceramics containing crystalline apatite and magnesium titanate were measured. It was concluded that magnesium titanate precipitated during ceramming, appeared to be an important factor in decreasing total transmittance and in determination of the color of glass-ceramics.

Apatites↗
PubMed2000

Unprecedented crystallization and X-ray crystal structure of racemic N(alpha)-(t-butyloxycarbonyl)-L-L-phenylalanine N-methoxy-N-methylamide.

Weinreb amide 3 was synthesized using isobutyl chloroformate, carbonyldiimidazole, or ethylcarbodiimide as the coupling agent in the reaction of Boc-phenylalanine with O,N-dimethylhydroxylamine hydrochloride. An optically active oil was isolated along with an optically inactive solid irrespective of the type of coupling agent used. Single crystal X-ray analysis of the solid revealed that it is a racemate. The molecular packing of the crystals reflect the stability of the racemate as opposed to an enantiomerically pure solid.

Calpain↗
PubMed2000

Dynamic analyses on induced-fit gaseous guest binding to organic crystals with a quartz-crystal microbalance

The inclusion behavior of gaseous guest molecules in a solid apohost, an orthogonal anthracene-bis(resorcinol)tetraol (1), was investigated with a quartz-crystal microbalance (QCM). Compound 1 forms crystals composed of molecular sheets bound together by an extensive hydrogen-bonded network. An apohost of 1 was cast onto a QCM and the binding of gaseous guest molecules was followed as a function of time by observing the decrease in the oscillation frequency, which is directly related to the increase in mass. Ethyl acetate and methyl ethyl ketone were significantly included into the apohost, whereas benzene and cyclohexane were simply adsorbed onto the surface of the solid; all these guests have similar vapor pressures at 25 degrees C. On the other hand, a host analogue 2, a tetramethoxy derivative of 1, barely included these guest molecules. The inclusion amount and the rate of inclusion of ethyl acetate or methyl ethyl ketone showed a drastic increase above a threshold concentration of guests in the gas phase. Thus, the structure of the apohost changed cooperatively in order to bind guest molecules above the threshold guest concentration. This cooperativity of the binding behavior was kinetically analyzed.

Journal Article↗
PubMed2004

Does hydrogen bonding matter in crystal engineering? Crystal structures of salts of isomeric ions.

The preparation and structure determinations of the crystalline salts [3,3'-H(2)bipy][PtCl(4)] (2), [2,2'-H(2)bipy][PtCl(4)] (3) and [1,4'-Hbipy][PtCl(4)] (4) and [3,3'-H(2)bipy][SbCl(5)] (6) and [1,4'-Hbipy][SbCl(5)] (8) are reported. In addition a redetermination of the structure of the metastable salt [4,4'-H(2)bipy][SbCl(5)] (5 b) in the corrected space group Pbcm is described. These structures are compared to those of the known salt [4,4'-H(2)bipy][PtCl(4)] (1), the stable triclinic form of [4,4'-H(2)bipy][SbCl(5)] (5 a) and [2,2'-H(2)bipy][SbCl(5)] (7). In the case of the salts of the rigid [PtCl(4)](2-) ion, structures 2, 3 and 4 are essentially isostructural despite the differing hydrogen-bonding capability of the cations. Similarly, among the salts of [SbCl(5)](2-) ions, structures 7 and 8 are essentially isostructural. Structure 6 differs from these in having a differing pattern of aggregation of the [SbCl(5)](2-) ions to form polymeric rather than tetrameric units. It is evident that local hydrogen-bonding interactions, although significant, are not the only or even the decisive influence on the crystal structures formed by these salts. These observations are not in good accord with the heuristic "sticky tecton" or supramolecular synthon models for synthetic crystallography or crystal engineering.

Journal Article↗
PubMed1992

The gene for human eosinophil Charcot-Leyden crystal protein directs expression of lysophospholipase activity and spontaneous crystallization in transiently transfected COS cells.

Expression of the gene encoding human eosinophil lysophospholipase, the Charcot-Leyden crystal (CLC) protein, was studied in transiently transfected COS cells. Recombinant CLC (rCLC) protein expression was demonstrated both by Western blot and radioimmunoassay inhibition analyses of transfected COS cell extracts and by immunofluorescent staining and ultrastructural immunogold analyses of intact cells. The rCLC protein was immunochemically indistinguishable from native eosinophil-derived CLC protein, and each transfected COS cell expressed approximately 11 pg of rCLC protein as determined by radioimmunoassay and assessment of transfection efficiency. Immunofluorescent microscopy and ultrastructural immunogold analyses localized rCLC protein to the nucleus, cytoplasm, and plasma membrane of COS cells. Lysates from transfected COS cells producing CLC protein expressed significant lysophospholipase activity. Furthermore, rCLC protein expressed in COS cells spontaneously formed the distinctive intracytoplasmic and intranuclear hexagonal bipyramidal crystals characteristic of the native eosinophil and basophil-derived protein. Expression of the CLC gene confirms the authenticity of the CLC cDNA, the expression of lysophospholipase activity by this unique eosinophil and basophil constituent, and will facilitate the routine purification of the active enzyme for in vitro and animal model studies of its role (or roles) in eosinophil and basophil associated allergic inflammation and eosinophil-parasite interactions.

Animals↗
PubMed1994

Crystallization and preliminary characterization of crystals of D-2-hydroxyisocaproate dehydrogenase from Lactobacillus casei.

D-2-hydroxyisocaproate dehydrogenase (D-HicDH) from Lactobacillus casei is a homodimeric enzyme with a molecular mass of 74.6 kDa. It catalyzes the reduction of a wide range of 2-ketocarboxylic acids to D-2-hydroxycarboxylic acids using NADH as co-substrate. The enzyme has been crystallized by vapor diffusion using ammonium sulfate as precipitant. The crystals belong to hexagonal space group type P6(3)22 with a = b = 134.1 A, c = 124.1 A and diffract X-rays to 3.0 A resolution. Packing considerations show that there are either one or two D-HicDH monomers in the asymmetric unit.

Alcohol Oxidoreductases↗
PubMed1999

The X-ray crystal structure of a Valpha2.6Jalpha38 mouse T cell receptor domain at 2.5 A resolution: alternate modes of dimerization and crystal packing.

We describe here the structure of a murine T cell receptor (TCR) Valpha2.6Jalpha38 (TCRAV2S6J38) domain, derived from a T cell hybridoma with specificity for the H-2Ddmajor histocompatibility complex class I molecule bound to a decamer peptide, P18-I10, from the HIV envelope glycoprotein gp120, determined by X-ray crystallography at 2.5 A resolution. Unlike other TCR Valpha domains that have been studied in isolation, this one does not dimerize in solution at concentrations below 1 mM, and the crystal fails to show dimer contacts that are likely to be physiological. In comparison to other Valpha domains, this Valpha2.6 shows great similarity in the packing of its core residues, and exhibits the same immunoglobulin-like fold characteristic of other TCR Valpha domains. There is good electron density in all three complementarity-determining regions (CDRs), where the differences between this Valpha domain and others are most pronounced, in particular in CDR3. Examination of crystal contacts reveals an association of Valpha domains distinct from those previously seen. Comparison with other Valpha domain structures reveals variability in all loop regions, as well as in the first beta strand where placement and configuration of a proline residue at position 6, 7, 8, or 9 affects the backbone structure. The great variation in CDR3 conformations among TCR structures is consistent with an evolving view that CDR3 of TCR plays a plastic role in the interaction of the TCR with the MHC/peptide complex as well as with CDR3 of the paired TCR chain.

Amino Acid Sequence↗
PubMed2000

Small crystals and small coils in variable-temperature single-crystal NMR.

Time savings by a factor of between 20 and 30 in the acquisition of multinuclear single-crystal (SC) NMR spectra have been obtained for submillimeter-size (0.01 to 0.03 mm(3)) single crystals when compared to recent results for (31)P and (87)Rb SC NMR. This gain in sensitivity is achieved by optimizing the filling factor using the smallest possible rf coil (2.0 mm inner diameter) for the specific SC probe design. Furthermore, this small coil is particularly useful for variable-temperature SC NMR studies. A probe design for such studies is presented and demonstrated experimentally.

Magnetic Resonance Spectroscopy↗
PubMed1988

The polarized UV-absorption spectra and the crystal structure of two different monoclinic crystal forms of the retinal homologue beta-8'-apocarotenal.

During the visual process, light absorption in the 11-cis retinylidene chromophore leads to a rapid cis-trans-isomerization which initiates the phototransduction step. Important spectroscopic properties of this chromophore can be derived from polarized UV-absorption spectra of crystalline 11-cis-retinal if a parallel X-ray structure analysis is performed. Several questions about the relation between molecular geometry and spectroscopic behavior could not be answered from these spectra. All crystal forms of 11-cis-retinal contain this molecule in its 6-s-cis-ring conformation. For the retinal homologue, beta-8'-apocarotenal (APC), however, two crystal forms with different ring conformation can be grown. The spectrum of alpha-APC (6-s-cis) shows a vibronic structure whereas that of beta-APC (6-s-trans) is diffuse but has a distinct shoulder on the low energy side of the main band. This S-band is typical for retinal spectra and has been ascribed to a transition into a 1Ag-*-state. The appearance of the S-band is not correlated with a 6-s-cis-conformation as suggested by the retinal spectra but is due to intermolecular interactions: beta-APC has a dense dimer packing and a strong electrostatic interaction between the pi-electron systems. This might cause the "forbidden" 1Ag-*-transition. On the other hand, this interaction is missing in the loose and polar packing of alpha-APC which favors vibration in the polyene chain. This finding is remarkable in view of the photodynamic behavior of the visual chromophore for which strong electrostatic interactions with the protein helices of its binding site have to be postulated.

Carotenoids↗
PubMed1988

Expression of the glyceraldehyde-3-phosphate dehydrogenase gene from the extremely thermophilic archaebacterium Methanothermus fervidus in E. coli. Enzyme purification, crystallization, and preliminary crystal data.

The gene of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the extremely thermophilic archaebacterium Methanothermus fervidus (growth optimum 82 degrees C) was cloned in vector pJF118EH and expressed in E. coli cells. As shown by molecular mass determination, protein sequencing, heat stability, and substrate saturation kinetics, the enzyme synthesized in E. coli is identical to the original enzyme from M. fervidus. The high thermostability of the E. coli-produced M. fervidus GAPDH allows rapid purification to homogeneity. From this enzyme protein crystals were grown which proved to be suitable for X-ray analysis. The crystals are of tetragonal space group P4(1)22 and contain a dimer per asymmetric unit.

Base Sequence↗
PubMed2006

Characterization and crystal structure of cadmium(II) halide complexes with amino acids and their derivatives: VII. Crystal structures of aquadibromo(3-aminopropanoic acid)cadmium(II), dichloro(4-aminobutanoic acid)cadmium(II), diaquabis(aminohexanoic acid)cadmium(II) tetrachlorocadmium(II), and dibromo(azetidine-3-carboxylic acid)cadmium(II).

Seven cadmium complexes: [CdX2(Hapro)(H2O)n] (X: Cl(1), Br(2)), [CdX2(Hgaba)] (X: Cl(3), Br(4)), [Cd(Hahex)2(H2O)2][CdCl4] (5), and [CdX2(Haze-3)](H2O)n (X: Cl(6), Br(7)) have been prepared and investigated by means of IR and FT Raman spectra. The crystal and molecular structures of 2, 3, 5 and 7 were determined by a single-crystal X-ray diffraction method. In complex 2, the cadmium atom is in a distorted octahedral geometry, ligated by two carboxyl oxygen atoms of Hapro, a water molecule, and three bromine atoms; one is terminal and each of the other two is bridging two cadmium atoms to make a polymer. The structure of 3 consists of one-dimensional polymers bridged by two chlorine atoms and a carboxyl group. The carboxyl oxygen atoms of Hgaba coordinate forkedly to two cadmium atoms. The cadmium atom of [Cd(Hahex)2(H2O)2]2+ in complex 5 is in a distorted octahedral geometry, ligated by four carboxyl oxygen atoms of two molecules of Hahex and by two water molecules. [Cd(Hahex)2(H2O)2]2+ exists between two layers which are formed of infinite [CdCl4]2- chains. The carboxyl oxygen atoms of Hahex coordinate to the same cadmium atom. In complex 7, the cadmium atom is ligated by two carboxyl oxygen atoms and four bridging bromine atoms to make a polymer.

Amino Acids↗
PubMed2000

Structure determination of tubular crystals of membrane proteins. II. Averaging of tubular crystals of different helical classes.

A set of programs has been developed for averaging the data from tubular crystals belonging to different helical classes. This was done either by (i) cutting out molecules constituting a unit cell from density maps, and aligning and averaging them in real space; (ii) transforming the densities in a unit cell to layer-line data according to a (possibly artificial) helical symmetry, aligning and averaging them in reciprocal space. These methods were applied to tubular crystals of Ca2+-ATPase. Either method worked well and substantially improved the data quality. Transforming the reconstructed images to the layer-line data has many advantages and is essential for fully exploiting the power of averaging.

Calcium-Transporting ATPases↗
PubMed2001

Growth, optical spectroscopy and crystal field investigation of YAl3(BO3)4 single crystals doped with tripositive praseodymium.

Single crystals of YAl3(BO3)4 doped with 1 and 10% Pr3+ were grown by spontaneous nucleation from a K2Mo3O10 and B2O3 flux. Polarised absorption and luminescence spectra in the visible, near infrared and infrared ranges were recorded at room and low temperatures on ground and polished samples of about 1 mm thickness. The microsymmetry of the Pr3+ sites is D3. The observed transitions were assigned and analysed on the basis of the selection rules for the D3 point group. A set of free ion and crystal field parameters in reasonable agreement with the observed energy level structure is reported. The possible applications of the material in the field of optical devices are considered.

Aluminum↗
PubMed2003

Syntheses, reactivity, and crystal structures of molybdenum complexes with pyridine-2-thionate (pyS)-containing ligands: crystal structures of [Mo(eta(3)-C(3)H(5))(CO)(2)](2)(mu-eta(1),eta(2)-pyS)(2), exo-[Mo(eta(3)-C(3)H(5))(CO)(eta(2)-pyS)(eta(2)-dppe)], [Mo(CO)(3)(eta(1)-SC(5)H(4)NH)(eta(2)-dppm)], and [Mo(CO)(eta(2)-pyS)(2)(eta(2)-dppm)].

The doubly bridged pyridine-2-thionate (pyS) dimolybdenum complex [Mo(eta(3)-C(3)H(5))(CO)(2)](2)(mu-eta(1),eta(2)-pyS)(2) (1) is accessible by the reaction of [Mo(eta(3)-C(3)H(5))(CO)(2)(CH(3)CN)(2)Br] with pySK in methanol at room temperature. Complex 1 reacts with piperidine in acetonitrile to give the complex [Mo(eta(3)-C(3)H(5))(CO)(2)(eta(2)-pyS)(C(5)H(10)NH)] (2). Treatment of 1 with 1,10-phenanthroline (phen) results in the formation of complex [Mo(eta(3)-C(3)H(5))(CO)(2)(eta(1)-pyS)(phen)] (3), in which the pyS ligand is coordinated to Mo through the sulfur atom. Four conformational isomers, endo,exo-complexes [Mo(eta(3)-C(3)H(5))(CO)(eta(2)-pyS)(eta(2)-diphos)] (diphos = dppm, 4a-4d; dppe, 5a-5d), are accessible by the reactions of 1 with dppm and dppe in refluxing acetonitrile. Homonuclear shift-correlated 2-D (31)P((1)H)-(31)P((1)H) NMR experiments of the mixtures 4a-4d have been employed to elucidate the four stereoisomers. The reaction of 4 and pySK or [Mo(CO)(3)(eta(1)-SC(5)H(4)NH)(eta(2)-dppm)] (6) and O(2) affords allyl-displaced seven-coordinate bis(pyridine-2-thionate) complex [Mo(CO)(eta(2)-pyS)(2)(eta(2)-dppm)] (7). All of the complexes are identified by spectroscopic methods, and complexes 1, 5d, 6, and 7 are determined by single-crystal X-ray diffraction. Complexes 1 and 5d crystallize in the orthorhombic space groups Pbcn and Pbca with Z = 4 and 8, respectively, whereas 6 belongs to the monoclinic space group C2/c with Z = 8 and 7 belongs to the triclinic space group Ponemacr; with Z = 2. The cell dimensions are as follows: for 1, a = 8.3128(1) A, b = 16.1704(2) A, c = 16.6140(2) A; for 5d, a = 17.8309(10) A, b = 17.3324(10) A, c = 20.3716(11) A; for 6, a = 18.618(4) A, b = 16.062(2) A, c = 27.456(6) A, beta = 96.31(3) degrees; for 7, a = 9.1660(2) A, b = 12.0854(3) A, c = 15.9478(4) A, alpha = 78.4811(10) degrees, beta = 80.3894(10) degrees, gamma = 68.7089(11) degrees.

Journal Article↗