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Query: UNIPROT:Q86TM3 (cage)
 29,987 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The hemoproteins (sperm whale myoglobin, hemoglobin from larvae of Chironomus thummi thummi, bovine hemoglobin) were studied in viscous solvents (saturated sucrose solution, glycerol and water-glycerol solutions) in the temperature range +50 divided by -100 degrees C. At low temperatures the three-phase kinetics of Mb recombination with CO was observed. The velocities of two "fast" reactions did not depend on ligand concentration. This fact indicates that they are due to a so called cage-effect. The formation of the cage is caused apparently by a local change of the solvent state in the heme region. To explain the biphasic "cage" kinetics it has been assumed that during some time after photodissociation myoglobin remains in the "ligand-bound" conformation and reacts with CO faster than the "normal" myoglobin. For other hemoproteins the "cage-effect" was not observed. For all the studied hemoproteins the quantum yield of photodissociation decreased as the temperature decreased. The decrease of quantum yield can be described by the Arrenius law. The rates of the decrease of quantum yield differ for different proteins.
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PMID:[The flash-photolysis study of recombination of hemoproteins with carbon monoxide at low temperatures]. 121 83

Single-crystal X-ray diffraction studies were carried out for the title compounds at room temperature. The crystal packings are of the cage-type and isomorphous to that of beta-cyclodextrin (beta CD) hydrate. In both crystal structures, disorder and extensive thermal vibrations of the complexed guest molecules are observed. In beta CD-ethylene glycol.8H2O, one ethylene glycol molecule (disordered over two discrete sites) and three water molecules (four discrete sites) are included in the beta CD cavity. Within the beta CD cavity, all oxygen sites (ordered and disordered) are in positions occupied by water molecules in beta CD.12H2O; this is only possible because the ethylene glycol molecule adopts the low-energy conformation with the O-C-C-O torsion angle approximately 60 degrees and an O...O separation of 2.9 A, in which its hydroxyl groups can directly substitute for two hydrogen-bonding water molecules. In beta CD-glycerol.7.2H2O, one glycerol molecule (disordered over two discrete sites) and two water molecules (two fully occupied sites) are included in the beta CD cavity. The general situation in both compounds parallels that found earlier in beta CD-ethanol.8H2O. It is assumed that the disorder is dynamic, i.e., associated with jumps between the partially occupied molecular sites.
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PMID:Crystal structures of cyclomaltoheptaose (beta-cyclodextrin) complexed with ethylene glycol.8.0H2O and glycerol.7.2H2O. 827 3

Magnetic field effect studies of alkylcobalamin photolysis provide evidence for the formation of a reactive radical pair that is born in the singlet spin state. The radical pair recombination process that is responsible for the magnetic field dependence of the continuous-wave (CW) quantum yield is limited to the diffusive radical pair. Although the geminate radical pair of adenosylcob(III)alamin also undergoes magnetic field dependent recombination (A.M. Chagovetz and C. B. Grissom, J. Am. Chem. soc. 115, 12152-12157, 1993), this process does not account for the magnetic field dependence of the CW quantum yield that is only observed in viscous solvents. Glycerol and ethylene glycol increase the microviscosity of the solution and thereby increase the lifetime of the spin-correlated diffusive radical pair. This enables magnetic field dependent recombination among spin-correlated diffusive radical pairs in the solvent cage. Magnetic field dependent recombination is not observed in the presence of nonviscosigenic alcohols such as isopropanol, thereby indicating the importance of the increased microviscosity of the medium. Paramagnetic radical scavengers that trap alkyl radicals that escape the solvent cage do not diminish the magnetic field effect on the CW quantum yield, thereby ruling out radical pair recombination among randomly diffusing radical pairs, as well as excluding the involvement of solvent-derived radicals. Magnetic field dependent recombination among alkylcobalamin radical pairs has been simulated by a semi-classical model of radical pair dynamics and recombination. These calculations support the existence of a singlet radical pair precursor.
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PMID:The origin of magnetic field dependent recombination in alkylcobalamin radical pairs. 876 May 70

Trypanosomatids have a striking cage-like arrangement of submembraneous microtubules. We previously showed that alpha- and beta- tubulins of these stable microtubules are extensively modified by polyglutamylation. Cytoskeletal microtubular preparations obtained by Triton extraction of Leishmania tarentolae and Crithidia fasciculata retain an enzymatic activity that incorporates radioactive glutamic acid in a Mg2+-ATP-dependent manner into alpha- and beta-tubulins. The tubulin polyglutamylase is extracted by 0.25 M salt. The Crithidia enzyme can be purified by ATP-affinity chromatography, glycerol-gradient centrifugation and ion-exchange chromatography. After extraction from the microtubular cytoskeleton the glutamylase forms a complex with alphabeta tubulin, but behaves after removal of tubulin as a globular protein with a molecular mass of 38x10(3). In highly enriched fractions a corresponding band is the major polypeptide visible in SDS-PAGE. The enzyme from Crithidia recognises mammalian brain tubulin, where it incorporates glutamic acid preferentially into the more acidic variants of both alpha- and beta-tubulins. Synthetic peptides with an oligoglutamyl side chain, corresponding to the carboxy-terminal end of brain alpha- and beta-tubulins, are accepted by the enzyme, albeit at low efficiency. The polyglutamylase elongates the side chain by up to 3 and 5 residues, respectively. Other properties of the tubulin polyglutamylase are also discussed.
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PMID:Isolation of tubulin polyglutamylase from Crithidia; binding to microtubules and tubulin, and glutamylation of mammalian brain alpha- and beta-tubulins. 1036 48

The equilibrium constant for the thermal isomerization of the diastereomeric alpha- and beta-(cyanomethyl)cobinamides (NCCH(2)Cbi(+)'s) has been measured over the temperature range 70-95 degrees C. Although the beta diastereomer is the thermodynamically more stable isomer, it is favored by the entropy change, but disfavored by the enthalpy change. In the presence of >/=5 x 10(-)(3) M concentration of the radical trap 4-hydroxy-2,2,6,6,-tetramethylpiperidinyloxy (4-HTEMPO), thermolysis of either isomer leads to cob(II)inamide and the trapped NCCH(2)(*) radical (NCCH(2)-4-HTEMPO) in high yield and no isomerization can be detected. The kinetics of the 4-HTEMPO-trapped thermal homolysis of alpha- and beta-NCCH(2)Cbi(+) have been studied in anaerobic glycerol/water mixtures of varying viscosity. The observed first-order rate constants for thermolysis show the expected inverse dependence on viscosity indicating that the process is at least partially diffusion controlled. From these data, the primary rate constant, k(1), for carbon-cobalt bond homolysis and the ratio of the rate constants for in-cage recombination and diffusional separation (k(c)/k(d)) can be extracted. The enthalpies of activation for Co-C bond homolysis are identical (29.0 +/- 0.3 kcal mol(-)(1)) while the entropy of activation is 2-fold higher for the alpha diastereomer. In water, the fractional cage efficiencies, F(c), are quite small (0.12 +/- 0.01, alpha; 0.049 +/- 0.008, beta) and invariant for each complex in the temperature range 75-95 degrees C. Assuming that the rate constant for diffusional separation of the caged radical pairs is the same for both isomers, the ratio of the in-cage recombination rate constants, k(c)(alpha)/k(c)(beta), can be calculated to be 2.6 +/- 0.6. This surprising kinetic preference for the alpha diastereomer results from enthalpic stabilization of the recombination transition state for the alpha diastereomer, since the beta diastereomer is entropically favored.
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PMID:Solvent Cage Effects in Organocobalt Corrinoid Chemistry: Thermal Homolysis of alpha- and beta-(Cyanomethyl)cobinamides(1). 1166 11

Methyl substituents on the distant benzene ring of the dppz ligand in the "light switch" complex [Ru(phen)(2)dppz](2+) have profound effects on the photophysics of the complexes in water as well as in the polyol solvents ethylene glycol, glycerol, and 1,2- and 1,3-propanediol. Whereas 11,12-dimethyl substitution decreases the rate of quenching by diminishing hydrogen bonding by solvent, the 10-methyl substituent in addition also decreases both the radiative and the nonradiative rate constant for decay to the ground state of the non-hydrogen-bonded excited state species. For both the 10-methyl and the 11,12-dimethyl derivatives, the effect of methyl substitution on the equilibrium of solvent hydrogen bonding to the excited state is due to changes in the entropy terms, rather than in the enthalpy, indicating that the effect is a steric perturbation of the solvent cage around the molecule. When intercalated into DNA, the effects of methyl substitution is smaller than those in polyol solvent or water, suggesting that the water molecules that quench the excited state by hydrogen bonding to the phenazine aza nitrogens mainly access them from the same groove as in which the Ru(II) ion resides. Since the Delta-enantiomer of [Ru(phen)(2)10-methyl-dppz](2+) has an absolute quantum yield of up to 0.23 when bound to DNA, a value 7000 times higher than in pure water solution, it is promising as a new luminescent DNA probe.
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PMID:Effects of methyl substitution on radiative and solvent quenching rate constants of [Ru(phen)2dppz]2+ in polyol solvents and bound to DNA. 1556 73

We report here the crystal structure of a trehalose-6-phosphate phosphatase-related protein (T6PP) from Thermoplasma acidophilum, TA1209, determined by the dual-wavelength anomalous diffraction (DAD) method. T6PP is a member of the haloacid dehalogenase (HAD) superfamily with significant sequence homology with trehalose-6-phosphate phosphatase, phosphoserine phosphatase, P-type ATPases and other members of the family. T6PP possesses a core domain of known alpha/beta-hydrolase fold, characteristic of the HAD family, and a cap domain, with a tertiary fold consisting of a four-stranded beta-sheet with two alpha-helices on one side of the sheet. An active-site magnesium ion and a glycerol molecule bound at the interface between the two domains provide insight into the mode of substrate binding by T6PP. A trehalose-6-phosphate molecule modeled into a cage formed by the two domains makes favorable interactions with the protein molecule. We have confirmed that T6PP is a trehalose phosphatase from amino acid sequence, three-dimensional structure, and biochemical assays.
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PMID:Crystal structure of trehalose-6-phosphate phosphatase-related protein: biochemical and biological implications. 1681 21

An experiment was conducted with laying hens to determine the AME(n) value of crude glycerol, a coproduct of biodiesel production. Crude glycerol (87% glycerol, 9% water, 0.03% methanol, 1.26% Na, and 3,625 kcal/kg of gross energy) was obtained from a commercial biodiesel production facility (Ag Processing Inc., Sergeant Bluff, IA). A total of forty-eight 40-wk-old laying hens (Hy-Line W-36) were placed in metabolic cages (2 hens/ cage) and given free access to the experimental diets. A corn and soybean meal-based basal diet (18% CP, 2,875 kcal/kg of AME(n), 4.51% Ca, 0.51% nonphytate P) was formulated with 15% glucose.H(2)O and 1% Celite. Four dietary treatments were created by substituting 0, 5, 10, or 15% crude glycerol for glucose.H(2)O (3,640 kcal/kg of AME(n)). After 7 d of dietary adaptation, excreta were collected twice daily for 3 d, freeze-dried, and analyzed for contents of DM, Kjeldahl N, acid-insoluble ash, and gross energy. Egg production was recorded daily, and eggs were collected on d 7 and 8 of the experiment for calculation of egg mass (egg production x egg weight). Feed consumption was measured over the 10-d experimental period. Egg-production data were analyzed by ANOVA with 4 treatments and 6 replications in a completely randomized experimental design. The AME(n) value of crude glycerol was estimated as the slope of the linear relationship between the inclusion rate of dietary crude glycerol and the glucose-corrected AME(n) value of the experimental diets. No significant treatment effects (P > 0.1) were apparent for egg-production rate (93.0%), egg weight (56.1 g), egg mass (52.2 g/d), or feed consumption (104 g/d). Linear regression analysis (P < 0.001, r(2) = 0.92, n = 24) revealed that the AME(n) value of the crude glycerol used in this study was 3,805 +/- 238 kcal/kg (mean +/- SEM; as-is basis) for laying hens.
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PMID:Nitrogen-corrected apparent metabolizable energy value of crude glycerol for laying hens. 1807 58

The kinetics of geminate recombination of multiatomic organic free radicals in glycerol solutions have been investigated. Radicals were produced by ns laser flash photolysis under photoreduction of carbonyl compounds. An external moderate magnetic field decelerates geminate recombination leading to smaller cage effect values. The duration of geminate recombination is discussed.
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PMID:Kinetics of geminate recombination of organic free radicals in viscous solvents. 1903 7

Inner-sphere (nonradical) and outer-sphere (radical-based) mechanisms have been suggested for cobalamin-mediated dechlorination of tetrachloroethylene (PCE) and trichloroethylene (TCE). In this study, the role of free vinyl radicals was investigated using deuterated radical traps: d(8)-isopropanol and d(8)-tetrahydrofuran. For both substrates, addition of trap resulted in production of deuterated dechlorination products, and higher concentrations of trap resulted in increased amounts of deuterated products. However, only a finite proportion of the products were trappable: 8% of the PCE-derived products and 86% of the TCE-derived products result from free radicals. The data show that the reaction does not proceed solely by either an inner-sphere or an outer-sphere mechanism and led to the hypothesis that caged radical intermediates were involved in the mechanism. The untrappable fraction of products are hypothesized to result from in-cage reactions. This hypothesis was investigated using d(5)-glycerol as a radical trap and viscogen. Although increased viscosity resulted in decreased formation of free-radical-derived products, consistent with the cage hypothesis, these data were inconclusive. The role of d(8)-isopropanol in enhancing the production of radicals in this system via an acetone ketyl radical chain mechanism was also investigated, and no evidence for such an effect was found.
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PMID:Reconciling disparate models of the involvement of vinyl radicals in cobalamin-mediated dechlorination reactions. 1994 73


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