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PubMed1985

Radioiodination of a photoactivatable heterobifunctional reagent.

The N-hydroxysuccinimide ester of 4-azidosalicylic acid, a photoactivable heterobifunctional reagent, can be radioiodinated. The low efficiency (3%) of the radioiodination by a previously published method (I. Ji and T. H. Ji, 1982, Anal. Biochem. 121, 286-289) has been increased to 63% by substituting the solvent, acetone, with others such as aqueous acetonitrile, dimethylformamide, or dimethyl sulfoxide. The resulting 125I reagent was used for derivatizing human choriogonadotropin. The radioactive hormone derivative was crosslinked to the alpha beta dimer upon photolysis.

Azides↗
PubMed1996

Volume and enthalpy changes in the early steps of bacteriorhodopsin photocycle studied by time-resolved photoacoustics.

We have studied the photoinduced volume changes, energetics, and kinetics in the early steps of the bacteriorhodopsin (BR) photocycle with pulsed, time-resolved photoacoustics. Our data show that there are two volume changes. The fast volume change ( < or = 200 ns) is an expansion (2.5 +/- 0.3 A3/molecule) and is observed exclusively in the purple membrane (PM), vanishing in the 3-[(3-cholamidopropyl)-dimethylammonio] -1-propane-sulfonate-sulfonate-solubilized BR sample; the slow change (approximately 1 micros) is a volume contraction (-3.7 +/- 0.3 A3/molecule). The fast expansion is assigned to the restructuring of the aggregated BR in the PM, and the 1-micros contraction to the change in hydrogen bonding of water at Asp 212 (Kandori et al. 1995. J. Am. Chem. Soc. 117:2118-2119). The formation of the K intermediate releases most of the absorbed energy as heat, with delta Hk = -36 +/- 8 kJ/mol. The activation energy of the K --> L step is 49 +/- 6 kJ/mol, but the enthalpy change is small, -4 +/- 10 kJ/mol. On the time scale we studied, the primary photochemical kinetics, enthalpy, and volume changes are not affected by substituting the solvent D2O for H2O. Comparing data on monomeric and aggregated BR, we conclude that the functional unit for the photocycle is the BR monomer, because both the kinetics (rate constant and activation energy) and the enthalpy changes are independent of its aggregation state.

Acoustics↗
PubMed2004

Binding of 9-methylguanine to [cis-Ru(2,2'-bpy)2]2+: First X-ray structure of a cis-bis purine complex of ruthenium.

Reaction of [cis-Ru(2,2'-bpy)2(O3SCF3)2] (1) with 9-methylguanine (9-MeG) affords the cis-[Ru(2,2'-bpy)2(9-MeG)2]2+ complex (2) in good yield. Two bases bind to the metal center via the N7 atoms. X-ray structure analysis of 2(SO3CF3)2 (monoclinic, P2(1)/n, a = 12.5159(6) A, b = 20.0904(13) A, c = 17.1202(9) A, beta = 98.981(6) degrees, V = 4252.1(4) A(3), Z = 4) reveals that the two bases are in a head-to-tail (HT) orientation with base-base dihedral angle of 60.4 degrees. NMR studies confirm that the complex is stable in water for hours, and no evidence for guanine substitution by solvent molecules was found.

Crystallography, X-Ray↗
PubMed2006

Synthesis, crystal structure, and luminescent properties of novel Eu3+ heterocyclic beta-diketonate complexes with bidentate nitrogen donors.

New tris(heterocyclic beta-diketonato)europium(III) complexes of the general formula Eu(PBI)3.L [where HPBI = 3-phenyl-4-benzoyl-5-isoxazolone and L = H2O, 2,2'-bipyridine (bpy), 4,4'-dimethoxy-2,2'-bipyridine (dmbpy), 1,10-phenanthroline (phen), or 4,7-diphenyl-1,10-phenanthroline (bath)] were synthesized and characterized by elemental analysis, Fourier transform infrared spectroscopy (FT-IR), 1H NMR, high-resolution mass spectrometry, thermogravimetric analysis, and photoluminescence (PL) spectroscopy. Single-crystal X-ray structures have been determined for the complexes Eu(PBI)3.H2O.EtOH and Eu(PBI)3.phen. The complex Eu(PBI)3.H2O.EtOH is mononuclear, and the central Eu3+ ion is coordinated by eight oxygen atoms to form a bicapped trigonal prism coordination polyhedron. Six oxygens are from the three bidentate HPBI ligands, one is from a water molecule, and another is from an ethanol molecule. On the other hand, the crystal structure of Eu(PBI)3.phen reveals a distorted square antiprismatic geometry around the europium atom. The room-temperature PL spectra of the europium(III) complexes are composed of the typical Eu3+ red emission, assigned to transitions between the first excited state (5D0) and the multiplet (7F0-4). The results demonstrate that the substitution of solvent molecules by bidentate nitrogen ligands in Eu(PBI)3.H2O.EtOH richly enhances the quantum yield and lifetime values. To elucidate the energy transfer process of the europium complexes, the energy levels of the relevant electronic states have been estimated. Judd-Ofelt intensity parameters (Omega2 and Omega4) were determined from the emission spectra for Eu3+ ion based on the 5D0 --> 7F2 and 5D0 --> 7F4 electronic transitions, respectively, and the 5D0 --> 7F1 magnetic dipole allowed transition was taken as the reference. The high values obtained for the 4f-4f intensity parameter Omega2 for europium complexes suggest that the dynamic coupling mechanism is quite operative in these compounds.

Journal Article↗
PubMed2004

Elimination-addition mechanism for nucleophilic substitution reaction of cyclohexenyl iodonium salts and regioselectivity of nucleophilic addition to the cyclohexyne intermediate.

The reaction of 4-substituted cyclohex-1-enyl(phenyl)iodonium tetrafluoroborate with tetrabutylammonium acetate gives both the ipso and cine acetate-substitution products in aprotic solvents. The isomeric 5-substituted iodonium salt also gives the same mixture of the isomeric acetate products. The reaction is best explained by an elimination-addition mechanism with 4-substituted cyclohexyne as a common intermediate. The cyclohexyne formation was confirmed by deuterium labeling and trapping to lead to [4 + 2] cycloadducts and a platinum-cyclohexyne complex. Cyclohexyne can also be generated in the presence of some other mild bases such as fluoride ion, alkoxides, and amines, though amines are less effective bases for the elimination. Kinetic deuterium isotope effects show that the anionic bases induce the E2 elimination (k(H)/k(D) > 2), while the amines allow formation of a cyclohexenyl cation in chloroform to lead to E1 as well as S(N)1 reactions (k(H)/k(D) approximately 1). Bases are much less effective in methanol, and methoxide was the only base to efficiently afford the cyclohexyne intermediate. Nucleophiles react with the cyclohexyne to give regioisomeric products in the ratio dependent on the ring substituent. The observed regioselectivity of nucleophilic addition to substituted cyclohexynes is rationalized from calculated LUMO populations, which are governed by the bond angles at the acetylenic carbons: The less deformed carbon has a higher LUMO population and is preferentially attacked by the nucleophile.

Acetates↗
PubMed2003

Stabilized and destabilized carbocations in the 1,6-methano[10]annulene series.

2-Chloromethyl and 3-chloromethyl-1,6-methano[10]annulene systems solvolyze in methanol to give simple substitution products. Solvent effect studies and the special salt effect support the involvement of cationic intermediates stabilized by the 1,6-methano[10]annulene group. Rate data indicate that the degree of cation stabilization greatly exceeds that of naphthyl groups. B3LYP/6-31G computational studies also suggest that the cationic intermediates are greatly stabilized by the 1,6-methano[10]annulene. By way of contrast to these findings, solvolytic and computational studies indicate that the 11-(1,6-methano[10]annulenyl) cation is a destabilized analogue of the cycloheptatrienyl cation. There are no favorable interactions with the annulene ring. Distortions from planarity prevent charge delocalization as in the analogous aromatic cycloheptatrienyl cation.

Journal Article↗
PubMed2006

The anharmonic vibrational potential and relaxation pathways of the amide I and II modes of N-methylacetamide.

We investigate the influence of isotopic substitution and solvation of N-methylacetamide (NMA) on anharmonic vibrational coupling and vibrational relaxation of the amide I and amide II modes. Differences in the anharmonic potential of isotopic derivatives of NMA in D2O and DMSO-d6 are quantified by extraction of the anharmonic parameters and the transition dipole moment angles from cross-peaks in the two-dimensional infrared (2D-IR) spectra. To interpret the effects of isotopic substitution and solvent interaction on the anharmonic potential, density functional theory and potential energy distribution calculations are performed. It is shown that the origin of anharmonic variation arises from differing local mode contributions to the normal modes of the NMA isotopologues, particularly in amide II. The time domain manifestation of the coupling is the coherent exchange of excitation between amide modes seen as the quantum beats in femtosecond pump-probes. The biphasic behavior of population relaxation of the pump-probe and 2D-IR experiments can be understood by the rapid exchange of strongly coupled modes within the peptide backbone, followed by picosecond dissipation into weakly coupled modes of the bath.

Acetamides↗
PubMed2005

Stepwise controlled immobilization of colloidal crystals formed by polymer-grafted silica particles.

Colloidal crystals formed by polymer-grafted silica particles were immobilized by a stepwise procedure consisting of gelation by radical copolymerization followed by solidification by ring-opening radical polymerization. In the first step, the poly(methyl methacrylate) (PMMA)-grafted silica colloidal crystal suspension was incorporated into the gel without altering the crystal structure by copolymerization of cross-linker, 1,2-dimethylacryloyloxyethane (DME) and methyl methacrylate (MMA). In the second step, ring-opening radical polymerization was performed after substituting the solvent with vinylidene-1,3-dioxolane. By this two-step procedure, the silica particle array of colloidal crystals was immobilized and made into durable material.

Journal Article↗
PubMed1984

Effect of single amino acid replacements on the thermal stability of the NH2-terminal domain of phage lambda repressor.

The thermal stabilities of mutant phage lambda repressors that have single amino acid replacements in the NH2-terminal domain have been studied by means of circular dichroism and differential scanning calorimetry. The variations in stability determined by these physical methods correlate with the resistance to proteolysis at various temperatures and can be compared with the temperature-sensitive activity of the mutants in vivo. In general, mutant proteins bearing solvent-exposed substitutions have thermal stabilities identical to wild type, whereas buried substitutions reduce stability. In one case, a single amino acid replacement increases the thermal stability of the repressor.

Amino Acids↗
PubMed2003

The mechanisms by which family 10 glycoside hydrolases bind decorated substrates.

Endo-beta-1,4-xylanases (xylanases), which cleave beta-1,4 glycosidic bonds in the xylan backbone, are important components of the repertoire of enzymes that catalyze plant cell wall degradation. The mechanism by which these enzymes are able to hydrolyze a range of decorated xylans remains unclear. Here we reveal the three-dimensional structure, determined by x-ray crystallography, and the catalytic properties of the Cellvibrio mixtus enzyme Xyn10B (CmXyn10B), the most active GH10 xylanase described to date. The crystal structure of the enzyme in complex with xylopentaose reveals that at the +1 subsite the xylose moiety is sandwiched between hydrophobic residues, which is likely to mediate tighter binding than in other GH10 xylanases. The crystal structure of the xylanase in complex with a range of decorated xylooligosaccharides reveals how this enzyme is able to hydrolyze substituted xylan. Solvent exposure of the O-2 groups of xylose at the +4, +3, +1, and -3 subsites may allow accommodation of the alpha-1,2-linked 4-O-methyl-d-glucuronic acid side chain in glucuronoxylan at these locations. Furthermore, the uronic acid makes hydrogen bonds and hydrophobic interactions with the enzyme at the +1 subsite, indicating that the sugar decorations in glucuronoxylan are targeted to this proximal aglycone binding site. Accommodation of 3'-linked l-arabinofuranoside decorations is observed in the -2 subsite and could, most likely, be tolerated when bound to xylosides in -3 and +4. A notable feature of the binding mode of decorated substrates is the way in which the subsite specificities are tailored both to prevent the formation of "dead-end" reaction products and to facilitate synergy with the xylan degradation-accessory enzymes such as alpha-glucuronidase. The data described in this report and in the accompanying paper indicate that the complementarity in the binding of decorated substrates between the glycone and aglycone regions appears to be a conserved feature of GH10 xylanases.

Bacterial Proteins↗
PubMed1999

A study on the equivalence of olive oil and the EU official substitute test media for migration testing at high temperatures.

As a consequence of an increasing awareness and findings about the technical and analytical difficulties related to the employment of triglycerides as fatty food simulants in migration testing, EU Directive 82/711/EEC on the basic rules of migration has been amended for the second time and adapted with the recent Commission Directive 97/48/EC. The major merit of this important amendment is to authorize alternative tests such as extraction tests and to allow substitute tests for the fat test with concrete indication of corresponding test conditions to be applied. As a novelty in food law compliance testing it authorizes a modified polyphenylene oxide (MPPO), well-known as Tenax, a thermostable and highly adsorptive porous polymer, as a 'solid' matrix to substitute fat simulant D at temperatures equal to or higher than 100 degrees C. In the study presented here, comparative migration testing--overall and specific--was carried out between fat simulants olive oil and 14C-labelled HB 307 and the substitute test media iso-octane, 95% ethanol and MPPO using polypropylene materials as examples at test temperatures of 100 degrees C to 120 degrees C and prescribed corresponding substitute test conditions. As a consequence, a number of conclusions were drawn which are relevant for overall and/or specific migration testing under the investigated test conditions. One of the major findings was that MPPO was generally more equivalent to the fat test than the other two substitute test media. The presence of volatile hydrocarbons in the test samples was found to play a crucial role with respect to the equivalence of the iso-octane-based substitute test. At high volatile concentrations in the test sample the iso-octane test underestimated the olive oil benchmark whereas low volatile concentrations led to satisfying equivalence. It is therefore recommended that the procedure is modified and GC-FID screening of the isooctane extract is carried out. As a logical consequence, the possibility of quantitative determination of the overall extract by GC-FID is recommendable and should be investigated in more depth. Concerning the overall migration test procedure in olive oil, the vacuum pre-conditioning at 60 degrees C should be given re-consideration to avoid the possibility of loss of volatile migrants whose determination should be within the scope of the overall migration test method itself. Finally, the specific migration related equivalence between olive oil, MPPO and iso-octane needs further investigations to clarify the net effect of strongly increased diffusion rates at the regular high temperature versus the substitute test solvent accelerated extraction effect at 60 degrees C. Stability aspects of migrants at the different test temperatures deserve further consideration.

Chromatography, Gas↗
PubMed2005

Two phosphate-imidazole complexes with and without a hydrogen-bonded guest molecule.

The molecular structures of the complexes imidazolium 6,6'-di-tert-butyl-4,4'-dimethyl-2,2'-thiodiphenyl phosphate, C(3)H(5)N(2)(+).C(22)H(28)O(4)PS(-), (I), and imidazolium 6,6'-di-tert-butyl-4,4'-dimethyl-2,2'-thiodiphenyl phosphate diisopropyl hydrazodicarboxylate hemisolvate, C(3)H(5)N(2)(+).C(22)H(28)O(4)PS(-).0.5C(8)H(16)N(2)O(4), (II), have been determined. While (I) forms the expected hydrogen-bonded chain utilizing the two imidazole N-bound H atoms, in (II), the substituted hydrazine solvent molecule inserts itself between the chains. Compound (I) exhibits a strong N-H...O hydrogen bond, with an N...O distance of 2.603 (2) A. The hydrazine solvent molecule in (II) lies about a twofold axis and the N-bound H atoms are involved in bifurcated hydrogen bonds with phosphate O atoms. A C-bound H atom of the imidazolium cation is involved in a C-H...O interaction with a carbonyl O atom of the hydrazine solvent molecule.

Journal Article↗
PubMed2006

Plastic-embedded protein crystals.

Rapid vitrification followed by the replacement of the vitrified water by a solvent (freeze substitution) and then resin is a widely used procedure for preparing biological samples for electron microscopy. The resulting plastic-embedded samples permit convenient room-temperature sectioning (microtomy) and can yield well preserved cellular structures. Here this procedure has been applied to crystalline protein samples, and it is shown that it is possible to freeze-substitute vitrified crystals while preserving some of their original diffraction properties. The plastic-embedded crystals were used to collect a series of complete room-temperature data sets at a powerful macromolecular crystallography synchrotron beamline. Whereas one normally observes specific damage to disulfide bonds upon X-ray radiation, no such damage was seen for the plastic-embedded sample. The X-ray diffraction data allowed an initial atomic analysis to be made of the effects of freeze-substitution and plastic embedding on biological samples.

Acrylic Resins↗
PubMed1991

Recent advances in electron immunocytochemistry.

Considerable progress has been made in the development of methods for the localisation of antigens at the ultrastructural level using both transmission and scanning electron microscopy. There is currently no technique which is appropriate for all antigens, although, almost without exception, colloidal gold-linked reagents provide the electron-dense marker. For post-embedding techniques, several approaches are available all utilising low temperatures during the preparative stages. Cryosectioning and embedding by the PLT method both require the antigen to withstand some degree of fixation. For fixation-sensitive antigens, freeze substitution in solvents lacking fixative agents is an approach offering considerable potential.

Frozen Sections↗
PubMed1992

Cofactor and DNA interactions in EcoRI DNA methyltransferase. Fluorescence spectroscopy and phenylalanine replacement for tryptophan 183.

EcoRI DNA methyltransferase contains tryptophans at positions 183 and 225. Tryptophan 225 is adjacent to residues previously implicated in S-adenosylmethionine (AdoMet) binding and to cysteine 223, previously shown to be the site of N-ethyl maleimide-mediated inactivation of the enzyme (Reich, N. O., and Everett, E. (1990) J. Biol. Chem. 265, 8929-8934; Everett, E. A., Falick, A. M., and Reich, N. O. (1990) J. Biol. Chem. 265, 17713-17719). The fluorescence spectra of the wild-type enzyme is centered at 338 nm indicating partial tryptophan solvent accessibility. Substitution of tryptophan 183 with phenylalanine results in a 45% drop in fluorescence intensity, but no shift in lambda max. DNA binding to the wild-type methyltransferase caused an increase in the fluorescence intensity, while binding to the tryptophan 183 mutant had a quenching effect, suggesting that DNA binding induces a conformational change near both tryptophans. Binding of AdoMet and various AdoMet analogs to the wild-type methyltransferase results in no change in the fluorescence spectrum when excitation occurs at 295 nm, suggesting that no conformational change occurs, and AdoMet does not interact with either tryptophan. In contrast, quenching was observed when excitation occurred at 280 nm, suggesting that AdoMet and its analogs may be quenching tyrosine to tryptophan energy transfer. Protein-ligand complexes were titrated with acrylamide, and the data also implicate conformational changes upon DNA binding but not upon AdoMet binding, consistent with previous limited proteolysis results (Reich, N. O., Maegley, K. A., Shoemaker, D.D., and Everett, E. (1991) Biochemistry 30, 2940-2946).

Acrylamide↗
PubMedDate not supplied

Nature of lysozyme-water interactions by proton NMR.

Proton spin-lattice relaxation measurements were performed in 10 mM lysozyme solution as a function of temperature and degree of substitution of solvent H2O with D2O. The results show that in the temperature range from 274 to 323 K, the intermolecular lysozyme proton water proton coupling contributes appreciably to the observed water proton relaxation rate. In this system exchange between water protons and labile protein protons does not dominate the behaviour with temperature of the water-lysozyme intermolecular contribution to the spin-lattice relaxation.

Kinetics↗