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PubMed1997

Titration kinetics of Asp-85 in bacteriorhodopsin: exclusion of the retinal pocket as the color-controlling cation binding site.

The spectrum (the purple blue transition) and function of the light-driven proton pump bacteriorhodopsin are determined by the state of protonation of the Asp-85 residue located in the vicinity of the retinal chromophore. The titration of Asp-85 is controlled by the binding/unbinding of one or two divalent metal cations (Ca2+ or Mg2+). The location of such metal binding site(s) is approached by studying the kinetics of the cation-induced titration of Asp-85 using metal ions and large molecular cations, such as quaternary ammonium ions, R4N+ (R = Et, Pr, a divalent 'bolaform ion' [Et3N+-(CH2)4-N+Et3] and the 1:3 molecular complex formed between Fe2+ and 1,10-phenanthroline (OP). The basic multi-component kinetic features of the titration, extending from 10(-2) to 10(4) s, are unaffected by the charge and size of the cation. This indicates that cation binding to bR triggers the blue --> purple titration in a fast step, which is not rate-determining. In view of the size of the cations involved, these observations indicate that the cation binding site is in an exposed location on, or close to, the membrane surface. This excludes previous models, which placed the color-controlling Ca2+ ion in the retinal binding pocket.

Aspartic Acid↗
PubMed1999

Automated one-step supercritical fluid extraction and clean-up system for the analysis of pesticide residues in fatty matrices.

An automated supercritical fluid extraction and in-line clean-up system has been developed for organochlorine and organophosphate pesticide residues contained in fats. This procedure utilizes supercritical carbon dioxide modified with 3% acetonitrile at 27.58 MPa and 60 degrees C to extract and separate the pesticide residues from the fat on a C1 bonded phase preparative column at 95 degrees C. The automated C1 system recovers 86 of 117 nonpolar to moderately polar organochlorine and organophosphate pesticides from fats. Ten of the 31 pesticides not recovered through the system are not recovered through the conventional clean-up sorbent, Florisil. Pesticide residues can be separated from 0.68 g of butter fat and 0.67 g corn oil, resulting in 2.9 mg of butterfat and 2.1 mg corn oil residue co-eluting into the pesticide fraction. Also, this integrated method can extract and clean-up a 5 g sample of fatty foods containing < 18% fat and 70% moisture. The automated C1 system is reproducible and the amount of co-extracted sample residue in the pesticide fraction yields results comparable to the current methodology, which uses organic solvent extraction and gel permeation chromatography, along with a final Florisil column clean-up step. This automated C1 system simplifies the extraction and clean-up step while reducing solvent usage and hazardous waste.

2-Propanol↗
PubMed1997

Effect of divalent metal ions on the binding of tissue factor and activated factor VII.

Surface plasmon resonance technology was used to study the binding of activated factor VII to tissue factor, in the presence of divalent metal ions. The binding was calcium-dependent, with the optimum calcium concentration at 5 mM. Only very minimal binding was observed in the absence of added calcium ions and presence of 10 mM EGTA. The effect of the calcium concentration on the apparent dissociation constants for the TF/VIIa complex formation was also investigated. In the absence of calcium ions but in the presence of either magnesium or zinc ions, no significant binding of activated factor VII to tissue factor was detected. However some binding was observed with manganese ions, indicating that manganese ions could partially replace calcium ions to support the formation of the TF/VIIa complex. These results are consistent with studies of the effect of divalent metal ions on the amidolytic activity of the TF/VIIa complex.

Calcium Chloride↗
PubMed2000

In vitro bioactivity of glass and glass-ceramics of the 3CaO x P2O5-CaO x SiO2-CaO x MgO x 2SiO2 system.

A glass of nominal composition (wt%) 40.0 CaO-34.5 SiO2-16.5 P2O5-8.5 MgO-0.5 CaF2 has been obtained (G13). The glass showed in vitro bioactivity evidenced by the formation on its surface of a calcium phosphate-rich layer when soaked in a solution with ionic composition analogous to human plasma. By thermal treatments of G13, a glass-ceramic (GC13) containing apatite, diopside, althausite and akermanite as crystalline phases was developed. GC13 as-made did not show in vitro bioactivity. However, after chemical treatment of GC13 with 1 M HCl (GC13-HCl), the in vitro studies showed the formation of an apatite-like layer covering certain areas of the material surface. The influence of both chemical and morphological factors on the in vitro bioactivity has been studied.

Calcium Compounds↗
PubMed2000

QED v 1.0: a software package for quantitative electron diffraction data treatment.

A new software package for quantitative electron diffraction data treatment of unknown structures is described. No "a priori" information is required by the package which is able to perform in successive steps the 2-D indexing of digitised diffraction patterns, the extraction of the intensity of the collected reflections and the 3-D indexing of all recorded patterns, giving as results the lattice parameters of the investigated structure and a series of data files (one for each diffraction pattern) containing the measured intensities and the relative e.s.d.s of the 3-D indexed reflections. The software package is mainly conceived for the treatment of diffraction patterns taken with a Gatan CCD Slow-Scan Camera, but it can also deal with generic digitised plates. The program is designed to extract intensity data suitable for structure solution techniques in electron crystallography. The integration routine is optimised for a correct background evaluation, a necessary condition to deal with weak spots of irregular shape and an intensity just above the background.

Algorithms↗
PubMed1992

A multinuclear magnetic resonance examination of the mineral grandidierite. Identification of a 27Al resonance from a well-defined AlO5 site.

11B, 27Al and 29Si magic angle spinning NMR results are reported for the boroaluminosilicate mineral grandidierite (Mg, Fe)Al3SiBO9. Three distinct aluminium sites are identified, two AlO6 and one AlO5. Despite overlap of the centrebands from these sites the use of three magnetic fields (9.4, 11.7 and 14.1 T) allows unambiguous values for the isotropic chemical shift (delta iso), quadrupolar coupling constant (Cq) and quadrupolar asymmetry parameter (eta) to be deduced for each site. The NMR spectrum from the AlO5 site is simulated with parameters Cq = 8.7 +/- 0.1 MHz, eta = 0.95 +/- 0.05 and delta iso = 41 +/- 1 ppm which are compared to values from other well-defined AlO5 units.

Aluminum↗
PubMed2000

Determination of titanium NMR parameters of ATiO3 compounds: correlations with structural distortion.

Solid state 47,49Ti NMR spectra have been obtained for a number of perovskite and ilmenite ATiO3 compounds. The 49Ti quadrupole coupling constant varies from 2.75 MHz (CaTiO3) to 15.5 MHz (MgTiO3) and the electric field gradient at the titanium site was found to correlate well with the shear strain, independent of structure. The chemical shift in the perovskite structures varies by approximately 160 ppm and correlates well with the mean Ti-O distance. The 25Mg and 113Cd NMR parameters are also reported for the relevant compounds.

Barium↗
PubMed2003

A personal thermoluminescence dosimeter using LiF:Mg,Cu,Na,Si detectors for photon fields.

A new personal thermoluminescence (TL) dosimeter for photon fields using LiF:Mg,Cu,Na,Si TL detector was developed by taking advantage of its dosimetric properties including energy dependencies. Solid pellet type LiF:Mg,Cu,Na,Si detector was developed and fabricated at Korea Atomic Energy Research Institute (KAERI) and has been studied on its dosimetric properties such as TL grow curve, dose response, energy response and reusability. Its dosimetric properties show the feasibility of application of LiF:Mg,Cu,Na,Si TL detector to personal dosimetry fields. A new dosimeter using LiF:Mg,Cu,Na,Si TL detector was designed and tested through irradiation experiments. This multi-element TL dosimeter allows the measurement of a personal dose equivalent Hp(d) in photon fields. Based on the experimental results of the proposed dosimeter, it was demonstrated that a personal TL dosimeter using sintered LiF:Mg,Cu,Na,Si TL detector is appropriate to estimate personal dose equivalent for wide range energy of photon fields.

Copper↗
PubMed2000

Chloroplast ribonuclease P does not utilize the ribozyme-type pre-tRNA cleavage mechanism.

The transfer RNA 5' maturation enzyme RNase P has been characterized in Bacteria, Archaea, and Eukarya. The purified enzyme from all three kingdoms is a ribonucleoprotein containing an essential RNA subunit; indeed, the RNA subunit of bacterial RNase P RNA is the sole catalytic component. In contrast, the RNase P activity isolated from spinach chloroplasts lacks an RNA component and appears to function as a catalytic protein. Nonetheless, the chloroplast enzyme recognizes a pre-tRNA substrate for E. coli RNase P and cleaves it as efficiently and precisely as does the bacterial enzyme. To ascertain whether there are differences in catalytic mechanism between an all-RNA and an all-protein RNase P, we took advantage of the fact that phosphodiester bond selection and hydrolysis by the E. coli RNase P ribozyme is directed by a Mg2+ ion coordinated to the nonbridging pro-Rp oxygen of the scissile bond, and is blocked by sulfur replacement of this oxygen. We therefore tested the ability of the chloroplast enzyme to process a precursor tRNA containing this sulfur substitution. Partially purified RNase P from spinach chloroplasts can accurately and efficiently process phosphorothioate-substituted pre-tRNAs; cleavage occurs exclusively at the thio-containing scissile bond. The enzymatic throughput is fivefold slower, consistent with a general chemical effect of the phosphorothioate substitution rather than with a metal coordination deficiency. The chloroplast RNase P reaction mechanism therefore does not involve a catalytic Mg2+ bonded to the pro-Rp phosphate oxygen, and hence is distinct from the mechanism of the bacterial ribozyme RNase P.

Base Sequence↗
PubMedDate not supplied

Synthesis of 3-(triethylstannyl)propanoic acid: an organotin mass label for DNA.

The synthesis of 3-(triethylstannyl)propanoic acid (TESPA), an organometallic reporter group that enables the mass labeling of oligonucleotides with stable isotopes of tin, is described. Synthesized from commercially available isotopically-enriched SnO2 in a five step process, the NHS ester of TESPA is produced with an overall yield of 40%. This simplification of the standard synthetic scheme, with two less synthetic steps and a coincident 60% yield increase, is accomplished through the use of the reagent N-(acryloxy)succinimide and the free radical initiator AMPN. The conditions for the attachment of the reporter group to priming oligonucleotides and the subsequent HPLC isolation of the labeled primers are also detailed.

Alloys↗
PubMedDate not supplied

A psoralen-conjugated triplex-forming oligodeoxyribonucleotide containing alternating methylphosphonate-phosphodiester linkages: synthesis and interactions with DNA.

A psoralen-conjugated oligodeoxyribopyrimidine (1443), PS-pTTTTCTTTTCTTCTT, where PS is trimethylpsoralen and C is 5-methyl-2'-deoxycytidine, that contains alternating methylphosphonate-phosphodiester internucleotide linkages was synthesized. The ability of 1443 to form triple-stranded complexes with a purine tract in a synthetic DNA duplex was studied. Irradiation of solutions containing the DNA target and 10 microM 1443 or 0.25 microM of a similar psoralen-conjugated oligodeoxyribonucleotide that contained all phosphodiester linkages, (1193), with long-wavelength UV light resulted in approximately 80% formation of interstrand cross-links at pH 7.0, 37 degrees C, in the presence of 20 mM magnesium chloride. The extent of triplex formation as monitored by photo-cross-linking decreased over the pH range 5.5-8.0, and the apparent pK of the 5-methylcytosines (C) in 1443 was approximately one-half of a pH unit less than that of the 5-methylcytosines in 1193. Oligomer 1443 formed triplexes in the absence of magnesium, and maximum triplex formation was observed in solutions containing 2.5 mM magnesium, whereas maximal triplex formation by the fully charged 1193 was not observed until the magnesium concentration was 10 mM or higher. Unlike the all-phosphodiester backbone of 1193, the alternating methylphosphonate-phosphodiester backbone of 1193 is resistant to hydrolysis by exonucleases in fetal calf serum. The nuclease resistance of 1443 and its ability to form triplexes at very low magnesium concentrations suggests that triplex-forming oligomers with alternating methylphosphonate-phosphodiester backbones may be good candidates for use as antigene reagents in cell culture.

Cross-Linking Reagents↗
PubMed1995

Higher order folding and domain analysis of the ribozyme from Bacillus subtilis ribonuclease P.

Folding of the ribozyme from Bacillus subtilis ribonuclease P (denoted P RNA) has been examined by Fe(II)-EDTA protection and bimolecular association. Fe(II)-EDTA results show that, in the presence of Mg2+, P RNA is folded into a core structure which includes most of the phylogenetically conserved nucleotides. Folding is cooperative and is complete at 5-6 mM Mg2+ with the [Mg2+]1/2 at 2-3 mM. The Hill constant indicates that this folding transition requires binding of at least three additional Mg2+ ions. Two RNA molecules consisting of nucleotides 62-239 [p(62-239)] and 240-401 + 1-61 [p(240-61)] of the B. subtilis P RNA have been constructed. These RNAs can in principle form the catalytically active structure primarily, if not solely, through tertiary interactions. Although either molecule by itself is inactive, the bimolecular complex is as active as the circularly permuted P RNAs from which it is derived. The binding constant of the complex can be as low as 0.1 microM and is strongly dependent on Mg2+ and K+ concentrations. Association of these molecules also induces a Mg2+ dependent cleavage at nucleotide 103 in p(62-239). p(62-239) gives a Fe(II)-EDTA protection pattern very similar to the wild-type P RNA at identical Mg2+ concentrations. However, Fe(II)-EDTA protection in p(240-61) is completely lost, even though it contains many nucleotides that are conserved among all P RNAs. These results suggest that, like other RNAs, P RNA contains domains that can fold in the absence of the rest of the molecule. The implications of these results are discussed in the context of the P RNA structure and catalysis.

Bacillus subtilis↗
PubMed1995

Identification of Asp258 as the metal coordinate of pigeon liver malic enzyme by site-specific mutagenesis.

Pigeon liver malic enzyme was inactivated by ferrous sulfate in the presence of ascorbate. Manganese and some other divalent metal ions provided complete protection of the enzyme against the Fe(2+)-induced inactivation. The inactivated enzyme was subsequently cleaved by the Fe(2+)-ascorbate system at Asp258-Ile259, which was presumably the Mn(2+)-binding site of the enzyme [Wei, C. H., Chou, W. Y., Huang, S. M., Lin, C. C., & Chang, G. G. (1994) Biochemistry 33, 7793-7936]. For identification of Asp258 as the putative metal-binding site of the enzyme, we prepared four mutant enzymes substituted at Asp258 with glutamate (D258E), asparagine (D258N), lysine (D258K), or alanine (D258A), respectively. These mutant proteins were recombinantly expressed in a bacterial expression system (pET-15b) with a stretch of histidine residues attached at the N-terminus and were successfully purified to apparent homogeneity by a single Ni-chelated affinity column. Among the four mutants, only D258E possessed 0.8% residual activity after purification; all other purified mutants had < 0.0001% residual activity in catalyzing the oxidative decarboxylation of L-malate. The D258E mutant was susceptible to inactivation by the Fe(2+)-ascorbate system, albeit with much slower inactivation rate, and was protected by the Mn2+ to a lesser extent as compared to the wild-type enzyme. None of the mutants were cleaved by the Fe(2+)-ascorbate system under conditions that cleaved the natural or wild-type enzyme at Asp258.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acids↗
PubMed1988

Cleavage of dT8 and dT8 phosphorothioyl analogues by Escherichia coli DNA topoisomerase I: product and rate analysis.

Escherichia coli DNA topoisomerase I catalyzes the cleavage of short, single-stranded oligodeoxynucleotides with dT8 as the shortest cleavable oligo(thymidylic acid). The 5'-32P-labeled products formed from the cleavage of [5'-32P]dT8 are dT5, dT4, and dT3 with over 70% of the substrate cleaved to dT4. Mg(II) ions affect this product distribution by increasing the percentage of dT4 formed. The substitution of a sulfur atom for a nonbridging oxygen atom in a phosphodiester linkage yields oligodeoxynucleotide phosphorothioyl (PS) analogues. The epimers of the analogues were separated, and the position and stereochemistry of the phosphorothiodiester bond were determined. Topoisomerase I is stereospecific in its reactivity toward these analogues. With the oligodeoxynucleotide PS analogue substrates, the rate of cleavage, the stereospecificity, and the product distribution depend upon the position and the stereochemistry of the phosphorothiodiester linkage.

DNA Topoisomerases, Type I↗
PubMed1981

Transient and steady-state kinetic studies of sodium-potassium adenosine triphosphatase using beta-(2-furyl)acryloyl phosphate as chromophoric substrate assay.

A convenient and highly specific continuous spectrophotometric assay for sodium-potassium adenosine triphosphate activity utilizing the rapidly hydrolyzed and high-affinity chromophoric substrate beta-(2-furyl)acryloyl phosphate (FAP) is described. The Na/K-ATPase-catalyzed hydrolysis of FAP is faster than that for ATP under all ionic conditions. The rate is neither inhibited nor activated by Na+; it is dependent on [K+] and on [Mg2+]. The hydrolysis of FAP to furylacrylate is accompanied by a large shift in the UV absorbance maximum. The spectrum of FAP, but not furylacrylate, is sensitive to noncovalent ligation with Mg2+, a happenstance which permits the identification of Mg2+FAP, and consequently allows for a probe of the role of Mg2+ in the catalysis. Mg2+ binding to the active site is essential for catalysis. MgFAP is more tightly bound to the site than is FAP2-, but the complex is not obligatory for catalysis. The formation of a phosphoryl-enzyme intermediate is not evident in the reaction of FAP with the enzyme. Transient kinetic experiments, utilizing an excess of MgFAP, demonstrate a unique steady-state rate-limiting production of furylacrylate. These results indicate that the pathway demonstrated with ATP is not appropriate to the FAPase mechanism. The results suggest that acyl phosphates are good "phosphatase" substrates either because they are analogues of the phosphatase-specific phosphoryl-enzyme or because they react exclusively with the isomerized "E2" form of the enzyme.

Acrylates↗
PubMed1981

Prenyltransferase; determination of the binding mechanism and individual kinetic constants for farnesylpyrophosphate synthetase by rapid quench and isotope partitioning experiments.

The 1'-4 condensation reaction catalyzed by farnesylpyrophosphate synthetase was examined by using rapid quench and isotope partitioning experiments. E.Mg2+-isopentyl-PP (PP = pyrophosphate) is not catalytically competent, as evidenced by failure to trap the complex with Mg2+-geranyl-PP at concentrations as high as 3.2 mM. In contrast, the concentration of Mg2+-isopentenyl-PP required for one-half maximal trapping (K 1/2) of E.Mg2+-geranyl-PP is 1.4 muM. The results strongly support an ordered mechanism for the 1'-4 condensation reaction, with addition of the allylic substrate before Mg2+-isopentenyl-PP. At short reaction times, a burst phase corresponding to accumulation of Mg2+-farnesyl-PP on the surface of the enzyme, followed by a slower, steady-state release of products, is observed. Evaluation of individual kinetic constants for the reaction indicates that the rates for addition of Mg2+-geranyl-PP to the enzyme (k1 = 4.9 X 10(6) M-1 s-1) and addition of Mg2+-isopentenyl-PP to E.Mg2+-geranyl-PP (k3 = 2 X 10(6) m-1 s-1) are below the diffusion-controlled limit. The rate-limiting step at steady state is isomerization of E.Mg2+-farnesyl-PP-Mg2+-PPi or release of products (k6 = 0.1 s-1). During the course of isotope partitioning experiments with E.Mg2+-geranyl-PP, a new dual isotope procedure was developed which minimizes difficulties encountered during workup. In addition, for enzymes such as farnesyl-PP synthetase that catalyze irreversible reactions, the dual isotope approach is both sensitive extremely easy to execute.

Alkenes↗