Estimation of glycosaminoglycans by atomic absorption determination of copper in their Alcian Blue complexes.
Explore the source record for details and available documents.
SEARCH · PubMed Health
Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Explore the source record for details and available documents.
In the development of biosensors, it is essential to understand how the signal-transducing element may perturb surface-bound proteins and nucleic acids. The tip of the atomic force microscope is such an element in atomic force microscopy. In this paper, we describe the influence of tip-sample interactions on the measured height of the DNA repair protein, Ku, that has been adsorbed onto a mica surface which was submerged in aqueous solution. We find that the measured height of the Ku molecule depends critically on whether or not it is associated with DNA. Additionally, we observed that the conditions (time and concentration) under which Ku is incubated with DNA, affect the appearance (number and type) of the DNA-Ku complexes observed.
The hydrate of glycolaldehyde is a substrate analogue that induces the formation of cob(II)alamin and 5'-deoxyadenosine from adenosylcobalamin at the active site of dioldehydrase, and the resulting complex is inactive. The carbon atoms of glycolaldehyde hydrate remain bound to this complex, and it has been postulated that the first step or steps of the catalytic process on glycolaldehyde hydrate generate an intermediate that undergoes a destructive side reaction leading to inactivation of the enzyme [Wagner, O. W., Lee, H. A., Jr., Frey, P. A., and Abeles, R. H. (1966) J. Biol. Chem. 249, 1751-1762]. All evidence suggests that dioldehydrase reaction proceeds by a radical mechanism, and the glycolaldehyde hydrate is expected to be converted initially into a radical. Electron paramagnetic resonance (EPR) spectroscopic analysis of the inactivated complex shows that glycolaldehyde is transformed into a cis-ethanesemidione radical that is weakly spin-coupled to the cob(II)alamin in the active site of the enzyme. This radical has been identified by analysis of EPR spectra obtained from samples with (13)C- and (2)H-labeled forms of glycolaldehyde. The analysis shows that the stable radical associated with the inactive complex is symmetrical and that it contains a single solvent-exchangeable proton, consistent with a cis-ethanesemidione. Glycolaldehyde also inactivates ethanolamine ammonia-lyase (EAL). EPR studies of ethanolamine ammonia-lyase reveal that treatment with glycolaldehyde also results in formation of an ethanesemidione radical bound in the active site. The suicide inactivation in both enzymatic reactions is postulated to result from formation of this stable radical, which cannot react further to abstract a hydrogen atom from 5'-deoxyadenosine. Analysis of the electron spin-spin coupling between the semidione radicals and cob(II)alamin in both enzymes indicates that the distance between the radical and Co(2+) is approximately 11 A in each case.
The rhenium(V) complex [(HCpz3)ReOCl2]+ ([1]+), the tris(pyrazolyl)methane analogue of the known tris(pyrazolyl)borate complex (HBpz3)ReOCl2 (2), has been prepared. The two complexes are strikingly similar, as are the phosphine oxide adducts [(HCpz3)ReCl2(OPPh3)]Cl ([3]Cl) and (HBpz3)ReCl2(OPPh3) (4), which have been characterized by X-ray crystallography. Comparison of the bimolecular reduction of [1]BF4 and 2 by triarylphosphines reveals a pronounced charge effect, with the cationic species being reduced by PPh3 about 1,000 times faster than its neutral analogue in CH2Cl2 at room temperature. Ligand substitution of the adducts [3]+ and 4 is dissociative, with the cationic complex dissociating phosphine oxide about 56 times more slowly than the neutral compound. The relative impact of charge on ground and transition states in atom transfer reactions is discussed.
A calcium (Ca)-DNA complex in a buffered aqueous solution was irradiated with monochromatic x-rays at around the K-shell absorption edge of the Ca atom. The energies were 4.030 and 4.071 keV, which correspond to slightly below and above the K-shell absorption edge of Ca (4.047 keV). The number of double-strand breaks (DSB) and single-strand breaks (SSB) per one molecule of Col E1 DNA was calculated using Povirk's equation after the electrophoretic separation of three forms of plasmid DNA (forms I, II and III, which are supercoiled closed circular, open circular and linear, respectively). In a solution with Ca ions, the DSB yield in DNA irradiated with 4.071 keV x-rays is 1.27 times higher than that with 4.030 keV x-rays. In contrast, in the absence of Ca ions, the DSB yield is the same at both the x-ray energies. The SSB yields are also independent of the x-ray energy in the presence and absence of Ca ions. A reference experiment regarding irradiation with 60Co gamma-rays shows that the ratio of the DSB yield to the SSB yield upon irradiation with 4.071 keV x-rays is higher (factor of 3.2) than that with 60Co gamma-rays.
When expressed in Escherichia coli, the heme domain [beta1(1-385)] of rat lung soluble guanylate cyclase (sGC) is isolated with a stoichiometric amount of bound heme [Zhao, Y., and Marletta, M. A. (1997) Biochemistry 36, 15959-15964]. Nitric oxide (NO) binding to the heme in beta1(1-385) leads to cleavage of the Fe-His bond and formation of a five-coordinate NO-heme complex. Addition of imidazole to the five-coordinate NO complex shifts the Soret peak from 399 to 420 nm, which appears to result from the formation of a six-coordinate NO complex. Removal of the added imidazole by gel filtration results in formation of the five-coordinate NO complex once again. The EPR spectrum of the putative six-coordinate NO complex has nine distinct derivative-shaped lines (a triplet of triplets), which is the signature spectrum of a six-coordinate NO complex with two nitrogen atoms as the axial ligands. [15N]Imidazole simplifies the six-coordinate NO complex EPR spectrum to six distinct derivative-shaped lines (a triplet of doublets), indicating that the other axial ligand in the six-coordinate NO complex is an imidazole molecule. These results show that NO binding to sGC not only leads to the cleavage of the Fe-His bond but also induces a conformational change which opens the heme proximal pocket large enough to accommodate an exogenous imidazole molecule. These observations have important implications for determining the NO activation mechanism of sGC.
The application of inductively coupled plasma atomic emission spectrometry (ICP-AES) to the determination of the concentration of complex boron-containing compounds in biological tissue samples is described. Tissue digestion is achieved with perchloric acid and hydrogen peroxide in 1 hr at 75 degrees C. The ICP-AES method gave a linear response for elemental boron concentration in the range 0.05 to 100 ppm and does not require the reduction of the boron to a simple species, such as boric acid. Complete recovery of boron in complex boron cluster compounds was obtained. The procedure has been applied to the determination of the boron content in compounds synthesised for neutron capture therapy and is suitable for use in biodistribution studies of such compounds.
Recognition of 'foreign' DNA by Type I restriction-modification (R-M) enzymes elicits an ATP-dependent switch from methylase to endonuclease activity, which involves DNA translocation by the restriction subunit HsdR. Type I R-M enzymes are composed of three (Hsd) subunits with a stoichiometry of HsdR2:HsdM2:HsdS1 (R2-complex). However, the EcoR124I R-M enzyme can also exist as a cleavage deficient, sub-assembly of HsdR1:HsdM2:HsdS1 (R1-complex). ATPS was used to trap initial translocation complexes, which were visualized by Atomic Force Microscopy (AFM). In the R1-complex, a small bulge, associated with a shortening in the contour-length of the DNA of 8 nm, was observed. This bulge was found to be sensitive to single-strand DNA nucleases, indicative of non-duplexed DNA. R2-complexes appeared larger in the AFM images and the DNA contour length showed a shortening of approximately 11 nm, suggesting that two bulges were formed. Disclosure of the structure of the first stage after the recognition-translocation switch of Type I restriction enzymes forms an important first step in resolving a detailed mechanistic picture of DNA translocation by SF-II DNA translocation motors.
The manganese(III) complex K[MnL(py)(2)].py (H(4)L = 1,2-bis(2-hydroxybenzamido)benzene, py = pyridine) reacted as a ligand complex at the two phenoxo oxygen atoms with metal(II) ion and 2,2'-bipyridine to give a series of heterometal complexes [Mn(MeOH)L(OH)M(bpy)](2) (M(II) = Zn (1); Cu (2); Ni (3); Mn (4)). X-ray structures were determined 1, C(68)H(74)N(8)O(18)Mn(2)Zn(2): a = 12.367(3) Å, b = 12.844(2) Å, c = 12.262(2) Å, alpha = 106.58(1) degrees, beta = 117.89(1) degrees, gamma = 78.57(2) degrees, triclinic, P&onemacr;, and Z = 1. 2, C(68)H(74)N(8)O(18)Mn(2)Cu(2): a = 13.447(1) Å, b = 12.670(2) Å, c = 21.732(1) Å, beta = 107.076(5) degrees, monoclinic, P2(1)/n, and Z =2. 3, C(68)H(74)N(8)O(18)Mn(2)Ni(2): a = 12.358(3) Å, b = 12.847(3) Å, c = 12.315(3) Å, alpha = 106.63(2) degrees, beta = 118.71(1) degrees, gamma = 78.32(2) degrees, triclinic, P&onemacr;, and Z = 1. 4, C(66)H(66)N(8)O(16)Mn(4): a = 12.511(2) Å, b = 21.129(3) Å, c = 12.811(1) Å, beta = 110.12(1) degrees, monoclinic, P2(1)/n, and Z = 2. The X-ray analyses confirmed that each of the crystals consists of an incomplete double-cubane molecule with a [Mn(2)M(2)O(6)] core, in which two M(II) ions are bridged by two hydroxo groups to form a planar dinuclear moiety bridged by di-&mgr;-hydroxo groups [(bpy)M(OH)(2)M(bpy)](2+) and the dinuclear moiety is sandwiched between two Mn(III) complexes [Mn(MeOH)L](-). The Mn(III) ion and the dinuclear M(II) moiety are triply bridged by the one hydroxo oxygen of the dinuclear moiety and two phenoxo oxygen atoms of the Mn(III) ligand complex. The two phenoxo oxygen atoms of the Mn(III) ligand complex coordinate as an axial ligand to two independent metal(II) ions of the dinuclear moiety. The magnetic susceptibilities of 1-4 were measured in the temperature range of 2-300 K. All the Mn(III) ions in these complexes are in a high-spin state of S(Mn) = 2 with a d(4) electronic configuration, and the metal(II) ions are in the spin states of S(Zn) = 0, S(Cu) = 1/2, S(Ni) = 1, and S(Mn(II)) = 1/2 (low-spin). The magnetic susceptibility data are well reproduced by the following spin Hamiltonian based on the rhombus spin coupling model with spin (S(1), S(2), S(3), S(4)) = (2, S(M), 2, S(M)), including a zero-field splitting term for the Mn(III) centers: H = g(Mn)beta(S(1) + S(3)).H + g(M)beta(S(2) + S(4)).H - 2J(S(1).S(2) + S(2).S(3) + S(3).S(4) + S(4).S(1)) - 2J'(S(2).S(4)) + D(Mn)[S(1z)(2) + S(3z)(2)], in which g(Mn) and g(M) are the g factors of the Mn(III) and M(II) ions, J and J' are the Mn(III)-M(II) and M(II)-M(II) Heisenberg coupling constants, and D is the zero-field splitting parameter of Mn(III). The calculated best-fit parameters are as follows: g(Mn) = 1.91, g(Cu) = 2.39, J = -4.5 cm(-)(1), J' = -8.1 cm(-)(1), and D(Mn) = -4.9 cm(-)(1) for 2; g(Mn) = 1.97, g(Ni) = 2.23, J = -1.5 cm(-)(1), J' = -2.6 cm(-)(1), and D(Mn) = -5.5 cm(-)(1) for 3; and g(Mn) =1.95, g(Mn(II)) = 2.29, J = -3.5 cm(-)(1), J' = -14.1 cm(-)(1), and D(Mn) = -12.0 cm(-)(1) for 4. The spin frustration due to the incomplete double-cubane structure is discussed.
The complexes formed between Escherichia coli single-stranded DNA binding protein (SSBP) and the heavy atom-modified single-stranded polynucleotides poly(5-BrU) and poly(5-HgU) are investigated using optically detected magnetic resonance (ODMR) methods. In these complexes the triplet state properties of the tryptophan residues are subjected to the external heavy atom effect generated by bromine and mercury atoms and are characterized by a shortened triplet state lifetime and the appearance of the otherwise dark [D] + [E] slow passage ODMR signal. These features provide direct evidence for close range interactions between tryptophan residue(s) and the nucleotide bases in the complexes. The extent of the triplet state lifetime reduction in the case of the SSBP-poly(5-HgU) complex together with steric considerations of the complex structure is consistent only with a van der Waals contact between the perturbed molecule and the heavy atom perturber by means of a stacking interaction. Fast passage ODMR measurements show a lifetime for a sublevel of the perturbed tryptophan chromophore(s) in this complex on the order of 1 ms. The amplitude-modulated phosphorescence microwave double resonance technique captures selectively the broadened and red-shifted phosphorescence spectrum of the heavy atom-perturbed tryptophan residue(s). This work supports a model for the binding of SSBP to single-stranded polynucleotides in which the bases are inserted into hydrophobic regions of the protein, where they are likely to undergo stacking interactions with the indole moiety of buried tryptophan residues.
A computational study of gold(II) disproportionation is presented for the atomic ion as well as complexes with chloride and neutral ligands. The Au2+ atomic ion is stable to disproportionation, but the barrier is more than halved to 119 kcal/mol in an aqueous environment vs 283 kcal/mol in the gas phase. For dissociative disproportionation of chloride complexes, the loss of chlorine, either as an atom (Delta G(aq) = +20 kcal/mol) or as an anion (Delta G(aq) = +15 kcal/mol) represents the largest calculated barrier. The calculated transition state for associative disproportionation is only 9 kcal/mol above separated Au(II)Cl3(-) anions. For the disproportionation of Au(II)L3 complexes with neutral ligands, disproportionation is highly endergonic in the gas phase. Calculations imply that for synthesis of a monometallic Au(II) complex, a nonpolar solvent is preferred. With the exception of [Au(CO)3]2+, disproportionation of Au(II)L3 complexes to Au(I)L and Au(III)L3 is exergonic in solution phase for the ligands investigated. The driving force is provided by the very favorable solvation free energy of the trivalent gold complex. The solvation free energy contribution to the reaction (Delta G(solv)) is very large for small and polar ligands such as ammonia and water. Furthermore, calculations imply that choosing ligands that would yield neutral species upon disproportionation may provide an effective route to thwart this decomposition pathway for Au(II) complexes. Likewise, bulkier ligands that yield larger, more weakly solvated complex ions would appear to be desirable.
Progress towards rapid and simple characterization of biomolecular samples by scanning probe microscopy is impeded mainly by limitations of the current approach to sample preparation. We are working on approaches based on chemical functionalization of mica. Treatment of mica with aminopropyltriethoxy silane (APTES) makes the surface positively charged (AP-mica) and able to hold DNA in place for imaging, even in water. We have shown that AP-mica is an appropriate substrate for numerous nucleoprotein complexes as well. The AFM images of the complex of DNA with RecA protein are stable and indicate a structural periodicity for this filament. AP-mica holds strongly such large DNA complexes as kinetoplast DNA (kDNA) and is an appropriate substrate for their imaging with AFM. We have further develop this approach for making hydrophobic substrates. Silylation of mica surface with hexamethyldisilazane (Me-mica) allowed us to get AFM images of chlorosomes, an antenna complex isolated from green photosynthetic bacteria. Me-mica may be converted into a positively charged substrate after treatment with water solutions of tetraethylammonium bromide or cetyltrimethylammonium bromide. These activated surfaces show high activity towards binding the DNA molecules.
To regulate the reactivity of dithiolene dioxomolybdenum(VI) complexes, two systems were studied: (1) chelate recognition with a diamide additive, 1,3-bis(isobutyrylamino)benzene (1); (2) a dithiolene complex with four amide substituents, (n-Pr(4)N)(2)[Mo(IV)O{S(2)C(2)(CONH(2))(2)}(2)].0.5(i-PrOH).DMF (2) (S(2)C(2)(CONH(2))(2) = 1,2-dicarbamoylethylene-1,2-dithiolate). Both amide compounds, the additive 1 and the complex 2, were designed to form NH.S and/or NH.O hydrogen bonding with thiolate ligands in (Mo(VI)O(2))(2+) and (Mo(IV)O)(2+) complexes. Titration analyses indicate the presence of a 1:1 complex in CH(2)Cl(2) solution. This association causes changes in solubility and reactivity of the molybdenum complexes. When the additive was mixed with a DMSO-d(6) solution of (NEt(4))(2)[Mo(IV)O{S(2)C(2)(COOMe)(2)}(2)] (3) (S(2)C(2)(COOMe)(2) = 1,2-di(methoxycarbonyl)ethylene-1,2-dithiolate), the rate of reduction of Me(3)NO was increased by a factor of 6. An acceleration was also observed for compound 2. It appeares that NH.S hydogen bonding is modulating the system.
The kinetics of reaction between triarylphosphanes and two newly prepared dioxorhenium(VII) compounds has been evaluated. The compounds are MeRe(VII)(O)(2)("O,S") in which "O,S" represents an alkoxo, thiolato chelating ligand. With MeReO(3), ligands derived from 1-mercaptoethanol and 1-mercapto-2-propanol form MeRe(O)(2)(met), 2, and MeRe(O)(2)(m2p), 3. These compounds persist in chloroform solution for several hours at room temperature and for 2-3 weeks at -22 degrees C, particularly when water is carefully excluded. They were obtained as red oils with clean (1)H NMR spectra, but attempts to obtain pure, crystalline products were not successful because one decomposition pathway shows a kinetic order >1. The fastest reaction occurs between P(p-MeOC(6)H(4))(3) and 2; k(298) = 215(7) L mol(-1) s(-1) in chloroform at 25(1) degrees C. The other rate constants follow a Hammett correlation against 3sigma, with rho = -0.69(7). This study relates to oxygen atom transfer reactions catalyzed by MeReO(mtp)PPh(3), 1, in which MeRe(O)(2)(mtp), 4, is a postulated intermediate that does not build up to a measurable concentration during the catalytic cycle. Compound 2 does not react with MeSTol, but MeS(O)Tol was formed when tert-butyl hydroperoxide was added. This suggests that equilibrium lies to the left in this reaction, 2 + MeSTol + L = MeReO(met)L + MeS(O)Tol, and is drawn to the right by a reaction between MeReO(met)L and the hydroperoxide. Triphenyl arsane does not react with 2, but thermodynamic versus kinetic barriers were not resolved.
The complex formed between methanol and tetrafluoromethane has been identified in argon and neon matrixes by help of FTIR spectroscopy. Three fundamentals (nu(OH), nu(FCF), and nu(CO)) were observed for the complex isolated in the two matrixes, and the OH stretch was red shifted in a neon matrix and blue shifted in an argon matrix with respect to the corresponding vibration of the methanol monomer. The theoretical studies of the structure and spectral characteristics of the complexes formed between CH(3)OH and CF(4) were carried out at the MP2 level of theory with the 6-311+G(2df,2pd) basis set. The calculations resulted in three stationary points from which two (I-1, I-2) corresponded to structures involving the O-H...F hydrogen bond and the third one (I-3) to the non-hydrogen-bonded structure. The topological analysis of the distribution of the charge density (AIM theory) confirmed the existence of the hydrogen bond in I-1, I-2 complexes and indicated weak interaction between the oxygen atom of CH(3)OH and three fluorine atoms of CF(4) in the I-3 complex. The comparison of the experimental and theoretical data suggests that in the matrixes only the non-hydrogen-bonded complex I-3 is trapped. The blue/red shift of the complex OH stretching vibration with respect to the corresponding vibration of CH(3)OH in argon/neon matrixes is explained by the different sensitivity of the complex and monomer vibrations to matrix material. The ab initio calculations performed for the ternary CH(3)OH-CF(4)-Ar systems indicated a negligible effect of an argon atom on the binary complex frequencies.
This paper describes an efficient combinatorial method for simplification of topological features in a 3D scalar function. The Morse-Smale complex, which provides a succinct representation of a function's associated gradient flow field, is used to identify topological features and their significance. The simplification process, guided by the Morse-Smale complex, proceeds by repeatedly applying two atomic operations that each remove a pair of critical points from the complex. Efficient storage of the complex results in execution of these atomic operations at interactive rates. Visualization of the simplified complex shows that the simplification preserves significant topological features while removing small features and noise.
Because of their intense white lines and large f" values, lanthanide atoms are of great interest for solving structures of biological macromolecules using single-wavelength anomalous diffraction (SAD) or multiple-wavelength anomalous diffraction (MAD) methods. In this work, a series of seven gadolinium complexes are described which provide excellent derivatives for anomalous diffraction experiments in biological systems. These highly soluble lanthanide complexes can easily be introduced into protein crystals either by soaking or by co-crystallization, without significantly affecting the crystallization conditions, by employing highly concentrated complex solutions ( approximately 100 mM). De novo phasing by the SAD method was carried out with several proteins of known as well as previously unknown structures by employing this new class of heavy-atom compounds. Diffraction data were collected either with a laboratory source, making use of the high anomalous signal (f" = 12 e(-)) of gadolinium with Cu Kalpha radiation, or with synchrotron radiation at the peak of the gadolinium L(III) absorption edge, which exhibits a strong white line (lambda = 1.711 A, f" = 28 e(-)). Using one of these gadolinium complexes, Gd-HPDO3A, the structure of a bacterial chimeric ornithine carbamoyl transferase, OTCase3630, a dodecameric protein of 450 kDa, was determined. Employed with the SAD method, these seven complexes could be of particular interest for high-throughput macromolecular crystallography.
The near-diffusion-controlled reactions of hydroxyl radical, hydrated electron, and hydrogen atom with platinum macrocyclic complex ions in aqueous media have been studied using pulse radiolysis in conjunction with UV-visible absorption and conductivity detection. The hydrated electron and hydrogen atom react with trans-[Pt(cyclam)(Cl)(2)](2+) where cyclam is 1,4,8,11-tetraazacyclotetradecane to yield platinum(III) transients that exhibit intense absorption peaks in the 280-300 nm region; however in the case of the H-atom, the reaction involves a competition between chloride abstraction and a minor process, suggested to be attack on the organic ligand. The platinum(III) products are kinetically labile toward loss of chloro ligands, but these reactions are reversible in the presence of added KCl. The reactions of hydroxyl radical with [Pt(cyclam)](2+) and with [Pt(tmc)](2+), where tmc is 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane, lead to platinum(III) intermediates absorbing in the 250-300 nm region. Depending on the presence or absence of added KCl and on the pH, the platinum(III) cyclam systems can react to form a product(s) exhibiting absorption peaks near 330 and 455 nm, and this species is proposed to be a long-lived amidoplatinum(III) complex. In support of this proposal is the observation that the tmc system does not give rise to a similar visible-absorbing product. The interrelations of the cyclam-based transients through acid-base, chloro-substitution and water-elimination processes are discussed.