MutY DNA glycosylase: base release and intermediate complex formation

MutY protein, a DNA glycosylase found in Escherichia coli, recognizes dA:dG, dA:8-oxodG, and dA:dC mismatches in duplex DNA, excising the adenine moiety. We have investigated the mechanism of action of MutY, addressing several points of disagreement raised by previous studies of this enzyme. MutY forms a covalent intermediate with its DNA substrate but does not catalyze strand cleavage. The covalent intermediate has a half-life of approximately 2.6 h, 2 orders of magnitude greater than the half-life of Schiff bases formed when E. coli formamidopyrimidine-DNA glycosylase (Fpg) and endonuclease III react with their respective substrates. The covalent complex between MutY and its DNA substrate involves Lys-142; however, the position of this residue in the presumptive active site differs from that of catalytic residues involved in Schiff base formation associated with endonuclease III and related DNA glycosylases/AP lyases. MutY converts DNA duplexes containing the dA:8-oxodG mispair to a product containing an abasic site; heat-induced cleavage of this product may account for the several reports in the literature that ascribe AP lyase activity to MutY. The MutY-DNA intermediate complex is highly stable and hinders access by Fpg to DNA, thereby avoiding a double-strand break. Cross-linking of MutY to DNA may play an important role in the regulation of base excision repair.     

Change in environment of the P1 side chain upon progression from the Michaelis complex to the covalent serpin-proteinase complex

Serpins inhibit proteinases by forming a kinetically trapped intermediate during a suicide substrate inhibition reaction. To determine whether the kinetic trap involves a repositioning of the P1 side chain of the serpin following formation of the initial Michaelis complex, we used the tryptophan of a P1 M-->W variant of human alpha1-proteinase inhibitor as a fluorescent reporter group of the environment of the P1 side chain. The P1W variant was a valid model serpin and formed SDS-stable complexes with both trypsin and chymotrypsin with a stoichiometry of inhibition close to 1.0. Rates of inhibition of chymotrypsin for wild-type and variant alpha1-proteinase inhibitor differred only approximately 1.8-fold. Rates of inhibition of trypsin were, however, 25-fold lower for the variant than for the wild-type inhibitor. Steady-state fluorescence spectra showed a change in environment for the P1 side chain upon forming both covalent complex with trypsin or chymotrypsin and noncovalent complex with anhydrochymotrypsin. The P1 environments in the chymotrypsin and anhydrochymotrypsin complexes were, however, different. Fluorescence quenching studies confirmed the burial of the P1 side chain upon formation of both the noncovalent and covalent complexes, but were not able to discriminate between the solvent accessibility in these complexes. Stopped-flow fluorescence measurements resolved the covalent intramolecular reaction that led to covalent complex and showed that, during the course of the covalent reaction, the environment of the P1 side chain changed consistent with a repositioning relative to residues of the proteinase active site as part of formation of the trap. This repositioning is likely to be a crucial part of the trapping mechanism.     

Microstructure and formation mechanism of complex chromium diffusion layer

Presentation of a new type of chromium diffusion layer obtained on 0.5 % C carbon steel by termit process. Microstructure, phase composition and chemical composition of the layer obtained after various chromizing conditions. Determination of the growth mechanism of layer based on Fe-Cr-C equilibrium diagrams.     

Modeling the interaction between FK506 and FKBP12: a mechanism for formation of the calcineurin inhibitory complex

FK506 is a naturally occurring immunosuppressant whose mode of action involves formation of an initial complex with the cytosolic protein FKBP12. The composite surface of this complex then binds to and inhibits the protein phosphatase calcineurin (PP2B). To investigate why FK506 does not inhibit calcineurin directly we have conducted molecular modeling and conformational studies on published structures of FK506 both alone and in complex with FKBP12. From studies of the structure of FK506 in CDCl3 and Z-Arg32-ascomycin in water (a water soluble analogue of FK506) we suggest that the FK506 molecule can be viewed as consisting of three separate regions. The pipecolate region which extends from C24 to C10 including the pipecolate ring shows strongly conserved conformation in both solvents. The loop region which extends from C25 to C16 shows general conservation of the loop structure and the pyranose region made up of the pyranose ring and C15-C17 which shows highly variable conformation depending on solvent. Comparison of the structure of Z-Arg32-ascomycin in water with structures of FK506 bound to FKBP12 indicate that the conformation of the pipecolate region is conserved during the binding process. The conformation of the loop region was generally conserved but a significant reduction (approximately 1.7 A) in the diameter of the loop in the bound structure was observed. The conformation of the pyranose ring and C15-C17 region was found to be significantly altered in the bound structure resulting in displacements of the C13 and C15 methoxyl groups of 2.8 and 3.5 A, respectively. From computer models and molecular dynamics simulations of interactions between FK506 and FKBP12 we suggest that the conformational changes observed in bound FK506 are induced by the interaction between the 80's loop of FKBP12 and the pyranose ring of FKBP12. These interactions result in the formation of a complex with the both correct shape and surface polarity for interaction with calcineurin.     

Catalytic mechanism of Kdo8P synthase: transient kinetic studies and evaluation of a putative reaction intermediate

The mechanistic pathway for the reaction catalyzed by Kdo8P synthase has been investigated, and the cyclic bisphosphate 2 has been examined as a putative reaction intermediate. Two parallel approaches were used: (1) chemical synthesis of 2 and evaluation as an alternate substrate for the enzyme and (2) transient kinetic studies using rapid chemical quench methodology to provide direct observation and characterization of putative intermediate(s) during enzyme catalysis. The putative cyclic bisphosphate intermediate 2, possessing the stereochemistry of the beta-pyranose form, was synthesized and evaluated as a substrate and as an inhibitor of Kdo8P synthase. The substrate activity was examined by monitoring the release of anomeric phosphate over time using proton-decoupled 31P NMR spectroscopy. A very similar time course for the formation of inorganic phosphate was found in each experiment and the corresponding control experiment; i.e., no enzyme-catalyzed acceleration in the anomeric phosphate hydrolysis was detected. It was found however that 2 binds to the enzyme and is a competitive inhibitor with respect to phosphoenolpyruvate binding, having a Ki value of 35 microM. In a parallel study, we have performed single-turnover rapid chemical quench experiments to examine both the forward and reverse directions to identify a putative enzyme intermediate(s). Our results clearly demonstrate that the cyclic bisphosphate intermediate 2 does not accumulate under single-enzyme turnover conditions. This observation, coupled with the results obtained through the evaluation of synthetic 2 as a substrate, strongly suggests that the Kdo8P synthase catalytic pathway does not involve the formation of 2 as a reaction intermediate. Taken together, these combined results support the original hypothesis [Hedstrom, L., and Abeles, R. H. (1988) Biochem. Biophys. Res. Commun. 157, 816-820], which suggests a reaction pathway involving an acyclic bisphosphate intermediate 1.     

Capillary electrophoretic study of the complex formation between DNA and cationic surfactants

Due to the growing interest in the use of cationic surfactants for the construction of liposomal genetic delivery systems, the study of complex formation between DNA and quaternary ammonium detergents is of fundamental importance. In this context, we undertook the study of this complex formation using capillary zone electrophoresis (CZE) with suppressed electroosmotic flow, a technique that allowed us to both monitor the change in mobility of DNA as a function of added surfactant in a precise and reproducible manner and evaluate the potential of CZE to reflect the change in hydrodynamic friction upon binding. Nevertheless, CZE must be applied with caution for binding studies where strong cooperativity occurs, because of the presence of peak splitting at concentrations close to the half-point of binding. Also, a comparison between this experiment and Manning's polyelectrolyte transport properties theory on one hand and Tirado and Garcia de la Torre expression for hydrodynamic friction of rod-like molecules on the other hand is given.     

Mechanism and intermediate for formation of 2'-deoxyoxanosine

A reaction mechanism for the direct formation of 2'-deoxyoxanosine (dOxo) from 2'-deoxyguanosine (dGuo) by nitrous acid (HNO2) or nitric oxide (NO) was explored by using guanosine (Guo) and its methyl derivatives. HNO2 treatment of 1-methylguanosine (1-Me-Guo) indicated that the exocyclic amino nitrogen (N5) of dOxo originates from imino nitrogen (N1) of dGuo. A short-lived intermediate detected in the Guo-HNO2 system by reversed phase (RP) HPLC was converted into oxanosine (Oxo) and xanthosine (Xao) at neutral pH. Based on these findings, we discuss the reaction mechanism for the formation of dOxo.     

Priming of simple and complex scene layout: Rapid function from the intermediate level.

Three experiments examined the time course of layout priming with photographic scenes varying in complexity (number of objects). Primes were presented for varying durations (800–50 ms) before a target scene with 2 spatial probes; observers indicated whether the left or right probe was closer to viewpoint. Reaction time was the main measure. Scene primes provided maximum benefits with 200 ms or less prime duration, indicating that scene priming is rapid enough to influence everyday distance perception. The time course of prime processing was similar for simple and complex scene primes and for upright and inverted primes, suggesting that the prime representation was intermediate level in nature. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

The complex interaction between measurement and national employment policy.

The long history of measurement in psychology was dramatically changed in the early 1960s when the role of measurement as a gate keeper to the rewards of American society achieved national attention. Since that time in the employment context, the U.S. Congress, state and city legislatures, and the courts have had strong roles in determining the future course of measurement. Debates in many circles continue to this day. Because of the results of a large amount of research focused on issues such as possible differential prediction and validity of tests for various societal groups, the focus of the debates has changed. The current issues are (a) alteration of test scores to achieve results consistent with some social policies, (b) accommodation of testing conditions for persons with disabilities, (c) limitations on the use of personality inventories in employee selection, and (d) substitution of alternate selection procedures for standardized tests. All of these issues have different bases in psychological research and present different problems. Particularly when the civil rights policies of the last 30 years are being challenged, psychologists must be even more diligent in efforts to ensure that policy deliberations are informed by sound research. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

The fine structure and formation mechanism of lower bainite

Isothermal transformation of austenite to lower bainite was studied by optical microscopy and transmission electron microscopy (TEM), in two high-purity Fe-C-4 wt pct Mn-2 wt pct Si alloys containing 0.4 and 0.6 wt pct carbon, in order to elucidate the fine structure and formation mechanism of lower bainite. The present results support a mechanism for lower bainite formation presented previously in which lower bainite sheaves result from the formation of an aggregate of fine ferrite crystals with thin austenite “gaps” between them; carbide precipitation occurs within these austenite gaps. This mechanism accounts for the carbides oriented at an angle to the sheaf axis repeatedly observed in lower bainite but is inconsistent with models based on the precipitation of a high-volume fraction of carbides within highly supersaturated ferrite formed by high-velocity shear. Observations by a number of other researchers are reviewed and shown to include morphological features consistent with the present mechanism. Finally, the orientation relationships typically observed among ferrite, austenite, and carbides in lower bainite are reviewed and shown in most (but not all) cases to be consistent with the view that carbides precipitate in austenite at ferrite-austenite boundaries, also in agreement with the present model. This article is based on a presentation made at the Pacific Rim Conference on the “Roles of Shear and Diffusion in the Formation of Plate-Shaped Transformation Products,” held December 18-22, 1992, in Kona, Hawaii, under the auspices of ASM INTERNATIONAL’S Phase Transformations Committee.     

Interaction between the antibiotic spiramycin and a ribosomal complex active in peptide bond formation

The inhibition of peptide bond formation by spiramycin was studied in an in vitro system derived from Escherichia coli. Peptide bonds are formed between puromycin (S) and Ac-Phe-tRNA, which is a component of complex C, i.e., of the [Ac-Phe-tRNA-70S ribosome-poly(U)] complex, according to the puromycin reaction: C+S (Ks)<==>CS (k3)==>C'+P [Synetos, D., & Coutsogeorgopoulos, C. (1987) Biochim. Biophys. Acta 923, 275-285]. It is shown that spiramycin (A) reacts with complex C and forms the spiramycin complex C*A, which is inactive toward puromycin. C*A is the tightest complex formed between complex C and any of a number of antibiotics, such as chloramphenicol, blasticidin S, lincomycin, or sparsomycin. C*A remains stable following gel chromatography on Sephadex G-200 and sucrose gradient ultracentrifugation. Detailed kinetic study suggests that C*A is formed in a variation of a two-step mechanism in which the initial encounter complex CA is kinetically insignificant and C*A is the product of a conformational change of complex CA according to the equation, C+A (kassoc)<==>(kdissoc) C*A. The rate constants of this reaction (spiramycin reaction) are kassoc = 3.0 x 10(4) M-1 s-1 and kdissoc = 5.0 x 10(-5) s-1. Such values allow the classification of spiramycin as a slow-binding, slowly reversible inhibitor; they also lead to the calculation of an apparent overall dissociation constant equal to 1.8 nM for the C*A complex. Furthermore, they render spiramycin a useful tool in the study of antibiotic action on protein synthesis in vitro. Thus, the spiramycin reaction, in conjunction with the puromycin reaction, is applied (i) to detect a strong preincubation effect exerted by chloramphenicol and lincomycin (this effect constitutes further evidence that these two antibiotics combine with complex C as slow-binding inhibitors) and (ii) to determine the rate constant for the regeneration (k7 = 2.0 x 10(-3) s-1) of complex C from the sparsomycin complex C*I [Theocharis, D. A., & Coutsogeorgopoulos, C. (1992) Biochemistry 31, 5861-5868] according to the equation, C+I (Ki)<==>CI (k6)<==>(k7) C*I. The determination of k7 enables us to calculate the apparent association rate constant of sparsomycin, (k7/Ki') = 1.0 x 10(5) M-1 s-1, where Ki' = Ki(k7/k6 + k7). It is also shown that Ac-Phe-tRNA bound to the sparsomycin complex C*I is protected against attack by hydroxylamine.(ABSTRACT TRUNCATED AT 400 WORDS)     

The propeptide of the vitamin K-dependent carboxylase substrate accelerates formation of the gamma-glutamyl carbanion intermediate

Vitamin K-dependent carboxylase catalyzes the post-translational gamma-carboxylation of 9-12 glutamyl residues of several blood coagulation proteins. Carboxylase purified from Chinese hamster ovary (CHO) cells as a recombinant FLAG-carboxylase fusion protein [Sugiura, I., et al. (1996) J. Biol. Chem. 271, 17837-17844] was utilized with pentapeptide substrate FL[3H-R,S]EAL with high specific radioactivity to probe the timing of glutamyl Cgamma-3H cleavage relative to Cgamma-COO- bond formation by 14CO2 incorporation rates. Studies were conducted over a range of NaH14CO3 concentrations to assess uncoupling of gamma-glutamyl carbanion formation and over a range of concentrations of ProPT18, the 18-residue peptide corresponding to the -18 to -1 propeptide region of prothrombin known to affect the catalytic efficiency of carboxylase. At saturation, ProPT18 accelerates Cgamma-3H cleavage 11-13-fold and Cgamma-14CO2- formation 6-7-fold, converting a Cgamma-3H cleavage/Cgamma-14CO2- formation ratio of 1.2-1.4 in the absence of ProPT18 to 2.3-2.8 in its presence, a relative increase in and uncoupling of Cgamma-3H cleavage from C-C bond formation. When the HCO3- concentration was varied, the V/K3H+/V/K14CO2 ratios rose as HCO3- fractional saturation dropped to a ratio of 9.3-10.8/l at low bicarbonate, indicating an uncoupling of nine out of ten gamma-glutamyl carbanion formations from carboxylative capture, consistent with prior reports on microsomal enzyme [Larson, A. E., et al. (1981) J. Biol. Chem. 256, 11032-11035]. These results with pentapeptide substrate FLEAL validate reversible gamma-glutamyl carbanion formation by pure carboxylase and indicate the ProPT18 increase in catalytic efficiency is in selective lowering of an energy barrier preceding the gamma-glutamyl carbanion intermediate.     

Spectrophotometric study of complex formation between oxovanadium (IV) and antiamebic drugs

Complex formation between oxovanadium(IV) and the antiamebic drugs 5, 7-dibromo-8-quinolinol and 5, 7-dichloro-8-quinolinol was studied in the pH 1.5-2.0 range, using ethanol, dioxane-water, and dimethylformamide as solvents. The composition of the formed complexes was determined by more than one procedure. In ethanol and dioxane-water, the 1:1 and 1:2 complexes were formed; in dimethylformamide, the 1:1, 1:2 and 1:3 complexes were formed. The stability constants were computed using two procedures: the molar ratio method and the extrapolation method. The reproducibility or results in satisfactory.     

Thermodynamic and kinetic studies of the formation of triple helices between purine-rich deoxyribo-oligonucleotides and the promoter region of the human c-src proto-oncogene

The thermodynamic and kinetic parameters of triplex formation between four purine-rich oligonucleotides and a 22 bp pyrimidine. purine tract in the promoter region of the c-src gene were determined by fluorescence polarization studies. Three of these four oligonucleotides were 11 nt in length, corresponding to the left, central or right portion of the tract, while the fourth was a 22mer covering the whole tract. Binding constants ( Ka) were measured as a function of Mg2+ concentration (0-10 mM) and temperature (0-41 degrees C). In 10 mM Mg2+, K a for the left, central and right 11mers were 0.26, 0.75 and 1.4 x 10(8)/M, respectively, while for the 22mer the value was 1.8 x 10(8)/M at 22 degrees C. Under the same conditions, Ka was estimated by an electrophoretic band shift technique. The agreement between the two methods was acceptable for the 22mer but not for the 11mers. Kinetic measurements demonstrated that the rate of dissociation of the 22mer from the triplex was significantly slower than that of the 11mers, providing an explanation for the observed discrepancy. The entropy and enthalpy of triplex formation were calculated from van't Hoff plots. In all cases the entropy was favourable, especially for the 22mer and for the 11mer with the lowest guanine content. The enthalpy was unfavourable for the 22mer and most favourable for the 11mer with the highest guanine content. These results provide a thermodynamic explanation for length and sequence effects on the formation of purine.pyrimidine.purine triplexes.     

Studies on mechanism about ATP inhibited the proliferation of MGC-803 cells

This experiment was to study the mechanism of ATP anticancer effects. By using flow cytometry, Scrape-Loading and dye transfer (SLDT), dot hybridization methods, changes of cell cycle phase distribution, gap junctional intercellular communication (GJIC), and oncogene expression were observed in human stomach mucous glandular carcinoma (MGC-803) cells treated with ATP (0.23 mg/ml). It was found that ATP inhibited the proliferation and arrested cell cycle in S phase. The ATP-treated MGC-803 cells increased in GJIC, and decreased in expression of c-Ha-ras oncogene. These results indicated that the inhibition of proliferation and increased GJIC was closely correlated with the reduction of c-Ha-ras oncogene expression.     

The relationship between vaccinia virus DNA replication and intermediate filaments

Various DNA components which were extracted with gentle cell fractionation from the HeLa cells after 4 h vaccinia virus infection were detected by dot hybridization technique. The virus DNA mainly exist in intermediate filament-lamina-nuclear matrix complex. With DGD embedment free technique and electron microscopic autoradiography, the newly synthesized virus DNA is found to be associated with intermediate filaments. The results of southwestern hybridization demonstrate that vaccinia virus DNA has specific affinity to intermediate filaments and some nuclear matrix proteins.     

Colocalization and complex formation between prosaposin and monosialoganglioside GM3 in neural cells

Prosaposin, the precursor of saposins A, B, C, and D, was recently identified as a neurotrophic factor in vitro as well as in vivo. Its neurotrophic activity has been localized to a linear 12-amino acid sequence located in the NH2-terminal portion of the saposin C domain. In this study, we show the colocalization of prosaposin and ganglioside GM3 on NS20Y cell plasma membrane by scanning confocal microscopy. Also, TLC and western blot analyses showed that GM3 was specifically associated with prosaposin in immunoprecipitates; this binding was Ca2+-independent and not disassociated during sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The association of prosaposin-GM3 complexes on the cell surface appeared to be functionally important, as determined by differentiation assays. Neurite sprouting, induced by GM3, was inhibited by antibodies raised against a 22-mer peptide, prosaptide 769, containing the neurotrophic sequence of prosaposin. In addition, pertussis toxin inhibited prosaptide-induced neurite outgrowth, as well as prosaptide-enhanced ganglioside concentrations in NS20Y cells, suggesting that prosaposin acted via a G protein-mediated pathway, affecting both ganglioside content and neuronal differentiation. Our findings revealed a direct and tight GM3-prosaposin association on NS20Y plasma membranes. We suggest that ganglioside-protein complexes are structural components of the prosaposin receptor involved in cell differentiation.     

The role of glutamate 87 in the kinetic mechanism of Thermus thermophilus isopropylmalate dehydrogenase

The kinetic mechanism of the oxidative decarboxylation of 2R,3S-isopropylmalate by the NAD-dependent isopropylmalate dehydrogenase of Thermus thermophilus was investigated. Initial rate results typical of random or steady-state ordered sequential mechanisms are obtained for both the wild-type and two mutant enzymes (E87G and E87Q) regardless of whether natural or alternative substrates (2R-malate, 2R,3S-tartrate and/or NADP) are utilized. Initial rate data fail to converge on a rapid equilibrium-ordered pattern despite marked reductions in specificity (kcat/Km) caused by the mutations and alternative substrates. Although the inhibition studies alone might suggest an ordered kinetic mechanism with cofactor binding first, a detailed analysis reveals that the expected noncompetitive patterns appear uncompetitive because the dissociation constants from the ternary complexes are far smaller than those from the binary complexes. Equilibrium fluorescence studies both confirm the random binding of substrates and the kinetic estimates of the dissociation constants of the substrates from the binary complexes. The latter are not distributed markedly by the mutations at site 87. Mutations at site 87 do not affect the dissociation constants from the binary complexes, but do greatly increase the Michaelis constants, indicating that E87 helps stabilize the Michaelis complex of the wild-type enzyme. The available structural data, the patterns of the kinetics results, and the structure of a pseudo-Michaelis complex of the homologous isocitrate dehydrogenase of Escherichia coli suggest that E87 interacts with the nicotinamide ring.     

Deuterium kinetic isotope effects and the mechanism of the bacterial luciferase reaction

A combined experimental and theoretical investigation of the deuterium isotope effects on the bacterial luciferase reaction is described. The experimental studies focus on determining if the unusual aldehydic deuterium isotope effect of approximately 1.5 observed in these reactions is an intrinsic isotope effect resulting from a single rate-limiting step or is a composite of multiple rate-limiting steps. The isotope effect observed is not significantly affected by variation in the aldehyde chain length, changes in the pH over a range of 6-9, use of alphaC106A and alphaC106S site-directed mutants, or chloride substitution at the 8-position of the reduced flavin, though the isotope effect is decreased when the 8-methoxy-substituted flavin is used as a substrate. From these observations it is concluded that the aldehydic isotope effect arises from the change in rate of a single kinetic step. A stopped-flow kinetic analysis of the microscopic rate constants for the reactions of 1-[1H]decanal and 1-[2H]decanal in the bacterial luciferase reaction was carried out, and aldehyde hydration isotope effects were determined. From the results it is estimated that the aldehydic deuterium isotope effect is approximately 1.9 after formation of an intermediate flavin C4a-hydroperoxy hemiacetal. Ab initio calculations were used to examine the transformation of the aldehyde into a carboxylic acid and to predict isotope effects for possible mechanisms. These calculations indicate that the mechanism involving rate-limiting electron transfer from the flavin C4a-hydroxide to an intermediate dioxirane is consistent with the enigmatic aldehydic isotope effect and that the intermediacy of a dioxirane is energetically plausible.