DNA interaction with RNase A alters protein conformation

DNA-RNase H adducts were used for site specific cleavage of RNA and DNA-RNA duplexes, whereas nonspecific DNA interaction with ribonuclease A (RNase A) has been observed. The aim of this study was to examine the complexation of calf-thymus DNA with RNase A at physiological condition, using constant DNA concentration (12.5 mM) and various protein contents (1 microM to 270 microM). FTIR, UV-visible, and CD spectroscopic methods were used to analyse protein binding mode, the binding constant and the effects of nucleic acid-enzyme interaction on both DNA and protein conformations. Our structural analysis showed a strong RNase-PO2 binding and minor interaction with G-C bases with overall binding constant of K = 6.1 x 10(4) M(-1). The RNase-DNA interaction alters the protein secondary structure with a major reduction of the alpha-helix and increase of the beta-sheet and random structure, while DNA remains in the B-family structure.     

Polyglutamine expansion in huntingtin alters its interaction with phospholipids

Huntingtin has an expanded polyglutamine tract in patients with Huntington's disease. Huntingtin localizes to intracellular and plasma membranes but the function of huntingtin at membranes is unknown. Previously we reported that exogenously expressed huntingtin bound pure phospholipids using protein-lipid overlays. Here we show that endogenous huntingtin from normal ( Hdh ^7Q/7Q) mouse brain and mutant huntingtin from Huntington's disease ( Hdh ^140Q/140Q) mouse brain bound to large unilamellar vesicles containing phosphoinositol (PI) PI 3,4-bisphosphate, PI 3,5-bisphosphate, and PI 3,4,5-triphosphate [PI(3,4,5)P3]. Huntingtin interactions with multivalent phospholipids were similar to those of dynamin. Mutant huntingtin associated more with phosphatidylethanolamine and PI(3,4,5)P3 than did wild-type huntingtin, and associated with other phospholipids not recognized by wild-type huntingtin. Wild-type and mutant huntingtin also bound to large unilamellar vesicles containing cardiolipin, a phospholipid specific to mitochondrial membranes. Maximal huntingtin-phospholipid association required inclusion of huntingtin amino acids 171–287. Endogenous huntingtin recruited to the plasma membrane in cells that incorporated exogenous PI 3,4-bisphosphate and PI(3,4,5)P3 or were stimulated by platelet-derived growth factor or insulin growth factor 1, which both activate PI 3-kinase. These data suggest that huntingtin interacts with membranes through specific phospholipid associations and that mutant huntingtin may disrupt membrane trafficking and signaling at membranes.     

Labelling of histone H5 and its interaction with DNA. 1. Histone H5 labelling with fluorescein isothiocyanate

Histone H5 has been labelled with fluorescein isothiocyanate (FITC) with particular attention to the reaction conditions (pH, reaction time and input FITC/H5 molar ratio) and to the complete elimination of non-covalently bound dye. We preferred to use reaction conditions which yielded non-specific uniform labelling rather than specific alpha-NH2 terminal labelling, in order to obtain higher sensitivity in further studies dealing with the detection of perturbation at the binding sites of H5 on DNA. FITC-labelled H5 was further characterized by absorption and circular dichroism spectroscopy, and the fluorescein probe titrated in the 4-8 pH range. The structural integrity of H5 was found to be preserved after labelling. The positive electrostatic potential of the environment in which the FITC probe is embedded in the arginine/lysine-rich tails of H5 is believed to be responsible for the drop of pK of 1 unit found for H5-FITC as compared to free FITC. For the globular part of H5, the pK of covalently-bound FITC was only slightly lowered; this is a consequence of the much lower content in positively-charged amino-acid side chains in this region.     

DNase I - DNA interaction alters DNA and protein conformations.

Human DNase I is an endonuclease that catalyzes the hydrolysis of double-stranded DNA predominantly by a single-stranded nicking mechanism under physiological conditions in the presence of divalent Mg and Ca cations. It binds to the minor groove and the backbone phosphate group and has no contact with the major groove of the right-handed DNA duplex. The aim of this study was to examine the effects of DNase I - DNA complexation on DNA and protein conformations.We monitored the interaction of DNA with DNase I under physiological conditions in the absence of Mg2+, with a constant DNA concentration (12.5 mmol/L; phosphate) and various protein concentrations (10-250 micromol/L). We used Fourier transfrom infrared, UV-visible, and circular dichroism spectroscopic methods to determine the protein binding mode, binding constant, and effects of polynucleotide-enzyme interactions on both DNA and protein conformations. Structural analyses showed major DNase-PO2 binding and minor groove interaction, with an overall binding constant, K, of 5.7 x 10(5) +/- 0.78 x 10(5) (mol/L)-1. We found that the DNase I - DNA interaction altered protein secondary structure, with a major reduction in alpha helix and an increase in beta sheet and random structures, and that a partial B-to-A DNA conformational change occurred. No DNA digestion was observed upon protein-DNA complexation.     

Inactivation of aminated horseradish peroxidase by interaction with S-Sepharose

Horseradish peroxidase which had been aminated by periodate oxidation and reductive amination was purified by cation-exchange chromatography on S-Sepharose. Instead of the expected single peak of aminated enzyme, two distinct peaks of protein were eluted from the column. Evaluation of the protein in each of the two distributions showed that peak number 1 had spectral properties and specific activity similar to those of native enzyme. Distribution number 2 had a threefold reduction in the extinction in the Soret region at 404 nm and was completely devoid of enzymatic activity. This inactivation was caused by a specific interaction between the aminated peroxidase and the S-Sepharose matrix, resulting in a displacement of the heme prosthetic group out of its native orientation. The inactivation of the aminated peroxidase was found to be dependent on time, pH, and the support matrix itself. These results indicate that the S-Sepharose and Mono-S resins are not interchangeable, despite the chemical similarities of the two resins.     

Histone peptide AKRHRK enhances H(2)O(2)-induced DNA damage and alters its site specificity

Histone proteins are involved in compaction of DNA and the protection of cells from oxygen toxicity. However, several studies have demonstrated that the metal-binding histone reacts with H(2)O(2), leading to oxidative damage to a nucleobase. We investigated whether histone can accelerate oxidative DNA damage, using a minimal model for the N-terminal tail of histone H4, CH(3)CO-AKRHRK-CONH(2), which has a metal-binding site. This histone peptide enhanced DNA damage induced by H(2)O(2) and Cu(II), especially at cytosine residues, and induced additional DNA cleavage at the 5'-guanine of GGG sequences. The peptide also enhanced the formation of 8-oxo-7,8-dihydro-2'-deoxyguanosine and ESR spin-trapping signal from H(2)O(2) and Cu(II). Cyclic redox reactions involving histone-bound Cu(II) and H(2)O(2), may give rise to multiple production of radicals leading to multiple hits in DNA. It is noteworthy that the histone H4 peptide with specific sequence AKRHRK can cause DNA damage rather than protection under metal-overloaded condition.     

The interaction of benzhydroxamic acid with horseradish peroxidase and its fluorescent analogs

Horseradish peroxidase (HRP) reconstituted with protoporphyrin IX or zinc protoporphyrin IX binds benzhydroxamic acid with affinities of 1.54 × 10⁴ and 8 × 10²m^?1, respectively. This interaction is competitive with respect to hydrogen donor substrates of peroxidase. The steady-state oxidation of benzhydroxamic acid by HRP was studied by monitoring the disappearance of the hydroxamate function and the formation of nitrite. The inhibition by benzhydroxamic acid of oxidation of HRP substrates may be classified as an inhibition by a competing substrate. In the case of HRP-catalyzed oxidation of ferrocyanide a marked activating effect of benzhydroxamic acid was observed. Mechanisms responsible for this effect are discussed.     

Oxidation of NAD dimers by horseradish peroxidase.

Horseradish peroxidase catalyses the oxidation of NAD dimers, (NAD)2, to NAD+ in accordance with a reaction that is pH-dependent and requires 1 mol of O2 per 2 mol of (NAD)2. Horseradish peroxidase also catalyses the peroxidation of (NAD)2 to NAD+. In contrast, bacterial NADH peroxidase does not catalyse the peroxidation or the oxidation of (NAD)2. A free-radical mechanism is proposed for both horseradish-peroxidase-catalysed oxidation and peroxidation of (NAD)2.     

Oxidation of glutathione by peroxidase isoenzymes in fenugreek

During the germination of fenugreek (Trigonella foenum graecum L.) sulfhydryl groups rapidly declined in cotyledon and seedling axis, while peroxidase activity increased. Studies on purified isoenzymes showed that GSH was oxidized by the isoenzymes and was accomplished in presence of cofactors, Mn²⁺ and DCP along with H₂O₂ (0.01 mM). This reaction was found to be peroxidatic in nature. The oxidation was inhibited by catechol but was enhanced by malic acid.     

Neocarzinostatin: controlled release of chromophore and its interaction with DNA

A nonagglutinating derivative of wheat germ agglutinin has been prepared that binds to platelets and precipitates an antibody to the lectin. Platelets treated with this inactive derivative released serotonin when exposed to bivalent F(ab′)₂, but not monovalent Fab, fragments of the lectin antibody. Bridging of platelet-bound Fab by an antibody again induced secretion. The F(ab′)₂ or Fab fragments plus IgG, without the derivative, did not induce secretion. This secretion was not affected by indomethacin showing a direct activation of platelets. Platelets treated with con A followed by F(ab′)₂ to con A did not secrete. In addition, lentil lectin failed to release platelet serotonin. The receptors of the lectin derivative are mobile on the platelet surface and their redistribution may lead to secretion.     

Histone H2AX participates the DNA damage-induced ATM activation through interaction with NBS1

Phosphorylated histone H2AX (γ-H2AX) functions in the recruitment of DNA damage response proteins to DNA double-strand breaks (DSBs) and facilitates DSB repair. ATM also co-localizes with γ-H2AX at DSB sites following its auto-phosphorylation. However, it is unclear whether γ-H2AX has a role in activation of ATM-dependent cell cycle checkpoints. Here, we show that ATM as well as NBS1 is recruited to damaged-chromatin in a γ-H2AX-dependent manner. Foci formation of phosphorylated ATM and ATM-dependent phosphorylation is repressed in H2AX-knockdown cells. Furthermore, anti-γ-H2AX antibody co-immunoprecipitates an ATM-like protein kinase activity in vitro and recombinant H2AX increases in vitro kinase activity of ATM from un-irradiated cells. Moreover, H2AX-deficient cells exhibited a defect in ATM-dependent cell cycle checkpoints. Taken together, γ-H2AX has important role for effective DSB-dependent activation of ATM-related damage responses via NBS1.     

Histone H1 structural changes and its interaction with DNA in the presence of high glucose concentration in vivo and in vitro

Histone H1 has an important role in the packing of chromatin and controlling gene expression. The effect of nonenzymatic glycation on the structure of histone H1 (a basic protein), the inhibitory role of spermine on this phenomenon and interaction of H1 with DNA is investigated here. H1 was extracted from the liver of normal and diabetic rats with or without receiving spermine as a chemical chaperone. Rat liver H1 was also incubated with glucose (50 mM) and its structure was compared with the protein obtained from diabetic rat. The results indicated a lower fluorescence emission and alpha-helical content of glycated H1; i.e., alteration in its folding; and reduced DNA (high molecular weight or specific sequences) binding in comparison with normal protein. Spermine partially (not completely) returns the studied parameters on glycated H1 toward the normal values. The changes in the structure and function of histone H1 is suggested as one of the possible mechanisms involved in diabetic complications.     

Oxidation of p-cresol by horseradish peroxidase compound I.

Rate constants for the reaction between horseradish peroxidase compound I and p-cresol have been determined at several values of pH between 2.98 and 10.81. These rate constants were used to construct a log (rate) versus pH profile from which it is readily seen that the most reactive form of the enzyme is its most basic form within this pH range so that base catalysis is occurring. At the maximum rate a second order rate constant of (5.1 +/- 0.3) x 10(-7) M-1 s-1 at 25 degrees is obtained. The activation energy of the reaction at the maximum rate was determined from an Arrhenius plot to be 5.0 +/- 0.5 kcal/mol. Evidence for an exception to the generally accepted enzymatic cycle of horseradish peroxidase is presented. One-half molar equivalent of p-cresol can convert compound I quantitatively to compound II at high pH, whereas usually this step requires 1 molar equivalent of reductant. The stoichiometry of this reaction is pH-dependent.     

Oxidation of 1-hydroxybenzotriazole by laccase and lignin peroxidase

A method to measure laccase and lignin peroxidase (LiP) activity at 408 nm (402–410 nm) using 1-hydroxybenzotriazole (HBT) was developed. The assay can be performed either as a kinetic measurement or as a stopped reaction using 5 mM Na-azide which improves the spectrum. Only white-rot fungal laccases and LiP were found to oxidize HBT to give shoulders or peaks at 402-410 nm. Phanerochaete and Phlebia manganese peroxidases did not give absorbance increase at 402–410 nm. © Rapid Science Ltd. 1998     

Oxidation of aromatic amines by peroxidase at pH 14

Horseradish peroxidase catalyzes the peroxidation of p-anisidine and other aromatic amines at pH 14. Sensitivity to KCN and thermal inactivation are characteristic of classical heme-enzyme catalysis.     

Oxidation of gonadotrophin (PMSG) by oxygen free radicals alters its structure and hormonal activity

The effect of oxygen free radicals produced by the Fenton reaction was used to induce oxidation and other structural changes in pregnant mare serum gonadotrophin (PMSG). Modifications in the spectrophotometric scan, an increase in exposed carbonyl groups, and the ability to reduce nitroblue tetrazolium, was achieved by the oxidized hormone when compared to the control PMSG. PMSG loses its biological activity when coming in contact with the free-radical generating system. This lack of activity is manifested as a loss of ovulation and a decrease in the weight of the ovaries and uterus. It was demonstrated that oxygen free radicals can induce structural and biological changes in the gonadotrophin.