Alaeddin Hakam

Molecular interactions between poly(ADP‐ribose) polymerase (PARP I) and topoisomerase I (Topo I): identification of topology of binding

The molecular interactions of poly(ADP‐ribose) polymerase I (PARP I) and topoisomerase I (Topo I) have been determined by the analysis of physical binding of the two proteins and some of their polypeptide components and by the effect of PARP I on the enzymatic catalysis of Topo I. Direct association of Topo I and PARP I as well as the binding of two Topo I polypeptides to PARP I are demonstrated. The effect of PARP I on the ‘global’ Topo I reaction (scission and religation), and the activation of Topo I by the 36 kDa polypeptide of PARP I and catalytic modifications by poly(ADP‐ribosyl)ation are also shown. The covalent binding of Topo I to circular DNA is activated by PARP I similar to the degree of activation of the ‘global’ Topo I reaction, whereas the religation of DNA is unaffected by PARP I. The geometry of PARP I–Topo I interaction compared to automodified PARP I was reconstructed from direct binding assays between glutathione S‐transferase fusion polypeptides of Topo I and PARP I demonstrating highly selective binding, which was correlated with amino acid sequences and with the ‘C clamp’ model derived from X‐ray crystallography.

Catalytic activities of synthetic octadeoxyribonucleotides as coenzymes of poly(ADP-ribose) polymerase and the identification of a new enzyme inhibitory site.

The catalytic activity of highly purified poly(ADP‐ribose) polymerase was determined at constant NAD+ concentration and varying concentrations of sDNA or synthetic octadeoxyribonucleotides of differing composition. The coenzymic activities of deoxyribonucleotides were compared in two ways: (i) graphic presentation of the activation of poly(ADP‐ribose) polymerase in the presence of a large concentration range of deoxyribonucleotides and (ii) by calculating kD values for the deoxyribonucleotides. As determined by method i, auto‐mono‐ADP‐ribosylation of the enzyme protein at 25 nM NAD+ was maximally activated at 1:1 octamer/enzyme molar ratios by the octadeoxyribonucleotide derived from the regulatory region of SV40 DNA (duplex C). At a 0.4:1 sDNA/enzyme ratio, sDNA was the most active coenzyme for monoADP‐ribosylation. At 200 μM NAD+, resulting in polymer synthesis and with histones as secondary polymer acceptors, duplex C was the most active coenzyme, and the octamer containing the steroid hormone receptor binding consensus sequence of DNA was a close second, whereas sDNA exhibited an anomalous biphasic kinetics. sDNA was effective on mono‐ ADP‐ribosylation at a concentration 150–200‐times lower than on polymer formation. When comparison of deoxyribonucleotides was based on method ii (kD values), by far the most efficiently binding coenzyme for both mono and polymer synthesis was sDNA, followed by duplex C, with (dA‐dT)8 exhibiting the weakest binding. The synthetic molecule 6‐amino‐1,2‐benzopyrone (6‐aminocoumarin) competitively inhibited the coenzymic function of synthetic octadeoxyribonucleotides at constant concentration of NAD+, identifying a new inhibitory site of poly(ADP‐ribose) polymerase.

Mechanisms of poly(ADP-ribose) polymerase catalysis; mono-ADP-ribosylation of poly(ADP-ribose) polymerase at nanomolar concentrations of NAD

Calf thymus and rat liver poly(ADP‐ribose) polymerase enzymes, and the polymerase present in extracts of rat liver nuclei synthesize unstable mono‐ADP‐ribose protein adducts at 100 nM or lower NAD concentrations. The isolated enzyme‐mono‐ADP‐ribose adduct hydrolyses to ADP‐ribose and enzyme protein at pH values slightly above 7.0 indicating a continuous release of ADP‐ribose from NAD through this enzyme‐bound intermediate under physiological conditions. NH2OH at pH 7.0 hydrolyses the mono‐ADP‐ribose enzyme adduct. Desamino NAD and some other homologs at nanomolar concentrations act as ‘forward’ activators of the initiating mono‐ADP‐ribosylation reaction. These NAD analogs at micromolar concentrations do not affect polymer formation that takes place at micromolar NAD concentrations. Benzamides at nanomolar concentrations also activate mono‐ADP‐ribosylation of the enzyme, but at higher concentrations inhibit elongation at micromolar NAD as substrate. In nuclei, the enzyme molecule extensively auto‐ADP‐ribosylates itself, whereas histones are trans‐ADP‐ribosylated to a much lower extent. The unstable mono‐ADP‐ribose enzyme adduct represents an initiator intermediate in poly ADP‐ribosylation.

Cellular regulation of poly(ADP) ribosylation of proteins. I. Comparison of hepatocytes, cultured cells and liver nuclei and the influence of varying concentrations of NAD.

The in vitro rates (vinit) of poly(ADP-ribose) polymerase of permeabilized rat hepatocytes and of nuclei, isolated from hepatocytes, did not differ significantly. Incubation beyond 3 min resulted in diminished poly(ADP) ribosylation in hepatocytes compared with nuclei, coinciding with high rates of plasma membrane-associated NAD-glycohydrolase. Cultured cells (Drosophila Kc cells, gliosarcoma 9L, human fibroblasts and mouse spleen lymphocytes) exhibit variations of NAD-glycohydrolase and poly(ADP-ribose) polymerase activities and the assessment of poly(ADP-ribose) polymerase activity in permeabilized cells requires simultaneous assay of NAD-glycohydrolase. In rat liver nuclei during 10 min incubation with 500 microM NAD, 40% of NAD is consumed, 10% ADP-ribose is bound to proteins, and 20% ADP-ribose, 5% AMP and 2.7% adenosine are liberated. As determined by solvent partitioning (Jackowski, G & Kun, E, J biol chem 258 (1983) 12587) [1], the phenol-soluble protein-ADP-ribose fraction represents largely mono(ADP)-ribose protein adducts, whereas the H2O-soluble phase contains poly(ADP)-ribosylated proteins. The quantity of ADP-ribose protein adducts, the chain length of oligomers and the nature of apparent acceptor proteins in liver nuclei vary significantly with the concentration of NAD as substrate. At 500 microM NAD concentration the quantity of ADP-ribose containing adducts was in the nmol per mg DNA range, the polymers are long chains and the acceptor proteins predominantly non-histone proteins. At 0.1 microM NAD as substrate pmol quantities of monomeric ADP-ribose adducts per mg DNA were formed and the main acceptors were sharply discernable on the basis of molecular mass as histones, high mobility non-histone proteins, two protein groups of a mass of 66 and 44 kD respectively, and the poly(ADP-ribose) polymerase enzyme protein of 119 kD mass. Whereas products in the presence of 0.1 microM NAD may indicate acceptors of highest reactivity, protein adducts formed in the presence of 500 microM NAD resemble a pattern found in vivo.

Separation of poly(adp-ribose) by high-performance liquid chromatography

The homopolymer of ADP-ribose, poly(ADP-ribose), was synthesized in vitro by liver nuclei from NAD. The protein-poly(ADP-ribose) adducts were isolated and, after base hydrolysis or proteolysis by proteinase K, the free polymers were separated from NAD, ADP-ribose, AMP and adenosine, and quantitatively determined by reversed-phase chromatography on an Ultrasphere ODS 5-micron column. Oxidation of the polymer by sodium periodate and labeling with 3H by borotritiation maintained the polymeric structure, but its modification was detectable by the chromatographic system employed.

Benzamide-DNA interactions: Deductions from binding, enzyme kinetics and from X-ray structural analysis of a 9-ethyladenine-benzamide adduct

The interaction of benzamide with the isolated components of calf thymus poly(ADP-ribose) polymerase and with liver nuclei has been investigated. A benzamide-agarose affinity gel matrix was prepared by coupling o-aminobenzoic acid with Affi-Gel 10, followed by amidation. The benzamide-agarose matrix bound the DNA that is coenzymic with poly(ADP-ribose) polymerase; the matrix, however, did not bind the purified poly(ADP-ribose) polymerase protein. A highly radioactive derivative of benzamide, the 125I-labelled adduct of o-aminobenzamide and the Bolton-Hunter reagent, was prepared and its binding to liver nuclear DNA, calf thymus DNA and specific coenzymic DNA of poly(ADP-ribose) polymerase was compared. The binding of labelled benzamide to coenzymic DNA was several-fold higher than its binding to unfractionated calf thymus DNA. A DNA-related enzyme inhibitory site of benzamide was demonstrated in a reconstructed poly(ADP-ribose) polymerase system, made up from purified enzyme protein and varying concentrations of a synthetic octadeoxynucleotide that serves as coenzyme. As a model for benzamide binding to DNA, a crystalline complex of 9-ethyladenine and benzamide was prepared and its X-ray crystallographic structure was determined; this indicated a specific hydrogen bond between an amide hydrogen atom and N-3 of adenine. The benzamide also formed a hydrogen bond to another benzamide molecule. The aromatic ring of benzamide does not intercalate between ethyladenine molecules, but lies nearly perpendicular to the planes of stacking ethyladenine molecules in a manner reminiscent of the binding of ethidium bromide to polynucleotides. Thus we have identified DNA as a site of binding of benzamide; this binding is critically dependent on the nature of the DNA and is high for coenzymic DNA that is isolated with the purified enzyme as a tightly associated species. A possible model for such binding has been suggested from the structural analysis of a benzamide-ethyladenine complex.

High-performance liquid chromatography of in vitro synthesized poly(ADP-ribose) on ion-exchange columns, separation of oligomers of varying chain length and estimation of apparent branching

Separated macromolecular fractions of in vitro synthesized poly(ADP-ribose) by liver nuclei were subjected to ion-exchange chromatography in a programmed high-performance liquid chromatographic elution system. The effects of ionic strength, pH and temperature on the separation of poly(ADP-ribose) chains were determined. Short chain oligomers (up to n = 11) were fractionated into individual components by baseline separation. Each fraction was analyzed for chain length. Trace amounts of Ado(P)Rib(P)Rib(P) found in phosphodiesterase digests were taken as indication of apparent branching. In phosphodiesterase digests of the shorter oligomers, besides traces of the above component, two other digestion products were also observed, presumably representing oligomer termini, one terminal fragment being dominant in short oligomers. Medium and long chain oligomers were partly resolved to individual components, and especially the long oligomers exhibited marked temperature dependent elution patterns. Apparent branching increased with increasing chain length up to about 3% for n = 44 and components presumably indicating termini diminished to mere traces. The adenine spectra of all fractions identified individual components.

Simultaneous determination of mono- and poly(ADP-ribose) in vivo by tritium labelling and direct high-performance liquid chromatographic separation

A microanalytical method for the determination of cellular mono-, oligo-and poly(ADP-ribose) has been developed that does not involve enzymatic degradation of oligomers to ribosyladenosine. The method consists of separation of protein-bound mono-, oligo- and poly(ADP-ribose) adducts from soluble nucleotides, followed by hydrolysis and quantitative isolation of AMP [derived from mono-(ADP-ribose)proteins], oligo- and poly(ADP-ribose) by boronate affinity chromatography and subsequent isolation of these nucleotides by HPLC. cis-Diols in AMP, oligo- and poly(ADP-ribose) are selectively oxidized by periodate, then reduced by [3H]borohydride. Conditions for the oxidation-reduction steps were optimized, and tritiated AMP, oligo- and poly(ADP-ribose) were quantitatively determined by radiochemical analysis of these components that were isolated by reversed-phase high-performance liquid chromatography. A 1-pmol ADP-ribose unit under standard conditions yields 2 X 10(3)-2.2 X 10(3) cpm 3H and this sensitivity can be amplified by increasing the specific radioactivity of [3H]borohydride.

Enzymatic mechanism of the tumoricidal action of 4-iodo-3-nitrobenzamide.

Activation of the prodrug 4-iodo-3-nitrobenzamide critically depends on the cellular reducing system specific to cancer cells. In non-malignant cells, reduction of this prodrug to the non-toxic amine occurs by the flavoprotein of complex?I of mitochondria receiving Mg2+-ATP-dependent reducing equivalents from NADH to NADPH via pyridine nucleotide transhydrogenation. This hydride transfer is deficient in malignant cells; therefore, the lethal synthesis of 4-iodo-3-nitrosobenzamide takes place selectively. Enzymatic evidence for this mechanism has been provided by cellular studies with lysolecithin-permeabilized cells and cell fractions, which have identified the defect in transhydrogenation in neoplastic cells to be located at the energy transfer site. Confirming previous results, the present study demonstrates the validity of the selective tumoricidal action of the prodrug in cell cultures.

Regulation of malignant phenotype and bioenergetics by a π-electron donor-inducible mitochondrial MgATPase

The recognition of poly ADP-ribose transferase-1 (PARP-1) as an ATP sensor receiving this energy source by way of a specific adenylate kinase ATP wire (AK) from mitochondrial ATP synthase (F0F1), and directly regulating cellular mRNA and DNA synthesis, was the first step towards the identification of an effect by PARP-1 that is of fundamental significance. The molecular target of AK-ATP is Arg 34 of the Zn finger I of PARP-1, which is also a site for cation-π interactions as a target of π-electron donors. We now identify this π-electron receptor site as the second active center of PARP-1 which by interaction with a π-electron donor-inducible MgATPase reversibly controls a malignant vs. non-malignant phenotype through energizing the NADH➝NADP+ transhydrogenase, a reaction which is the metabolic connection of PARP-1 to cell function. The specific enzyme-inducing action of the π-electrons is executed by the PARP-1 -topoisomerase I - DNA complex of the nuclei regulating both the nature and the quantity of cellular enzymes that constitute cell-specific physiology.