[Studies of the resistance of the human immunodeficiency virus to azidothymidine. I. Kinetic studies of the interaction between reverse transcriptase and a series of its mutant forms with substrates and azidothymidine-5'-trisphosphate]

Prolonged therapy of AIDS patients with azidothymidine results in the development of resistance to the drug. This phenomenon is accompanied by the appearance of point mutations in the pol gene coding for reverse transcriptase (RT). Kinetic studies of interactions of wild type RT and its forms containing the above-mentioned mutations with substrates and azidothymidine 5'-triphosphate have been carried out. Considerable differences in the affinities of RT and the mutants for RNA and DNA heteropolymer templates were established. The mutations did not affect the RT affinity for dNTP; however, its location influenced considerably the inhibition of the reaction with azidothymidine 5'-triphosphate.

[Functional studies of mutant forms of bacteriophage T7 RNA polymerases containing point substitutions in the motif at the active site of the enzyme]

Monomeric DNA and RNA polymerases contain a number of conserved motifs. By means of random and oligonucleotide-directed mutagenesis the point mutants of bacteriophage T7 RNA polymerase containing the amino acid substitutions in motif B which is the part of the active site were obtained. The kinetic properties of the mutants were studied. The results obtained suggest that amino acid residues 636, 639 and 646 are involved in the binding of the initiating GTP, the selection of correct nucleoside triphosphate and interaction with the promoter, respectively.

Interactions of the HIV-1 reverse transcriptase 'AZT-resistant' mutant with substrates and AZT-TP

To investigate the biochemical basis of the HIV-1 resistance to AZT we obtained the RT mutant containing four amino acid substitutions by an oligonucleotide-directed mutagenesis technique. Enzymatic properties of the wild type and mutant RTs were compared. 'AZT-resistant' mutations in RT were shown to be associated with the reduced capability of AZT-TP to block the DNA- but not RNA-directed DNA synthesis.

Random mutagenesis of the gene for bacteriophage T7 RNA polymerase

Random mutagenesis of the gene for bacteriophage T7 RNA polymerase was used to identify functionally essential amino acid residues of the enzyme. A two-plasmid system was developed that permits the straightforward isolation of T7 RNA polymerase mutants that had lost almost all catalytic activity. It was shown that substitutions of Thr and Ala for Pro at the position 563, Ser for Tyr571, Pro for Thr636, Asp for Tyr639 and of Cys for Phe646 resulted in inactivation of the enzyme. It is noteworthy that all these mutations are limited to two short regions that are highly conservative in sequences of monomeric RNA polymerases.

Tyr-571 is involved in the T7 RNA polymerase binding to its promoter

The in vitro studies of three T7 RNA polymerase point mutants suggest that substitutions of Ala and Thr for Pro-563 and of Ser for Tyr-571 have little effect on the enzyme catalytic competence, but result in its inability to utilize the promoter. Both P563A and P563T mutants retain the promoter-binding ability, whereas the promoter affinity of the Y571S mutant drops drastically.

[Study of the form of bacteriophage T7 RNA polymerase containing point substitutions in the region of functionally important amino acid residues]

A study was carried out on the influence of point mutations of the functional amino acid residues on the secondary and ternary structure of bacteriophage T7 RNA polymerase as well as on the activity of the enzyme. A change in residue 631 is accompanied by significant changes in secondary structure (alpha-->beta transition). The substitution Lys-172 Leu changes both the secondary and ternary structures whereas the deletion of residues 172-173 does not lead to such changes. Changes in residues 631-632 do not affect the ability of the enzyme to bind the promoter and/or the synthesis of a full-length transcript but disturbs phosphodiester bond formation.

[Study of phage T7 DNA-dependent RNA-polymerase using GTP analogs. Affinity modification and study of interaction with matrices using fluorescent markers]

Interactions of the bacteriophage T7 DNA-dependent RNA polymerase with three GTP analogs have been studied. All of the three analogs tested contained substituted naphthalenesulphamide groups and were shown to be under appropriate conditions irreversible covalent inhibitors of the enzyme, the modified enzyme possessing fluorescent properties. One of these analogs contained the reactive 2-bromoethyl phosphonate group and was shown to cause the loss of the enzyme affinity for polynucleotide templates. The other two modifiers which contained the azide reactive group did not alter the enzyme-template affinity, the polynucleotide binding leading to a notable increase of the enzyme fluorescence intensity. The latter two modifiers are supposed to be convenient for fluorescent labelling of the active site of RNA polymerase for enzyme-template binding studies.

[Site-specific mutagenesis of residue Lys-172 of phage T7 RNA polymerase: characterization of transcription properties of mutant proteins]

Lys-172 residue of bacteriophage T7 RNA polymerase (T7RP) was substituted for Leu and Gly and Lys-172, Arg-173 were deleted by the site-directed mutagenesis using synthetic oligonucleotides. The specific activity of all mutant enzymes did not differ significantly from that of the wild-type (w.t.) T7RP while for Gly-172 mutant (G172) it was somewhat lower. Leu-172 (L172) and deletion (DEL172-3) mutants were able to direct RNA synthesis on the templates lacking the T7 promoter. DEL172-3 was not able to synthesize extraneous RNA sequences in addition to the expected run-off transcripts. L172 and DEL172-3 mutants revealed altered template specificity toward various DNA templates and showed the lower stability of enzyme-promoter complexes. The possible role of Lys-172 likely belonging to an interdomain "stretch" is discussed.

On the functional role of the Tyr-639 residue of bacteriophage T7 RNA polymerase

Substitution of Asp for a Tyr residue normally present at position 639 of the bacteriophage T7 RNA polymerase leads to a drastic drop in the enzymatic activity. This mutation does not affect the enzyme-promoter interaction but decreases the ability of the RNA polymerase to discriminate between GTP and ATP molecules, resulting in a decrease in the rate of the incorporation of the nucleotide into the RNA chain.

[Genetic system of selecting point mutations of bacteriophage T7 RNA polymerase]

Random mutagenesis of the bacteriophage T7 gene 1 was used to delineate the functionally important amino acids residues of its product--T7 RNA polymerase. A two-plasmid system has been constructed for the phenotypic selection of the mutants. Nine mutants were isolated; the RNA polymerase with Tyr-639----Asp substitution has been shown to be completely inactive. Methods were developed for the rapid purification of plasmid-encoded mutant proteins, facilitating their future biochemical analysis.

[Reverse transcriptase of the human immunodeficiency virus: cloning, expression in Escherichia coli, purification of the enzyme, and production of monoclonal antibodies]

To express HIV-1 reverse transcriptase in E. coli a number of genetic constructions containing reverse transcriptase and virus protease nucleotide sequences was obtained. The products of expression were characterized; monoclonal antibodies to reverse transcriptase were produced. The purification of reverse transcriptase was carried out. The substantial proteolysis of reverse transcriptase during purification was shown. The purified preparation is predominantly, an active protein with Mr 57 kDa. Some properties of this protein differed from the reverse transcriptase isolated from HIV.

Lys631 residue in the active site of the bacteriophage T7 RNA polymerase. Affinity labeling and site-directed mutagenesis

A highly selective affinity labeling of T7 RNA polymerase with the o-formylphenyl ester of GMP and [alpha-32P]UTP was carried out. The site of the labeling was located using limited cleavages with hydroxylamine, bromine, N-chlorosuccinimide and cyanogene bromide and was identified as the Lys631 residue. Site-directed mutagenesis using synthetic oligonucleotides was used to substitute Lys631 by a Gly, Leu or Arg residue. Kinetic studies of the purified mutant enzymes showed alterations of their polymerizing activity. For the Lys----Gly mutant enzyme, anomalous template binding was observed.

Inactivation of bacteriophage T7 DNA-dependent RNA polymerase by 5'-p-fluorosulfonylbenzoyladenosine. Identification of the modification site and the effect of the modification on enzyme action

Bacteriophage T7 RNA polymerase was covalently modified by 5'-[4-fluorosulfonyl)benzoyl]adenosine (4-FSO2BzAdo). The modified enzyme lacks the ability to catalyze RNA synthesis from the phi 10 promoter of bacteriophage T7; both promoter and GTP binding being markedly decreased. The mild hydrolysis of the ester bond of 4-FSO2BzAdo within the covalent enzyme-inhibitor complex restores the RNA synthesis at a lower rate. Sequence studies show that Lys172 is the target of modification by 4-FSO2BzAdo. This residue, which is situated in the polypeptide region connecting two domains of RNA polymerase, was shown to be the primary site of the limited proteolysis occurring in vivo [Ikeda, R. A. & Richardson, C. C. (1987) J. Biol. Chem. 262, 3790-3799]. We propose that Lys172 is located outside the active site. Once this residue has reacted with 4-FSO2BzAdo, the nucleoside moiety of the analog is fixed in the NTP-binding site of the active centre and prevents binding of the substrates. Here, Lys172 per se is not important for the activity but serves as an 'anchor' for binding of the inhibitor.

[The study of nucleoside triphosphate-binding center of DNA-dependent RNA-polymerase of phage T7 using GTP analogs]

The NTP binding site of bacteriophage T7 DNA-dependent RNA polymerase was studied using GTP analogs. For four analogs the irreversible inhibition was demonstrated. The kinetic parameters for competitive (Ki) and irreversible (KI and k3) inhibition were determined. One of the analogs, 5'[2-hydroxy(4-iodoacetamido)benzoyl]guanosine, was shown to inactivate the enzyme rapidly due to the modification of SH-groups. Some suggestions on the structure of the RNA polymerase active site have been made.

[Preparation and characteristics of monoclonal antibodies to DNA-dependent RNA-polymerase of bacteriophage T7]

The monoclonal antibodies to DNA-dependent RNA-polymerase of bacteriophage T7 have been obtained. Twenty of the obtained 500 clones have inhibited the enzyme activity. Three specificity groups were identified for seven of the clones supporting their affinity for different antigenic determinants.

[Affinity modification of DNA-dependent RNA-polymerase from phage T7 with 5'-p-fluorosulfonylbenzoyl adenosine: the effect of modification on the interaction with substrates]

T7 RNA polymerase, covalently modified with 5'-p-fluorosulfonylbenzoyl adenosine, looses the ability of binding the promoter (pGEM-2 plasmid) and poly(dC) template as well as the initiating nucleoside triphosphate (GTP). However the enzyme retains the unspecific binding with DNA fragments of considerable length.

[A thermostable protein inhibitor of protein kinase from the swine brain. Isolation of the inhibitor and interaction with the enzyme]

A heat-stable protein inhibitor of cAMP-dependent protein kinase has been isolated from pig brain tissue. During gel filtration the protein is eluted in three peaks corresponding to the tetramer, dimer and monomer. The monomer fraction was purified 609-fold. The molecular mass of the monomeric form as determined by gel filtration and electrophoresis is equal to 11,000 Da and 8000 Da, respectively. The inhibition of the phosphotransferase reaction with respect to ATP occurs via a non-competitive mechanism, while that for histone--via a competitive mechanism. A formal kinetic analysis of various modes of the inhibitor binding to different protein kinase forms, e. g., the cAMP-dependent protein kinase catalytic subunit, protein kinase holoenzyme in the presence and absence of cAMP as well as of holoenzyme preparations modified by dimethylsuberimidate and cupric 1,10-phenanthroline, has been carried out. It was demonstrated that 3-4 inhibitor molecules are involved in the interaction with protein kinase.

[Mechanism of cAMP-dependent protein kinase activation. Covalent modification of the holoenzyme by dimethylsuberimidate]

Modification of the holoenzyme of cAMP-dependent protein kinase from porcine brain by dimethylsuberimidate was studied. It was demonstrated that a protein conjugate with a molecular mass of 180,000 Da and a stoichiometric formula of R2C2 evolves as a result of intermolecular cross-link formation in the holoenzyme molecule. The regulatory subunit partly protects the catalytic subunit from the inhibition by dimethylsuberimidate. The cross-linked holoenzyme retains the ability to be activated by cAMP. The experimental data testify to the non-identity of activation and dissociation of protein kinase.

[Mechanism of action of cAMP-dependent protein kinase. V. Free energy spectra]

The catalytic subunit of cAMP-dependent protein kinase from pig brain was shown to catalyse an isotope exchange reaction ATP in equilibrium with ADP. The kinetic parameters of the exchange were determined. The enzyme can also use GTP as the donor substrate; phosphotransferase and "GTPase" reactions were investigated. Based on the kinetic data obtained in this and in the previous paper the free energy profiles of protein kinase catalysed reactions are discussed.

[Problems of cellular activity regulation by secondary messengers]

The paper surveys the data obtained during the last years in the Laboratory of Regulation of Cellular Activity of the Institute of Molecular Biology. The data mostly concern the enzymes taking part in metabolism and in biological action of the secondary messengers, as well as the mechanisms of regulation of some metabolic pathways in the cultured cells. The results pertinent to the mechanisms of chromatin condensation and based on this genetic control processes are also discussed.

Physico-chemical principles of cAMP-dependent protein phosphorylation. Catalysis of phosphoryl group transfer to nucleophilic agents

The specificity of pig brain protein kinase towards high- and low-Mr 'analogs' of protein substrate was studied. Solvolysis of the phosphoenzyme intermediate by various nucleophilic agents is shown. The transition state structure of the phosphoryl transfer reaction is discussed.

[Mechanism of action of cAMP-dependent protein kinase. IV. Interaction of the enzyme catalytic subunit with structural analogs of histone H1]

A study was made of the specificity of the catalytic subunit of cAMP-dependent pig brain protein kinase with respect to structural analogs of the protein substrate, histone H1, namely: a) high-molecular-weight histone fragments obtained as the result of specific cleavage of histone with trypsin and N-bromsuccinimide; b) synthetic peptides-substrates; c) synthetic peptides-inhibitors. Analysis of the kinetic parameters estimated for these compounds allowed to evaluate the individual contribution of various elements of the primary and three-dimensional structure of histone in the processes of binding and phosphorylation. Factors of "near" and "remote" specificity in the protein substrate binding are suggested.

[cAMP-dependent phosphorylation in the pig brain]

Protein phosphorylation in the cytosol, membranes and nuclei of pig brain cells was investigated. Endogenous cAMP-dependent phosphorylation was observed in all fractions studied. The degree of activation of this process by cAMP was different, depending on the fraction. The molecular weights of the endogenous protein substrates were found to be equal to 60 000, 45 000 and 28 000 for the nuclei, 80 000, 71 000, 31 000, 25 000, 16 000 and 11 000 for the membranes and 280 000, 80 000, 67 000, 53 000, 32 000, 25 000 and 22 000 for cytosol. It was shown that the majority of these proteins can be phosphorylated by the exogenous cAMP-dependent pig brain protein kinase.

Studies on the mechanism of action of the histone kinase dependent on adenosine 3',5'-monophosphate. Fast kinetics of histone H1 phosphorylation

The transient phase of histone H1 phosphorylation was studied by the quenched-flow method. A 'minimal' kinetic scheme of the above process was proposed. A formal kinetic analysis was given to a four-step mechanism of the reaction. Computer simulation of the transient-phase kinetics of H1 phosphorylation and the steady-state kinetics of phosphate transfer from the enzyme phosphoform to histone permitted us to estimate all kinetic constants of the proposed mechanism.

Studies on the mechanism of action of the histone kinase dependent on adenosine 3',5'-monophosphate. Investigation of protein-protein interaction by electron spin-resonance spectroscopy and stopped-flow methods

The interaction of the cAMP-dependent protein kinase catalytic subunit with its protein substrate, histone H1, was studied. The H1 molecule was specifically converted into the aminotyrosine-72 derivative. Fluorescent and spin labels were introduced into this residue. The changes in the ESR and fluorescence spectra of respective derivatives were observed upon the interaction of the latter with the catalytic subunit, thus enabling us to determine some kinetic and equilibrium parameters of this process. Stopped-flow investigation of the transient phase of the binding reaction indicates that the kinetic curve is described by a three-exponential function. The rate of protein-protein interaction is close to the rate of phosphate transfer from phosphoenzyme intermediate to protein substrate.