Adenine Nucleotide Binding Proteins Research Articles

Design and Synthesis of ATP-Based Nucleotide Analogues and Profiling of Nucleotide-Binding Proteins

Two nucleotide-based probes were designed and synthesized in order to enrich samples for specific classes of proteins by affinity-based protein profiling. We focused on the profiling of adenine nucleotide-binding proteins. Two properties were considered in the design of the probes: the bait needs to bind adenine nucleotide-binding proteins with high affinity and carry a second functional group suitable and easily accessible for coupling to a chromatography resin. For this purpose, we synthesized p-biotinyl amidobenzoic acid-ATP (p-BABA-ATP) and p-biotinyl aminomethylbenzoic acid-ATP (p-BAMBA-ATP). p-BABA-ATP and p-BAMBA-ATP both bind to ATP-binding cassette (ABC) proteins with at least 10-fold higher affinity than ATP. Several ABC transporters could be enriched using p-BABA-ATP or p-BAMBA-ATP.

Irreversible inhibition of human natural killer cell natural cytotoxicity by modification of the extracellular membrane by the adenine nucleotide analog 5′- p-(fluorosulfonyl)benzoyl adenosine

Extracellular adenine nucleotides are inhibitors of the human natural killer cell line NK3.3 natural cytotoxicity activity. Natural cytotoxicity was inhibited approximately 26% by 1 m M ATP and 21% by 1 m M ADP. 5′-Adenylyl imidodiphosphate, a nonhydrolyzable ATP analog, inhibited natural cytotoxicity by 41% at a concentration of 1 m M and > 97% at a concentration of 10 m M. In contrast, AMP was not inhibitory. Adenosine was a weak inhibitor of natural cytotoxicity and may represent an alternate regulatory pathway. Removal of the nucleotides resulted in the restoration of control levels of natural cytotoxicity activity. The affinity label 5′- p-(fluorosulfonyl)benzoyladenosine (5′-FSBA) is a synthetic analog of ATP or ADP containing an electrophilic fluorosulfonyl group capable of covalently modifying proteins at adenine di- and triphosphate nucleotide-binding sites. Natural cytotoxicity was irreversibly inhibited by modification of the extracellular membrane of NK3.3 cells by 5′-FSBA. This inhibition was concentration dependent with an I 50 ∼ 100 μ M and complete inhibition at 1 m M. Modification of NK3.3 by 5′-FSBA did not affect the formation of effector—target cell conjugates; however, granule release was inhibited. This targets the site of inhibition by 5′-FSBA modification to a pathway preceding granule release. Irreversible, covalent modification of surface adenine nucleotide-binding proteins by 5′-FSBA provides a probe to study the role of specific adenine nucleotide-binding proteins in the extracellular regulation of natural killer cytolytic activity by adenine nucleotides.

Immunochemical detection of adenine nucleotide-binding proteins with antibodies to 5′- p-fluorosulfonylbenzoyladenosine

5′- p-Fluorosulfonylbenzoyladenosine (FSBA) is a useful reagent for the affinity labeling of adenine nucleotide binding proteins. We have developed an immunochemical approach to the detection of proteins that have been covalently modified with FSBA, which provides an alternative to the use of a radiolabeled ligand. Antibodies have been prepared against FSBA-modified glutamate dehydrogenase and purified by chromatography on ATP-agarose. The resulting affinity-purified antibodies react on Western blots only with proteins that have been labeled previously with the affinity reagent. The degree of immunoreactivity on Western blots correlates well with the extent of covalent modification as shown by studies on the modification and inhibition of the catalytic subunit of cAMP-dependent protein kinase. In crude cellular extracts, numerous proteins can be labeled with FSBA and then detected by using this approach. The labeling and subsequent detection of these proteins can be blocked by including an excess of MgATP, which competes with FSBA for nucleotide-binding sites. The labeling of specific proteins in crude mixtures is saturable, as shown by labeling studies of p56 lck , a protein-tyrosine kinase that is abundantly expressed in membranes from the T lymphoma cell line LSTRA.

Design and applications of biomimetic anthraquinone dyes: III. Anthraquinone-immobilised C.I. Reactive Blue 2 analogues and their interaction with horse liver alcohol dehydrogenase and other adenine nucleotide-binding proteins

C.I. Reactive Blue 2 analogues were bonded onto an agarose support matrix by a novel method which entailed immobilisation by the anthraquinone ring 1-amino group as opposed to the usual triazine ring coupling methods. Dyes with spacer arms attached to the anthraquinone ring 1-amino group were synthesised by reacting methoxytriazine analogues of C.I. Reactive Blue 2 with chloroacetyl chloride and ethylenediamine. Unlike the blue parent dyes, all C.I. Reactive Blue 2 analogues with derivatised anthraquinone ring 1-amino groups were of a characteristic red colour. This change of chromaticity was entirely expected since the anthraquinone ring 1-amino group is an important component of the C.I. Reactive Blue 2 chromophore. Chromatographic studies indicated that, in comparison to adsorbents comprising triazine ring-immobilised dyes, adsorbents formed from C.I. Reactive Blue 2 analogues immobilised by the anthraquinone ring were better suited to the isolation of horse liver alcohol dehydrogenase and other adenine nucleotide-requiring enzymes. Similarities between C.I. Reactive Blue 2 analogues immobilised by the anthraquinone ring and N 6-(6-aminohexyl)adenine nucleotide derivatives could be identified which may account for these observations. These studies confirm that highly effective affinity ligands based on synthetic textile dyes can be designed in a rational manner.

Homology of histone H1 variants with adenine nucleotide-binding proteins

Significant homology was observed between the adenine nucleotide-binding domain in the catalytic subunit of bovine protein kinase A and the carboxy-terminal half of the globular domain of histone H1. A consensus sequence deducible from several previously characterized adenine nucleotide-binding sites is totally conserved in H1. In addition, several putative phosphate binding-sites were observed within the carboxyterminal tail and one in the cluster of basic amino acids in the aminoterminal tail. Both the putative adenine and phosphate-binding sites are well conserved through evolution in various species and in different H1 variants. The present data thus suggest that histone H1 variants may bind to adenine derivatives and imply that they may recognize a specific nucleotide sequence in DNA.

Covalent modification of the inhibitor-binding site(s) of Escherichia coli ADP-glucose synthetase. Isolation and structural characterization of 8-azido-AMP-incorporated peptides.

The photoaffinity inhibitor analog [2-3H]8-azido-AMP is specifically and covalently incorporated into Escherichia coli ADP-glucose synthetase. The reaction site(s) of [2-3H]8-azido-AMP with the enzyme was identified by reverse phase high performance liquid chromatography isolation and chemical characterization of CNBr and mouse submaxillary arginyl protease-generated peptides containing the labeled analog. Three regions of modification, represented by six labeled peptides, accounted for over 85% of the covalently bound label. The major binding region of the azido analog, composed of residues 108-128, contained approximately 55% of the recovered covalently bound radioactivity. A single residue, Tyr-113, contained between 50 and 75% of the label found in the major binding region. This site is the same as the major binding region of the substrate site-specific probe, 8-azido-ADP-[14C]glucose (Lee, Y. M., and Preiss, J. (1986) J. Biol. Chem. 261, 1058-1064). Conformational analysis of this region predicts that it is a part of a Rossmann fold, the supersecondary structure found in many adenine nucleotide-binding proteins. Two minor reaction regions of the enzyme with [2-3H]8-azido-AMP were also identified by chemical characterization. One region, containing 20% of the covalently bound label, was composed of residues 11-68. This region contains Lys-38, the previously determined pyridoxal phosphate-modified allosteric activator site (Parsons, T. F., and Preiss, J. (1978) J. Biol. Chem. 253, 7638-7645). The third minor region of modification, residues 222-254, contained approximately 15% of the covalently bound label. The three modified peptide regions may be juxtaposed in the enzyme's tertiary structure.

Complete nucleotide sequence of recD, the structural gene for the alpha subunit of Exonuclease V of Escherichia coli.

Intracellular amplification of the Escherichia coli RecB and RecC proteins does not result in an increase in Exonuclease V activity unless the level of a third protein, encoded between the recB and argA genes, is also amplified. Nucleotide sequence analysis of this region reveals a 1,824 nucleotide open reading frame which would encode a protein of 608 amino acids with a calculated molecular weight of 66,973. This is assumed to be the structural gene for the alpha subunit of Exonuclease V, recently designated recD. The proposed initiation codon of the recD gene overlaps the termination codon of the upstream recB gene by one nucleotide, suggesting that these genes may form an operon. The deduced amino acid sequence of the RecD protein contains a region which is homologous to highly conserved sequences in adenine nucleotide binding proteins.

Nucleotide sequence of the Escherichia coli replication gene dnaZX.

The Escherichia coli 2.2 kilobase dnaZX region contains one 1929 nucleotide reading frame which directs the synthesis of two protein products involved in DNA polymerization. The larger consists of 643 amino acids in a deduced 71,114 dalton chain which could be the tau subunit of DNA polymerase III. The smaller, the DNA polymerase III gamma subunit, is encoded by the same reading frame as the larger. The dnaZX sequence contains a region homologous to ATP binding sites, suggesting that these replication factors are adenine nucleotide binding proteins.

The nucleotide sequence of theRAD3gene ofSaccharomyces cerevisiae: a potential adenine nucleotide binding amino acid sequence and a nonessential acidic carboxyl terminal region

The RAD3 gene of Saccharomyces cerevisiae is required for excision of pyrimidine dimers and is essential for viability. We present the nucleotide sequence of the RAD3 protein coding region and its flanking regions, and the deduced primary structure of the RAD3 protein. In addition, we have mapped the 5' end of RAD3 mRNA. The predicted RAD3 protein contains 778 amino acids with a calculated molecular weight of 89,779. A segment of the RAD3 protein shares homology with several adenine nucleotide binding proteins, suggesting that RAD3 protein may react with ATP. The twenty carboxyl terminal amino acids of RAD3 protein are predominantly acidic; however, deletion of this acidic region has no obvious effect on viability or DNA repair.

The nucleotide sequence of the uvrD gene of E. coli.

The nucleotide sequence of a cloned section of the E. coli chromosome containing the uvrD gene has been determined. The coding region for the UvrD protein consists of 2,160 nucleotides which would direct the synthesis of a polypeptide 720 amino acids long with a calculated molecular weight of 82 kd. The predicted amino acid sequence of the UvrD protein has been compared with the amino acid sequences of other known adenine nucleotide binding proteins and a common sequence has been identified, thought to contribute towards adenine nucleotide binding.

Identification of adenine nucleotide binding proteins in human platelet membranes by affinity labeling with 5'-p-flurosulfonylbenzoyl adenosine.

Identification of adenine nucleotide binding proteins in human platelet membranes by affinity labeling with 5'-p-flurosulfonylbenzoyl adenosine.