Peptides Interacting with Nucleic Acids

At the end of this chapter, cyclic peptides will be mentioned one of them (a mixture) being indeed the first antibiotic peptide ever isolated actinomycin from cultures of Streptomyces antibioticus by Waksman and Woodruff in 1940. The different actinomycins are orange-red peptides all containing the same chromo-phore, an aminophenoxazinone dicarboxylic acid, whose carboxyl groups are connected via the amino group of threonine with two identical cyclic depsipep-tide rings consisting of five amino acids. In Fig. 28 the cyclic part of actinomycin C3 is depicted as determined by H. Brockmann (Plate 13) and associates, who in the fifties contributed most to the analytical and synthetic chemistry of this class of compounds. 

The antibiotic (and highly toxic) effect of the actinomycins is due to their strong binding by intercalation to the double helix of DNA so inhibiting transcription into RNA even with minimal concentrations [63]. 

Another group of cytostatic, antiviral and antibacterial yet highly toxic peptides are the quinoxalines [64] with two quinoxaline-carboxylic acids attached to eight membered, disulfide bridged symmetric peptide-lactone rings. Further inhibitors of protein biosynthesis isolated from Streptomyces species here mentioned only by name are streptogramin B and the tuberactinomycins (e.g. Viomycin) isolated, elucidated and synthesized mainly by T. Shiba s group in Osaka. 

Hofmann, H. Ott, R. Griot, P.A. Stadler, A.J. Frey, Synthese von Ergotamin, Helv. Chim. Acta 46 2306-2336 (1963) 

The formation of cyclols from N-hydroxyacyl lactames. Tetrahedron 19 1661-1673 (1963) 

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In theory, if the net charge, q, on a molecule is known, it should be possible to measure / and obtain information about the hydrodynamic size and shape of that molecule by investigating its mobility in an electric field. Attempts to define /by electrophoresis have not been successful, primarily because Equation 4.3 does not adequately describe the electrophoretic process. Important factors that are not accounted for in the equation are interaction of migrating molecules with the support medium and shielding of the molecules by buffer ions. This means that electrophoresis is not useful for describing specific details about the shape of a molecule. Instead, it has been applied to the analysis of purity and size of macromolecules. Each molecule in a mixture is expected to have a unique charge and size, and its mobility in an electric field will therefore be unique. This expectation forms the basis for analysis and separation by all electrophoretic methods. The technique is especially useful for the analysis of amino acids, peptides, proteins, nucleotides, nucleic acids, and other charged molecules. 

Bioactive macromolecules like peptides, proteins, and nucleic acids have been successfully embedded in planar LbL films. An important question is the retention of the bioactivity of the film-embedded biomolecules. The structural properties and stability of the LbL films formed from synthesized polypeptides of various amino acid sequences were recently reported [50]. The authors showed that control over the amino acid sequence enables control over non-covalent interpolypeptide interaction in the film, which determines the film properties. Haynie and coworkers showed by circular dichroism spectroscopy that the extent of adsorption of poly(L-glutamic acid) (PGA) and poly(L-lysine) (PLL) in the LbL films scales with the extent of secondary structure of the polypeptides in solution [51]. Boulmedais demonstrated that the secondary structure of the film composed of these polypeptides is the same as the peptide structure in the complex formed in solution [52], as found by Fourier transform IR spectroscopy (FUR). 

Several other natural products systems have been studied, some quite extensively, by NMR methodology, however space constraints prohibt detailed discussion of these systems therefore only important leading references will be given. Extensive NMR studies on amino acids and small peptides have been performed by Lauterwein and coworkers [116-119], by Fiat and coworkers [120-123] and others [124]. Several studies have used l O-enriched dioxygen and carbon monoxide to study by NMR techniques the interactions of these biochemically important small molecules with various proteins [125-128]. A number of investigators have explored the properties and interactions of nucleic acid bases [129,130], nucleosides [131,132], nucleotides [133-138] and one report has appeared in which NMR spectroscopy approaches were applied to the study of small molecule-DNA interactions [139]. A recent report describes the careful analysis of the effect of structure on NMR chemical shifts of over forty hydroxyterpenoids [140]. A study of the 1 0 NMR spectroscopy of over thirty steroid ketones, acids, esters and alcohols enriched with has recently appeared [141]. 

Dimicoli, J. L. and Helene, C., Interactions of aromatic residues of proteins with nucleic acids. I. Proton magnetic resonance studies of the binding of tryptophan-containing peptides to poly(adenylic acid) and deoxyribonucleic acid, Biochemistry, 13(4], 714, 1974. 

Gabbay, E. J., Sanford, K., Baxter, C. S., Kapicak, L. (1973). Specific interaction of peptides with nucleic acids. Evidence for a selective bookmark recognition hypothesis, Biochemistry, 12 4021. 

The interaction of artificial metal ions/complexes with peptides/proteins [11], nucleic acids/DNA [12,13], enzymes [14], steroids [15] and carbohydrates [16] forms a bridge between natural and artificial macromolecular metal complexes. Biometal-organie chemistry concentrates on such complexes [17]. The reason for the increasing interest in this field lies in medical applications of metal complexes (cancer, photodynamic therapy of cancer, immunoassays, fluorescence markers, enantioselective catalysis, template orientated synthesis of peptides, etc.). Figure 2-4 presents an overview of metals in medicine [18]. Some examples are given below. 

The mechanism of carcinogenesis by PAHs is believed to involve alkylation of an informational macromolecule in a critical, but at present unknown, manner. Such an interaction with a protein has been modelled by alkylation of a peptide this showed a conformational change occurred on alkylation. It has not yet been possible to study the structure of DNA alkylated by an activated carcinogen this is because DNA is a fiber and the structural order in it is not sufficient for a crystal structure determination. However the crystal structures of some alkylated portions of nucleic acids are described, particularly some nucleosides alkylated by chloromethyl derivatives of DMBA. In crystals of these alkylation products the PAH portion of the adduct shows a tendency to lie between the bases of other nucleoside... 

The general types of protein-protein interactions that occur in cells include receptor-ligand, enzyme-substrate, multimeric complex formations, structural scaffolds, and chaperones. However, proteins interact with more targets than just other proteins. Protein interactions can include protein-protein or protein-peptide, protein-DNA/RNA or protein-nucleic acid, protein-glycan or protein-carbohydrate, protein-lipid or protein-membrane, and protein-small molecule or protein-ligand. It is likely that every molecule within a cell has some kind of specific interaction with a protein. 

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