The role of the cyclic depsipeptide rings in antibiotics

The physical and biological roles of the cyclic depsipeptides of actinomycin, quinomycin and triostin antibiotic families are proposed by examining the crystal structures of d(GC)-actinomycin D and d(CGTACG)-triostin A. The analyses suggest that not only are DNA-amino acid hydrogen-bonding and chromophore-base pair stacking crucially important for DNA-antibiotic interaction, but also that the unique structure of the cyclic depsipeptides (the perfect hydrophobic character of the inner surface) is equally necessary to insure that these interactions are directed, unambiguous and screened from interference by solvent. Beyond this, the characteristic nature of the outer surfaces suggests a further hypothesis for the biological role of the cyclic depsipeptide rings; when the antibiotics bind in the region around the pause or rho-dependent termination sites on the DNA, the drugs actually terminate transcription by RNA polymerase and cause release of a premature RNA transcript. Termination is likely because the antibiotics carry five to six consecutive apparent A/T sequences on the surface of the cyclic depsipeptide rings, thus presenting a deceptive termination signal to the polymerase.