Molecular dynamics study of the binding of elsamicin A to DNA

Title	Molecular dynamics study of the binding of elsamicin A to DNA
Publication Type	Journal Article
Year of Publication	1995
Authors	Alhambra, C, Luque FJ, Portugal J, Orozco M
Journal	European journal of biochemistry / FEBS
Volume	230
Issue	2
Pagination	555 - 566
Date Published	1995/06/01/
Keywords	Aminoglycosides; Anti-Bacterial Agents/metabolism; Antibiotics, Antineoplastic/metabolism; Base Sequence; Binding Sites; Carbohydrate Sequence; DNA/metabolism; Electrochemistry; Models, Molecular; Molecular Sequence Data
Abstract	Molecular mechanics (MM) and dynamics (MD) were used to examine the conformational flexibility of elsamicin A, an antitumour antibiotic, in aqueous solution. Furthermore, MM and MD simulations were performed to obtain the first three-dimensional model of the elsamicin-A-DNA complex. Comparison of MD simulations of free and DNA-bound elsamicin A provided insight into the mechanism of DNA cleavage. Moreover, the drug-DNA complexes were analyzed to investigate specific drug-DNA interactions, as well as the role of the solvent water molecules in the drug-DNA binding. On the basis of the results derived from these simulations, several issues related to the sequence-selective binding of elsamicin A to DNA are discussed.

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