Energetics of interaction of oligopeptide (lac 53–57) with DNA base sequences and origin of sequence-specific recognition

Computer model building with a dynamic energy minimization procedure is used here to study the interaction of a pentapeptide sequence from the lac repressor headpiece (lac 53–57) with different base sequences of DNA. The peptide fragment for this purpose was considered in the classical β-antiparallel as well as the β-associated conformation. The model of its interaction with DNA was optimised for various binding positions and base sequences. Partitioning of energy is analysed for different dielectric constant values and the main contributing factors to sequence-specific binding are discussed.