STRUCTURES AND ELECTRONIC PROPERTIES OF MONOMER, DIMER AND TETRAMER OF LACTOSE REPRESSOR PROTEIN: MOLECULAR MECHANICS, MOLECULAR DYNAMICS, MOLECULAR ORBITAL AND CHARGE EQUILIBRATION CALCULATIONS

Abstract

Tetramer of lactose repressor (LacR) protein plays an essential role in controlling the transcription of DNA. The previous experimental studies elucidated that the carboxyl-terminal domain of LacR is important for the tetramerization of LacR. In the present study, we investigated stable structures of monomers, dimers and tetramer of LacR by molecular mechanics and molecular dynamics simulations, based on AMBER force field to elucidate the effect of the tetramerization domain on LacR structure. The obtained stable structures for both the LacR tetramers, with and without the tetramerization domain, indicate that this domain is essential for constructing a compact structure of LacR tetramer. On the other hand, this domain does not affect the structure of LacR dimer. Furthermore, we investigated the charge distributions and binding energies for these stable structures by the charge equilibration and semiempirical molecular orbital methods. The results elucidate how the removal of the tetramerization domain causes the change in the electrostatic interaction between LacR dimers in the LacR tetramer, resulting in the separation of LacR dimers without the domain.