Albany 2015:Book of Abstracts

Albany 2015
Conversation 19
June 9-13 2015
©Adenine Press (2012)

Effect of ligand-binding on specific interactions between DNA and regulatory protein: molecular simulations based on MD and ab initio fragment MO methods

The transcriptional mechanism of gene information from DNA to mRNA in a cell is essentially controlled by DNA-binding regulatory proteins such as lactose repressor protein (LacR) and catabolite activator protein (CAP). Although the ligand-binding to these proteins was found to change the mechanism drastically, the effect of ligand-binding on the conformation of protein+DNA complex has not been clarified at atomic and electronic levels. In our previous study (Ohyama et al., 2011), we elucidated the specific interactions between LacR-monomer, DNA and ligand, using molecular simulations combined with classical molecular mechanics (MM) and ab initio fragment molecular orbital (FMO) methods. In the present study, we investigated the change in conformation for the LacR-dimer+DNA+ligand as well as CAP-dimer+DNA+ligand complexes by the molecular dynamics (MD) simulation in water. In addition, electronic states of these complexes were investigated by FMO, in order to elucidate the effect of ligand-binding on the specific interactions between LacR-dimer or CAP-dimer and DNA.

Figure 1 shows schematic pictures for the interactions between LacR-dimer, ligand and DNA in the complexes obtained by the MD simulations. As shown in Fig. 1a, the binding of inducer IPTG (green) to the ligand-binding pocket of LacR induces the shift of the α-helix domain (orange) of Monomer-B (blue) out of the pocket. This domain becomes hydrogen bonded to the DNA binding domain of Monomer-A (pink), leading to a significant tilt of the regulatory domain of the Monomer-B. As a result, the symmetry of the LacR-dimer+DNA complex is completely broken, and the binding of LacR-dimer to DNA is weakened. In contrast, as shown in Fig. 1b, the anti-inducer ONPF (red) binding to LacR-dimer+DNA does not affect significantly on the structure of the ligand-binding pocket of LacR as well as the conformation of the LacR-dimer and DNA, keeping the symmetric and rigid structure of the LacR-dimer+DNA complex. These changes in structure induced by IPTG or ONPF are consistent with their functions as inducer and anti-inducer, respectively. The specific interactions in the LacR+DNA+ligand complexes evaluated by FMO and the results for CAP-dimer+DNA+ligand complex will be presented at the conference.


Fig. 1 Schematic pictures of the effect of ligand-binding on the interaction between LacR-dimer and DNA; (a) LacR-dimer+DNA+IPTG and (b) LacR-dimer+DNA+ONPF

T. Ohyama, M. Hayakawa, S. Nishikawa, N. Kurita, J. Comput. Chem., 2011, 32, 1661.

K. Shimamura
Y. Matsushita
M. Oishi,
T. Ohyama
N. Kurita*

Toyohashi University of Technology
Aichi, 441-8580, Japan Tel. & Fax.: +81-532-44-6875