The headpiece structure of lac-repressor (LacI) is as an ideal system to investigate the nonspecific binding of the whole LacI to DNA. The hinge region in the headpiece plays a key role in the specific binding process of the LacI to DNA, while its role in the nonspecific binding process is still unknown. We report that the hinge region strengthens the nonspecific interaction between the headpiece of the LacI and DNA using molecular dynamics simulation, umbrella sampling technique, and continuum electrostatic calculations. The hinge region makes a 50 % contribution to the free energy for micro-dissociation. Without the hinge region, the calculated microscopic dissociation rate of the LacI from the DNA is reduced by 2~3 orders of magnitude. The hinge region contributes significantly to the electrostatic energy for binding, the salt dependence of electrostatic energy between the LacI and the DNA, and the number of salt ions excluded from binding.
The modified PDMS surface with paeonol shows good antibacteria activity. We simulated the absorption of paeonol to PDMS surface using molecular dynamics. We calculated the mass center distance between the groups of paeonol and PDMS. In the first 1 ns, paeonol gets close to the PDMS surface. We calculated that after 5.5 ns, when the absorption process is stabilized, the hydrophobic group is the farthest from the surface of PDMS. We explore the driving force responsible for the adsorption process. the total non-bonded energy is mainly composed of vdW energy, the electrostatic interaction energy is close to zero. Therefore, the vdW is the main interaction to decrease the non-bonded interaction energy and drive the paeonol to absorb on the surface of PDMS.