Abstract
Here, we describe the results of computer simulations for some retinal proteins. In our simulations, the membrane environments surrounding the proteins were treated at three different levels of approximation : 1) neglect of the membrane (protein placed in vacuo), 2) low dielectric continuum, and 3) more realistic model that explicitly takes into account all the atoms of phospholipids and water molecules. Under approximation 1), we calculated the excitation energies of several retinal proteins using a QM/MM-CI theory recently developed by us. There was found a good correlation between the calculated and observed data. Under approximation 2), the binding affinity between phoborhodopsin and transducer protein (HtrII) was estimated using linear-scaling molecular orbital calculations. According to our calculations, the tendency of the observed binding affinity, including the effect of mutation at Tyr199, was successfully reproduced if the dielectric constant of the membrane region is assumed to be about 4. Finally, we discuss the outlook for molecular dynamic simulations based on approximation 3).
