A molecular-dynamics study of the rhodopsin chromophore using ultrasoft pseudopotentials

Abstract

We investigate the effect of different environments on the chromophore of the protein rhodopsin by using the Vienna ab initio simulation package which is based on Density Functional Theory with a plane wave basis set and the implementation of Vanderbilt's ultrasoft pseudopotentials. We have calculated the energy dependence of 11-cis-retinal on the C11-C12 double bond twist angle in the ground state and our results show that the isomerization in the ground state of the retinal chromophore is more difficult in the presence of the counter ion than without it.