Ab initio, tight-binding and QM/MM calculations of the rhodopsin chromophore in its binding pocket

Abstract

We present results of ab initio and combined ab initio and force field calculations for the conformational changes of the rhodopsin chromophore in its binding pocket subject to various constraints like the inclusion of a water molecule near the counterion Glu113. Furthermore, the influence of other charged groups on the stability of the protonated Schiff base is investigated as well as the role of the amino acid threonine (Thr94). The calculations yield a stable protonated Schiff base and a highly twisted conformation of the chromophore which is in agreement with the latest refined set of structure data.

Keywords:

• Rhodopsin; Ab initio molecular dynamics and force field simulations

Acknowledgements

This work is supported by the Graduated School Structure and Dynamics of Heterogeneous Systems at the University of Duisburg and the Research Group Molecular Mechanisms of Retinal Protein Action through the Deutsche Forschungsgemeinschaft.