Calculation Of The Relative Binding Free-Energy Of 3 Inhibitors Of The Photosynthetic Reaction Center Of Rhodopseudomonas-Viridis Using The Molecular-Dynamics Free-Energy Perturbation Method

The results of the relative changes in binding free energy between the complex of the bacterial photosynthetic reaction center (RC) of Rhodopseudomonas viridis with inhibitors ametryn, atraton, and prometon are presented. These results were determined by using molecular dynamics, free energy perturbation methods. Force field parameters for the cofactors and non-heme iron of the RC along with the inhibitors are developed from a combination of quantum mechanical calculations and previous spectroscopic and molecular modeling studies. The calculated free energy changes compare well with the measured data and lie within thc error limits of this method. The calculations yielded a ranking of the relative stabilities of the inhibitors as atraton < prometon < ametryn. The relative free energy of solvation and the relative free energy of the complexes between the inhibitors and the RC both favor a hydrophobic substituent for better binding.