QUANTUM-CHEMISTRY - MOLECULAR-DYNAMICS STUDY OF THE DARK-ADAPTATION PROCESS IN BACTERIORHODOPSIN

Molecular dynamics simulations and quantum chemistry calculations have been combined to describe the dark adaptation in bacteriorhodopsin (b R). The process involves the reversible thermally activated transforma tion of retinal from an all-trans to a 13-cis,15-syn configuration. Th e potential surface governing the thermal isomerization of retinal aro und two (13-14, 15-N) double bonds has been determined for representat ive protein configurations taken from molecular dynamics trajectories. CASSCF(8,8)/6-31G level ab initio calculations (within Gaussian94) we re carried out for this purpose. The charge distributions of all atoms in the protein are represented by partial point charges and explicitl y included in the electronic Hamiltonian. Placement of retinal into bR is found to reduce the calculated isomerization barrier. Thermal fluc tuations of the protein lead to a further effective reduction of this barrier. The isomerization process is shown to be catalyzed by the pro tonation of an aspartic acid (Asp85) side group of bacteriorhodopsin.