Paper Citing NAMD - Abstract
Huntress, Mark M.; Gozem, Samer; Malley, Konstantin R.; Jailaubekov, Askat E.; Vasileiou, Chrysoula; Vengris, Mikas; Geiger, James H.; Borhan, Babak; Schapiro, Igor; Larsen, Delmar S.; Olivucci, Massimo
Toward an Understanding of the Retinal Chromophore in Rhodopsin Mimics
JOURNAL OF PHYSICAL CHEMISTRY B, 117:10053-10070, SEP 5 2013
Recently, a rhodopsin protein mimic was constructed by combining mutants of the cellular retinoic acid binding protein II (CRABPII) with an all-trans retinal chromophore. Here, we present a combine computational quantum mechanics/molecular mechanics (QM/MM) and experimental ultrafast kinetic study of CRABPII. We employ the QM/MM models to study the absorption (lambda(a)(max)), fluorescence (lambda(f)(max)), and reactivity of a CRABPII triple mutant incorporating the all-trans protonated chromophore (PSB-KLE-CRABPII). We also study the spectroscopy of the same mutant incorporating the unprotonated chromophore and of another double mutant incorporating the neutral unbound retinal molecule held inside the pocket. Finally, for PSB-KLE-CRABPII, stationary fluorescence spectroscopy and ultrafast transient absorption spectroscopy resolved two different evolving excited state populations which were computationally assigned to distinct locally excited and charge-transfer species. This last species is shown to evolve along reaction paths describing a facile isomerization of the biologically relevant 11-cis and 13-cis double bonds. This work represents a first exploratory attempt to model and study these artificial protein systems. It also indicates directions for improving the QM/MM models so that they could be more effectively used to assist the bottom-up design of genetically encodable probes and actuators employing the retinal chromophore.
