In the photosynthetic purple bacterium Rhodobacter Sphaeroides, the primary stages of the conversion of sunlight to chemical energy occurs in the Reaction Center (RC), a bacterial analog of the eukaryotic photosystem II protein. RC is bound to the inner membrane of Rb. Sphaeroides, and upon the absorption of visible light, initiates a series of electron and proton transfer reactions that result in the flow of cytoplasmic protons to the periplasm, which, in turn, generates the proton-motive force driving ATP synthesis and NAD+ reduction. The rate limiting step for RC involves an electron transfer reaction from a bound primary quinone (Qa) to a diffusible secondary quinone (Qb). Owing to the transient nature of Qb binding and to the fact that several energetic electron transfer parameters are simply not direct experimental observables, studies of this reaction have proven difficult. This work presents a microscopic picture of the Qa- to Qb electron transfer reaction from atomistic molecular dynamics (MD) simulations of a POPC membrane-bound RC protein. Systems have been simulated for multiple microseconds with traditional MD on the Anton supercomputer, and with collective-variable biased metadynamics MD simulations with NAMD on the Stampede supercomputer to calculate free energies of electron transfer as a function of Qb binding mode and Qa-Qb distance. In brief, this hypothesis-driven computational approach employs over 13 microseconds of atomistic trajectory data to show how modulating the Qb binding site within the protein, in principle the intermolecular Qa-Qb distance, can radically alter the reorganization energy, driving force, and Stokes shift for the rate-limiting reaction in RC.

Large-scale computational study of the distance-dependent properties of the Qa- to Qb electron transfer reaction from a membrane-bound reaction center protein

248th National Meeting (2014)

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