Slow Dissociation of a Charged Ligand: Analysis of the Primary Quinone QA Site of Photosynthetic Bacterial Reaction Centers

Reaction centers (RCs) are integral membrane proteins that undergo a series of electron transfer reactions during the process of photosynthesis. In the QA site of RCs from Rhodobacter sphaeroides, ubiquinone-10 is reduced, by a single electron transfer, to its semiquinone. The neutral quinone and anionic semiquinone have similar affinities, which is required for correct in situ reaction thermodynamics. A previous study showed that despite similar affinities, anionic quinones associate and dissociate from the QA site at rates ≈104 times slower than neutral quinones indicating that anionic quinones encounter larger binding barriers (Madeo, J.; Gunner, M. R. Modeling binding kinetics at the QA site in bacterial reaction centers. Biochemistry2005, 44, 10994–11004). The present study investigates these barriers computationally, using steered molecular dynamics (SMD) to model the unbinding of neutral ground state ubiquinone (UQ) and its reduced anionic semiquinone (SQ–) from the QA site. In agreement with experiment, the SMD unbinding barrier for SQ– is larger than for UQ. Multi Conformational Continuum Electrostatics (MCCE), used here to calculate the binding energy, shows that SQ– and UQ have comparable affinities. In the QA site, there are stronger binding interactions for SQ– compared to UQ, especially electrostatic attraction to a bound non-heme Fe2+. These interactions compensate for the higher SQ– desolvation penalty, allowing both redox states to have similar affinities. These additional interactions also increase the dissociation barrier for SQ– relative to UQ. Thus, the slower SQ– dissociation rate is a direct physical consequence of the additional binding interactions required to achieve a QA site affinity similar to that of UQ. By a similar mechanism, the slower association rate is caused by stronger interactions between SQ– and the polar solvent. Thus, stronger interactions for both the unbound and bound states of charged and highly polar ligands can slow their binding kinetics without a conformational gate. Implications of this for other systems are discussed

Charge Separation Related to Photocatalytic H\u3csub\u3e2\u3c/sub\u3e Production from a Ru–Apoflavodoxin–Ni Biohybrid

The direct creation of a fuel from sunlight and water via photochemical energy conversion provides a sustainable method for producing a clean source of energy. Here we report the preparation of a solar fuel biohybrid that embeds a nickel diphosphine hydrogen evolution catalyst into the cofactor binding pocket of the electron shuttle protein, flavodoxin (Fld). The system is made photocatalytic by linking a cysteine residue in Fld to a ruthenium photosensitizer. Importantly, the protein environment enables the otherwise insoluble Ni catalyst to perform photocatalysis in aqueous solution over a pH range of 3.5–12.0, with optimal turnover frequency 410 ± 30 h–1 and turnover number 620 ± 80 mol H2/mol hybrid observed at pH 6.2. For the first time, a reversible light-induced charge-separated state involving a Ni(I) intermediate was directly monitored by electron paramagnetic resonance spectroscopy. Transient optical measurements reflect two conformational states, with a Ni(I) state formed in ∼1.6 or ∼185 μs that persists for several milliseconds as a long-lived charge-separated state facilitated by the protein matrix