Comparison of Proton Transfer Paths to the Q_Aand Q_BSites of theRb. sphaeroidesPhotosynthetic Reaction Centers

Abstract

The photosynthetic bacterial reaction centers from purple non-sulfur bacteria use light energy to drive the transfer of electrons from cytochrome c to ubiquinone. Ubiquinone bound in the QA site cycles between quinone, QA, and anionic semiquinone, QA•−, being reduced once and never binding protons. In the QB site, ubiquinone is reduced twice by QA&•−, binds two protons and is released into the membrane as the quinol, QH2. The network of hydrogen bonds formed in a molecular dynamics trajectory was drawn to investigate proton transfer pathways from the cytoplasm to each quinone binding site. QA is isolated with no path for protons to enter from the surface. In contrast, there is a complex and tangled network requiring residues and waters that can bring protons to QB. There are three entries from clusters of surface residues centered around HisH126, GluH224, and HisH68. The network is in good agreement with earlier studies, Mutation of key nodes in the network, such as SerL223, were previously shown to slow proton delivery. Mutational studies had also shown that double mutations of residues such as Asp M17 and AspL210 along multiple paths in the network presented here slow the reaction, while single mutations do not. Likewise, mutation of both HisH126 and HisH128, which are at the entry to two paths reduce the rate of proton uptake.

Proton-mediated photoprotection mechanism in photosystem II

“…The proton-mediated photoprotection mechanism is pronounced exclusively in PSII, as the bicarbonate ligand is replaced with Glu-M234 in PbRC from Rhodobacter sphaeroides (Figure 8). The mechanism of the low-barrier H-bond formation caused by the loss of the bicarbonate ligand may also be associated with the Q A H 2 formation under high light in PSII (Vass et al, 1992;Noguchi, 2002), as Glu-M234 exists permanently and Q A never leaves in PbRC (Wei et al, 2022). These findings could elucidate how the type-II reaction centers show notable structural differences not only on the lumenal oxygen-evolving side but also on the stromal electron acceptor side.…”

Characterizing Protein Protonation Microstates Using Monte Carlo Sampling

“…42 However, as is customary, all water molecules in the crystal structure are deleted and replaced by implicit solvent in lysozyme while 28 crystallographic waters are retained in the RCs, as explicit water molecules play an important role in the proton transfer pathway. 43,44 All protonatable residues (Glu, Asp, Arg, Lys, His, Tyr, and Cys and N-and C-termini) have both charged and neutral conformers available. At each charge state, sidechain conformers are made that differ in the number and position of polar side-chain protons.…”