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Protons participate in many reactions. In proteins, protons need paths to move in and out of buried active sites. The vectorial movement of protons coupled to electron transfer reactions establishes the transmembrane electrochemical gradient used for many reactions, including ATP synthesis. Protons move through hydrogen bonded chains of waters and hydroxy side chains via the Grotthuss mechanism and by proton binding and release from acidic and basic residues. MCCE analysis shows that proteins exist in a large number of protonation states. Knowledge of the equilibrium ensemble can provide a rational basis for setting protonation states in simulations that fix them, such as molecular dynamics (MD). The proton path into the QB site in the bacterial reaction centers (RCs) of Rb. sphaeroides is analyzed by MD to provide an example of the benefits of using protonation states found by the MCCE program. A tangled web of side chains and waters link the cytoplasm to QB. MCCE analysis of snapshots from multiple trajectories shows that changing the input protonation state of a residue in MD biases the trajectory shifting the proton affinity of that residue. However, the proton affinity of some residues is more sensitive to the input structure. The proton transfer networks derived from different trajectories are quite robust. There are some changes in connectivity that are largely restricted to the specific residues whose protonation state is changed. Trajectories with QB•− are compared with earlier results obtained with QB [Wei et. al Photosynthesis Research volume 152, pages153–165 (2022)] showing only modest changes. While introducing new methods the study highlights the difficulty of establishing the connections between protein conformation. [ABSTRACT FROM AUTHOR]

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 AspM17 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. [ABSTRACT FROM AUTHOR]

The oxidation of water to O2 is catalyzed by the Oxygen Evolving Complex (OEC), a Mn4CaO5 complex in Photosystem II (PSII). The OEC is sequentially oxidized from state S0 to S4. The S2 state, (MnIII)(MnIV)3, coexists in two redox isomers: S2,g=2, where Mn4 is MnIV and S2,g=4.1, where Mn1 is MnIV. Mn4 has two terminal water ligands, whose proton affinity is affected by the Mn oxidation state. The relative energy of the two S2 redox isomers and the protonation state of the terminal water ligands are analyzed using classical multi-conformer continuum electrostatics (MCCE). The Monte Carlo simulations are done on QM/MM optimized S1 and S2 structures docked back into the complete PSII, keeping the protonation state of the protein at equilibrium with the OEC redox and protonation states. Wild-type PSII, chloride-depleted PSII, PSII in the presence of oxidized YZ/protonated D1-H190, and the PSII mutants D2-K317A, D1-D61A, and D1-S169A are studied at pH 6. The wild-type PSII at pH 8 is also described. In qualitative agreement with experiment, in wild-type PSII, the S2,g=2 redox isomer is the lower energy state; while chloride depletion or pH 8 stabilizes the S2,g=4.1 state and the mutants D2-K317A, D1-D61A, and D1-S169A favor the S2,g=2 state. The protonation states of D1-E329, D1-E65, D1-H337, D1-D61, and the terminal waters on Mn4 (W1 and W2) are affected by the OEC oxidation state. The terminal W2 on Mn4 is a mixture of water and hydroxyl in the S2,g=2 state, indicating the two water protonation states have similar energy, while it remains neutral in the S1 and S2,g=4.1 states. In wild-type PSII, advancement to S2 leads to negligible proton loss and so there is an accumulation of positive charge. In the analyzed mutations and Cl− depleted PSII, additional deprotonation is found upon formation of S2 state. [ABSTRACT FROM AUTHOR]

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 Q A site cycles between quinone, Q A , and anionic semiquinone, Q A ·- , being reduced once and never binding protons. In the Q B site, ubiquinone is reduced twice by Q A ·- , binds two protons and is released into the membrane as the quinol, QH 2 . 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. Q A 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 Q B . 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 AspM17 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., (© 2022. The Author(s), under exclusive licence to Springer Nature B.V.)

The oxidation of water to O 2 is catalyzed by the Oxygen Evolving Complex (OEC), a Mn 4 CaO 5 complex in Photosystem II (PSII). The OEC is sequentially oxidized from state S 0 to S 4 . The S 2 state, (Mn III )(Mn IV ) 3 , coexists in two redox isomers: S 2,g=2 , where Mn4 is Mn IV and S 2,g=4.1 , where Mn1 is Mn IV . Mn4 has two terminal water ligands, whose proton affinity is affected by the Mn oxidation state. The relative energy of the two S 2 redox isomers and the protonation state of the terminal water ligands are analyzed using classical multi-conformer continuum electrostatics (MCCE). The Monte Carlo simulations are done on QM/MM optimized S 1 and S 2 structures docked back into the complete PSII, keeping the protonation state of the protein at equilibrium with the OEC redox and protonation states. Wild-type PSII, chloride-depleted PSII, PSII in the presence of oxidized Y Z /protonated D1-H190, and the PSII mutants D2-K317A, D1-D61A, and D1-S169A are studied at pH 6. The wild-type PSII at pH 8 is also described. In qualitative agreement with experiment, in wild-type PSII, the S 2,g=2 redox isomer is the lower energy state; while chloride depletion or pH 8 stabilizes the S 2,g=4.1 state and the mutants D2-K317A, D1-D61A, and D1-S169A favor the S 2,g=2 state. The protonation states of D1-E329, D1-E65, D1-H337, D1-D61, and the terminal waters on Mn4 (W1 and W2) are affected by the OEC oxidation state. The terminal W2 on Mn4 is a mixture of water and hydroxyl in the S 2,g=2 state, indicating the two water protonation states have similar energy, while it remains neutral in the S 1 and S 2,g=4.1 states. In wild-type PSII, advancement to S 2 leads to negligible proton loss and so there is an accumulation of positive charge. In the analyzed mutations and Cl - depleted PSII, additional deprotonation is found upon formation of S 2 state.