Tracing the Pathways of Waters and Protons in Photosystem II and Cytochrome c Oxidase

Abstract

Photosystem II (PSII) uses water as the terminal electron donor, producing oxygen in the Mn4CaO5 oxygen evolving complex (OEC), while cytochrome c oxidase (CcO) reduces O2 to water in its heme–Cu binuclear center (BNC). Each protein is oriented in the membrane to add to the proton gradient. The OEC, which releases protons, is located near the P-side (positive, at low-pH) of the membrane. In contrast, the BNC is in the middle of CcO, so the protons needed for O2 reduction must be transferred from the N-side (negative, at high pH). In addition, CcO pumps protons from N- to P-side, coupled to the O2 reduction chemistry, to store additional energy. Thus, proton transfers are directly coupled to the OEC and BNC redox chemistry, as well as needed for CcO proton pumping. The simulations that study the changes in proton affinity of the redox active sites and the surrounding protein at different states of the reaction cycle, as well as the changes in hydration that modulate proton transfer paths, are described.

Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient

“…Experiments show chloride depletion blocks the advancement of S-state transition beyond S 2 ( Ono et al, 1986 ; Pokhrel and Brudvig, 2014 ). Simulations show depletion of chloride leads to formation of a salt bridge between D1-Asp 61 and D2-Lys 317 hindering proton loss ( Rivalta et al, 2011 ; Amin et al, 2016 ; Kaur et al, 2019 ).…”

Temperature effect on water dynamics in tetramer phosphofructokinase matrix and the super-arrhenius respiration rate

“…Control by temperature that the channels make a close and open form by the amino acid to influence the water-protein interactions in the channel. The channel water diffusion may make a key role in controlling the respiration reaction for the proton coupled electron transfer 26,[47][48][49] and the O 2 reduction. It has been found that the protons released need requires a proton-transferring pathway (a "proton well") in the relevant protein.…”

Identifying the proton loading site cluster in the ba cytochrome c oxidase that loads and traps protons

“…Pumps have proton loading sites (PLS), a residue or group of residues whose proton affinity changes dramatically through the reaction cycle, so a proton is loaded, held and then released through the reaction cycle. A requirement for a pump to function is that the PLS proton affinity must change so that its effective pK a shifts substantially, from several pH units above the pH for proton loading to several pH units below the pH for proton unloading [6,7]. Smaller changes in affinity or those where the change of effective pK a s in different states that do not cross the pH of the surroundings will not cause the PLS to alter protonation state.…”

“…In CcO the energy required is provided by the reduction of oxygen at the Binuclear center (BNC) located in the center of the protein. The BNC consists of a heme group and a copper site and a covalently-linked Tyr residue [7,9,10]. In the overall redox reaction cycle CcO reduces one oxygen molecule to water, driving a reaction cycle that results in uptake of 4 protons from the N-side for chemistry and additional protons pumped from N-to P-side [7,9]: ,…”