Probing the Accessibility of the Mn4Ca Cluster in Photosystem II: Channels Calculation, Noble Gas Derivatization, and Cocrystallization with DMSO

Abstract

Using the 2.9 A resolution structure of the membrane-intrinsic protein-cofactor complex photosystem II (PSII) from the cyanobacterium Thermosynechococcus elongatus, we calculated and characterized nine possible substrate/product channels leading to/away from the Mn(4)Ca cluster, where water is oxidized to dioxygen, protons, and electrons. Five narrow channels could function in proton transport, assuming that no large structural changes are associated with water oxidation. Four wider channels could serve to supply water to or remove oxygen from the Mn(4)Ca cluster. One of them might be regulated by conformational changes of Lys134 in subunit PsbU. Data analyses of Kr derivatized crystals and complexes with dimethyl sulfoxide (DMSO) confirm the accessibility of the proposed dioxygen channels to other molecules. Results from Xe derivatization suggest that the lipid clusters within PSII could serve as a drain for oxygen because of their predominant hydrophobic character and mediate dioxygen release from the lumen.

Mobile hydrogen carbonate acts as proton acceptor in photosynthetic water oxidation

“…Special pathways or channels have been discussed for guiding protons away from the water-splitting Mn 4 CaO 5 cluster (32,33). We show that HCO − 3 can compete for protons from water splitting with up to 300 times higher MES − concentration (at 10 mM MES) and that the CO 2 yield observed is time-dependent (Fig.…”

“…We therefore propose that HCO − 3 is able to penetrate more deeply into PSII to accept protons than MES molecules, which are not present in vivo. Inspection of the 1.9-Å PSII crystal structure (3ARC code) reveals that HCO − 3 should indeed be able to penetrate easily into the entrance regions of all postulated channels; some channels are even wide and flexible enough to allow glycerol molecules to penetrate far inside (32,33). In contrast, access to these channels for the even larger MES molecules would be more restricted.…”

Mutations in the CP43 Protein of Photosystem II Affect PSII Function and Cytochrome C550 Binding

“…Interestingly, the current crystal structure identified a third chloride ion bound near the C-terminal amino acid of PsbU, which is located between PsbU and cytochrome c 550 Kawakami et al, 2011). This chloride is ligated by water molecules and lies close to the exit of a proposed hydrogen-bonding network leading from the Mn 4 CaO 5 cluster to the lumen that could possibly serve to transport anions, water or protons (Gabdulkhakov et al, 2009;Vassiliev et al, 2010;Kawakami et al, 2011 …”

Radiolytic Mapping of Solvent-Contact Surfaces in Photosystem II of Higher Plants

“…Additionally, we have examined only the core subunits of PS II -D1, D2, CP43, and CP47. It is probable that residues of other proteins within the complex may participate in the formation of water channels (22,24,26,41). It should also be cautioned that the lack of observed modification of an amino acid residue in no way suggests that the residue is not in contact with water.…”

“…Murray and Barber (22) used the CAVER Program (23) to examine the 3.5 Å crystal structure of Thermosynechococcus elongatus (12). Gabdulkhakov et al (24) used nobel gas and dimethyl sulfoxide co-crystallization studies in combination with CAVER to examine the 2.9 Å structure of T. elongatus (14), and Ho and Styring calculated solvent-accessible surfaces for the 3.0 Å T. elongatus structure of Loll et al (13). Molecular dynamic simulations have also been used to probe for water channels within the photosystem (25,26), the latter study being performed on the recent high resolution PS II structure (15).…”