The mammalian circadian system is comprised of a central clock in the suprachiasmatic nucleus (SCN) and a network of peripheral oscillators located in all of the major organ systems. The SCN is traditionally thought to be positioned at the top of the hierarchy, with SCN lesions resulting in an arrhythmic organism. However, recent work has demonstrated that the SCN and peripheral tissues generate independent circadian oscillations in Per1 clock gene expression in vitro. In the present study, we sought to clarify the role of the SCN in the intact system by recording rhythms in clock gene expression in vivo. A practical imaging protocol was developed that enables us to measure circadian rhythms easily, noninvasively, and longitudinally in individual mice. Circadian oscillations were detected in the kidney, liver, and submandibular gland studied in about half of the SCN-lesioned, behaviorally arrhythmic mice. However, their amplitude was decreased in these organs. Free-running periods of peripheral clocks were identical to those of activity rhythms recorded before the SCN lesion. Thus, we can report for the first time that many of the fundamental properties of circadian oscillations in peripheral clocks in vivo are maintained in the absence of SCN control.

In photosystem II (PSII), the Mn4CaO5 cluster catalyses the water splitting reaction. The crystal structure of PSII shows the presence of a hydrogen-bonded water molecule directly linked to O4. Here we show the detailed properties of the H-bonds associated with the Mn4CaO5 cluster using a quantum mechanical/molecular mechanical approach. When O4 is taken as a μ-hydroxo bridge acting as a hydrogen-bond donor to water539 (W539), the S0 redox state best describes the unusually short O4–OW539 distance (2.5 Å) seen in the crystal structure. We find that in S1, O4 easily releases the proton into a chain of eight strongly hydrogen-bonded water molecules. The corresponding hydrogen-bond network is absent for O5 in S1. The present study suggests that the O4-water chain could facilitate the initial deprotonation event in PSII. This unexpected insight is likely to be of real relevance to mechanistic models for water oxidation.

The crystal structure of photosystem II (PSII) analyzed at a resolution of 1.9 Å revealed a remarkably short H-bond between redox-active tyrosine Y(Z) and D1-His190 (2.46 Å donor-acceptor distance). Using large-scale quantum mechanical/molecular mechanical (QM/MM) calculations with the explicit PSII protein environment, we were able to reproduce this remarkably short H-bond in the original geometry of the crystal structure in the neutral [Y(Z)O···H···N(ε)-His-N(δ)H···O═Asn] state, but not in the oxidized states, indicating that the neutral state was the one observed in the crystal structure. In addition to the appropriate redox/protonation state of Y(Z) and D1-His190, we found that the presence of a cluster of water molecules played a key role in shortening the distance between Y(Z) and D1-His190. The orientations of the water molecules in the cluster were energetically stabilized by the highly polarized PSII protein environment, where the Ca ion of the oxygen-evolving complex (OEC) and the OEC ligand D1-Glu189 were also involved.

Photosystem II uses light to drive water oxidation and plastoquinone (PQ) reduction. PQ reduction involves two PQ cofactors, Q A and Q B , working in series. Q A is a one-electron carrier, whereas Q B undergoes sequential reduction and protonation to form Q B H 2 . Q B H 2 exchanges with PQ from the pool in the membrane. Based on the atomic coordinates of the Photosystem II crystal structure, we analyzed the proton transfer (PT) energetics adopting a quantum mechanical/molecular mechanical approach. The potential-energy profile suggests that the initial PT to Q B•-occurs from the protonated, D1-His252 to Q B •-via D1-Ser264. The second PT is likely to occur from D1-His215 to Q B H − via an H-bond with an energy profile with a single well, resulting in the formation of Q B H 2 and the D1-His215 anion. The pathway for reprotonation of D1-His215-may involve bicarbonate, D1-Tyr246 and water in the Q B site. Formate ligation to Fe 2+ did not significantly affect the protonation of reduced Q B , suggesting that formate inhibits Q B H 2 release rather than its formation. The presence of carbonate rather than bicarbonate seems unlikely because the calculations showed that this greatly perturbed the potential of the nonheme iron, stabilizing the Fe 3+ state in the presence of Q B•-, a situation not encountered experimentally. H-bonding from D1-Tyr246 and D2-Tyr244 to the bicarbonate ligand of the nonheme iron contributes to the stability of the semiquinones. A detailed mechanistic model for Q B reduction is presented.electron transfer gating | purple bacterial reaction center | low-barrier hydrogen bond | photoinhibition | tyrosine peroxide T he core of the Photosystem II (PSII) reaction center is composed of D1/D2, a heterodimer of protein subunits containing the cofactors involved in photochemical charge separation, quinone reduction, and water oxidation. These reactions are driven by light absorption by pigments absorbing around 680 nm (P680). P680 is composed of four chlorophyll a (Chla) molecules, P D1 /P D2 , Chl D1 /Chl D2 , and two pheophytin a molecules (Pheo D1 /Pheo D2 ). Excitation of P680 initially leads to the formation of a range of charge separated states, with the Chl D1•+ Pheo D1•− state dominating. After a short time the secondary radical pair, [P D1 /P D2 ], is formed in nearly all centers. This state is stabilized by electron transfer to the first quinone, Q A , and by electron donation from a tyrosine residue, D1-Tyr160 (TyrZ), to P D1• then oxidizes the Mn 4 CaO 5 cluster, which catalyzes the subsequent water splitting reaction. Q A /Q A •− acts as a one-electron redox couple, accepting electrons from Pheo D1•− and donating to the second quinone, Q B , without undergoing protonation itself. In contrast, Q B reduction involves two consecutive one-electron reduction reactions with a series of associated proton uptake reactions (reviewed in 1-6).Q B is located near the nonheme Fe 2+ and the ligand to the Fe 2+ , D1-His215, donates an H-bond to the Q B carbonyl O atom that is nearer to the Fe complex (...