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

Kaur, Divya; Cai, Xiuhong; Khaniya, Umesh; Zhang, Yingying; Mao, Junjun; Mandal, Manoj; Gunner, M. R.

doi:10.3390/inorganics7020014

Cited by 16 publications

(21 citation statements)

References 157 publications

(265 reference statements)

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“…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 ).…”

Section: Photosystem IImentioning

confidence: 99%

Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient

et al. 2021

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Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome c oxidase (CcO), are reviewed. These proteins all use water filled proton transfer paths. The proton pumps, that move protons uphill from low to high concentration compartments, also utilize Proton Loading Sites (PLS), that transiently load and unload protons and gates, which block backflow of protons. PLS and gates should be synchronized so PLS proton affinity is high when the gate opens to the side with few protons and low when the path is open to the high concentration side. Proton transfer paths in the proteins we describe have different design features. Linear paths are seen with a unique entry and exit and a relatively straight path between them. Alternatively, paths can be complex with a tangle of possible routes. Likewise, PLS can be a single residue that changes protonation state or a cluster of residues with multiple charge and tautomer states.

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Section: Photosystem IImentioning

confidence: 99%

Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient

et al. 2021

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“…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.…”

Section: Features Of Tetramer Pfk-1s With Interior Site Connection Wamentioning

confidence: 99%

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

Yang

et al. 2021

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Advances in understanding the temperature effect on water dynamics in cellular respiration are important for the modeling of integrated energy processes and metabolic rates. For more than half a century, experimental studies have contributed to the understanding of the catalytic role of water in respiration combustion, yet the detailed water dynamics remains elusive. We combine a super-Arrhenius model that links the temperature-dependent exponential growth rate of a population of plant cells to respiration, and an experiment on isotope labeled 18O2 uptake to H218O transport role and to a rate-limiting step of cellular respiration. We use Phosphofructokinase (PFK-1) as a prototype because this enzyme is known to be a pacemaker (a rate-limiting enzyme) in the glycolysis process of respiration. The characterization shows that PFK-1 water matrix dynamics are crucial for examining how respiration (PFK-1 tetramer complex breathing) rates respond to temperature change through a water and nano-channel network created by the enzyme folding surfaces, at both short and long (evolutionary) timescales. We not only reveal the nano-channel water network of PFK-1 tetramer hydration topography but also clarify how temperature drives the underlying respiration rates by mapping the channels of water diffusion with distinct dynamics in space and time. The results show that the PFK-1 assembly tetramer possesses a sustainable capacity in the regulation of the water network toward metabolic rates. The implications and limitations of the reciprocal-activation–reciprocal-temperature relationship for interpreting PFK-1 tetramer mechanisms are briefly discussed.

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“…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.…”

Section: Introductionmentioning

confidence: 99%

“…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]: ,…”

Section: Introductionmentioning

confidence: 99%

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

Cai

Son

Mao

et al. 2020

Biochimica et Biophysica Acta (BBA) - Bioenergetics

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

Cited by 16 publications

References 157 publications

Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient

Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient

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

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

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