Engineering topics
Gunner, M. R.
Publications and source records attributed to Gunner, M. R..
Computing the Relative Affinity of Chlorophylls a and b to Light-Harvesting Complex II
In plants and algae, the primary antenna protein bound to photosystem II is light-harvesting complex II (LHCII), a pigment–protein complex that binds eight chlorophyll (Chl) a molecules and six Chl b molecules. Chl a and Chl b differ only in that Chl a has a methyl group (–CH 3 ) on one of its pyrrole rings, while Chl b has a formyl group (–CHO) at that position. This blue-shifts the Chl b absorbance relative to Chl a . It is not known how the protein selectively binds the right Chl type at each site. Knowing the selection criteria would allow the design of light-harvesting complexes that bind different Chl types, modifying an organism to utilize the light of different wavelengths. The difference in the binding affinity of Chl a and Chl b in pea and spinach LHCII was calculated using multiconformation continuum electrostatics and free energy perturbation. Both methods have identified some Chl sites where the bound Chl type ( a or b ) has a significantly higher affinity, especially when the protein provides a hydrogen bond for the Chl b formyl group. However, the Chl a sites often have little calculated preference for one Chl type, so they are predicted to bind a mixture of Chl a and b . The electron density of the spinach LHCII was reanalyzed, which, however, confirmed that there is negligible Chl b in the Chl a -binding sites. Finally, it is suggested that the protein chooses the correct Chl type during folding, segregating the preferred Chl to the correct binding site.
Helical allophycocyanin nanotubes absorb far-red light in a thermophilic cyanobacterium
To compete in certain low-light environments, some cyanobacteria express a paralog of the light-harvesting phycobiliprotein, allophycocyanin (AP), that strongly absorbs far-red light (FRL). Using cryo–electron microscopy and time-resolved absorption spectroscopy, we reveal the structure-function relationship of this FRL-absorbing AP complex (FRL-AP) that is expressed during acclimation to low light and that likely associates with chlorophyll a–containing photosystem I. FRL-AP assembles as helical nanotubes rather than typical toroids due to alterations of the domain geometry within each subunit. Spectroscopic characterization suggests that FRL-AP nanotubes are somewhat inefficient antenna; however, the enhanced ability to harvest FRL when visible light is severely attenuated represents a beneficial trade-off. The results expand the known diversity of light-harvesting proteins in nature and exemplify how biological plasticity is achieved by balancing resource accessibility with efficiency.
High-resolution cryo-electron microscopy structure of photosystem II from the mesophilic cyanobacterium, Synechocystis sp. PCC 6803
Significance Photosystem II (PSII) is a photo-oxidoreductase that harnesses light energy to use water to make fuel. Water oxidation occurs at a metal cluster in the active site called the oxygen-evolving complex (OEC). Understanding PSII function has provided design principles for synthetic solar fuel catalysts; however, the details of water oxidation are obscured by the multiple states through which the mechanism proceeds, differences between species, and lability of the OEC. To better understand PSII function, we solved its structure from Synechocystis sp. PCC 6803. We observe significant differences compared with PSII from thermophilic cyanobacteria that highlight the need for reexamination of previous data using this structure for interpretation. The structure also provides a platform for studies of site-directed mutations of PSII.
Toward understanding the S2-S3 transition in the Kok cycle of Photosystem II: Lessons from Sr-substituted structure
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Proton exit pathways surrounding the oxygen evolving complex of photosystem II
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Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient
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.
Identification of a Na + -Binding Site near the Oxygen-Evolving Complex of Spinach Photosystem II
The oxygen-evolving complex (OEC) of photosystem II (PSII) is an oxomanganese cluster composed of four redox-active Mn ions, and one redox-inactive Ca 2+ ion, with two nearby bound Cl – ions. Sodium is a common counter-ion of both chloride and hydroxide anions, and a sodium-specific binding site has not been identified near the OEC. Furthermore, we find that the oxygen-evolution activity of spinach PSII increases with [Na + ], particularly at high pH. A Na + -specific binding site next to the OEC, upon deprotonation of the D1-H337 amino-acid residue, is suggested by the analysis of two recently published PSII cryo-EM maps in combination with quantum mechanical calculations and molecular dynamics simulations.
Efficiency of Photosynthesis in a Chl d-Utilizing Cyanobacterium is Comparable to or Higher than that in Chl a-Utilizing Oxygenic Species
The cyanobacterium Acaryochloris marina uses chlorophyll d to carry out oxygenic photosynthesis in environments depleted in visible and enhanced in lower-energy, far-red light. However, the extent to which low photon energies limit the efficiency of oxygenic photochemistry in A. marina is not known. Here, we report the first direct measurements of the energy-storage efficiency of the photosynthetic light reactions in A. marina whole cells,and find it is comparable to or higher than that in typical, chlorophyll a-utilizing oxygenic species. This finding indicates that oxygenic photosynthesis is not fundamentally limited at the photon energies employed by A. marina, and therefore is potentially viable in even longer-wavelength light environments.