Coupling of electron transfer to proton uptake at the QB site of the bacterial reaction center: A perspective from FTIR difference spectroscopy

Contribution of Protonation to the Dielectric Relaxation Arising from Bacteriopheophytin Reductions in the Photosynthetic Reaction Centers of Rhodobacter sphaeroides

The pH dependence of the free energy level of the flash-induced primary charge pair P+IA- was determined by a combination of the results from the indirect charge recombination of P+QA- and from the delayed fluorescence of the excited dimer (P*) in the reaction center of the photosynthetic bacterium Rhodobacter sphaeroides, where the native ubiquinone at the primary quinone binding site QA was replaced by low-potential anthraquinone (AQ) derivatives. The following observations were made: (1) The free energy state of P+IA- was pH independent below pH 10 (-370 ± 10 meV relative to that of the excited dimer P*) and showed a remarkable decrease (about 20 meV/pH unit) above pH 10. A part of the dielectric relaxation of the P+IA- charge pair that is not insignificant (about 120 meV) should come from protonation-related changes. (2) The single exponential decay character of the kinetics proves that the protonated/unprotonated P+IA- and P+QA- states are in equilibria and the rate constants of protonation konH +koffH are much larger than those of the charge back reaction kback ~103 s-1. (3) Highly similar pH profiles were measured to determine the free energy states of P+QA- and P+IA-, indicating that the same acidic cluster at around QB should respond to both anionic species. This was supported by model calculations based on anticooperative proton distribution in the cluster with key residues of GluL212, AspL213, AspM17, and GluH173, and the effect of the polarization of the aqueous phase on electrostatic interactions. The larger distance of IA- from the cluster (25.2 Å) compared to that of QA- (14.5 Å) is compensated by a smaller effective dielectric constant (6.5 ± 0.5 and 10.0 ± 0.5, respectively). (4) The P* → P+QA- and IA-QA → IAQA- electron transfers are enthalpy-driven reactions with the exemption of very large (>60%) or negligible entropic contributions in cases of substitution by 2,3-dimethyl-AQ or 1-chloro-AQ, respectively. The possible structural consequences are discussed.

Conformational control over proton-coupled electron transfer in metalloenzymes

From the reduction of dinitrogen to the oxidation of water, the chemical transformations catalysed by metalloenzymes underlie global geochemical and biochemical cycles. These reactions represent some of the most kinetically and thermodynamically challenging processes known and require the complex choreography of the fundamental building blocks of nature, electrons and protons, to be carried out with utmost precision and accuracy. The rate-determining step of catalysis in many metalloenzymes consists of a protein structural rearrangement, suggesting that nature has evolved to leverage macroscopic changes in protein molecular structure to control subatomic changes in metallocofactor electronic structure. The proton-coupled electron transfer mechanisms operative in nitrogenase, photosystem II and ribonucleotide reductase exemplify this interplay between molecular and electronic structural control. We present the culmination of decades of study on each of these systems and clarify what is known regarding the interplay between structural changes and functional outcomes in these metalloenzyme linchpins.

Mechanism of Proton Transfer through the D1-E65/D2-E312 Gate during Photosynthetic Water Oxidation

In photosystem II, the D1-E65/D2-E312 dyad in the Cl-1 channel has been proposed to play a pivotal role in proton transfer during water oxidation. However, the precise mechanism remains elusive. Here, the proton transfer mechanism within the Cl-1 channel was investigated using quantum mechanics/molecular mechanics calculations. The molecular vibration of the E65/E312 dyad and its deuteration effect revealed that the recently suggested stepwise proton transfer, i.e., initial proton release from the dyad followed by slow reprotonation, does not occur in the Cl-1 channel. Instead, proton transfer is proposed to take place via a conformational change at the E65/E312 dyad, acting as a gate. In its closed form, a proton is trapped within the dyad, preventing forward proton transfer. This closed form converts into the open form, where protonated D1-E65 provides a hydrogen bond to the water network, thereby facilitating fast Grotthuss-type proton transfer.

Electron Transfer Route between Quinones in Type-II Reaction Centers

In photosynthetic reaction centers from purple bacteria (PbRCs) and photosystem II (PSII), the photoinduced charge separation is terminated by an electron transfer between the primary (QA) and secondary (QB) quinones. Here, we investigate the electron transfer route, calculating the superexchange coupling (HQA-QB) for electron transfer from QA to QB in the protein environment. HQA-QB is significantly larger in PbRC than in PSII. In superexchange electron tunneling, the electron transfer via unoccupied molecular orbitals of the nonheme Fe complex (QA → Fe → QB) is pronounced in PbRC, whereas the electron transfer via occupied molecular orbitals (Fe → QB followed by QA → Fe) is pronounced in PSII. The significantly large HQA-QB is caused by a water molecule that donates the H-bond to the ligand Glu-M234 in PbRC. The corresponding water molecule is absent in PSII due to the existence of D1-Tyr246. HQA-QB increases in response to the Ser-L223···QB H-bond formation caused by an extension of the H-bond network, which facilitates charge delocalization over the QB site. This explains the observed discrepancy in the QA-to-QB electron transfer between PbRC and PSII, despite their structural similarity.

Influence of Polar Mutations on the Electronic and Structural Properties of QA-· in Bacterial Reaction Centers

Reaction centers from Rhodobacter sphaeroides with residue M265 mutated from isoleucine to threonine, serine, and asparagine (M265IT, M265IS, and M265IN, respectively) in the Q_A^-· state are studied by high-resolution electron spin echo envelope modulation (ESEEM) and electron nuclear double resonance spectroscopy methods to investigate the structural characteristics of these mutants influencing the redox properties of the Q_A site. All three mutants decrease the redox midpoint potential (E_m) of Q_A by ∼0.1 V, yet the mechanism for this drop in E_m is unclear. In this work, we examine (i) the hydrogen bonding interactions between Q_A^-· and residues histidine M219 and alanine M260, (ii) the electron spin density distribution of the semiquinone, and (iii) the orientations of the ubiquinone methoxy substituents. ¹³C measurements show no significant contribution of methoxy dihedral angles to the observed decrease in E_m for the Q_A mutants. Instead, ¹⁴N three-pulse ESEEM data suggest that electrostatic or hydrogen bond formation between the mutated M265 side chain and His-M219 N_δ may be involved in the observed lowering of the Q_A midpoint potential. For mutant M265IN, analysis of the proton hyperfine couplings reveals a weakened hydrogen bond network, resulting in an altered Q_A^-· spin density distribution. The magnetic resonance study presented here is most consistent with an electrostatic or structural perturbation of the His-M219 N_δ hydrogen bond in these mutants as a mechanism for the ∼0.1 V decrease in Q_A E_m.

Control of electron transfer by protein dynamics in photosynthetic reaction centers

Trehalose and glycerol are low molecular mass sugars/polyols that have found widespread use in the protection of native protein states, in both short- and long-term storage of biological materials, and as a means of understanding protein dynamics. These myriad uses are often attributed to their ability to form an amorphous glassy matrix. In glycerol, the glass is formed only at cryogenic temperatures, while in trehalose, the glass is formed at room temperature, but only upon dehydration of the sample. While much work has been carried out to elucidate a mechanistic view of how each of these matrices interact with proteins to provide stability, rarely have the effects of these two independent systems been directly compared to each other. This review aims to compile decades of research on how different glassy matrices affect two types of photosynthetic proteins: (i) the Type II bacterial reaction center from Rhodobacter sphaeroides and (ii) the Type I Photosystem I reaction center from cyanobacteria. By comparing aggregate data on electron transfer, protein structure, and protein dynamics, it appears that the effects of these two distinct matrices are remarkably similar. Both seem to cause a "tightening" of the solvation shell when in a glassy state, resulting in severely restricted conformational mobility of the protein and associated water molecules. Thus, trehalose appears to be able to mimic, at room temperature, nearly all of the effects on protein dynamics observed in low temperature glycerol glasses.

Infrared Difference Spectroscopy of Proteins: From Bands to Bonds

Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.

Thermodynamic View of Proton Activated Electron Transfer in the Reaction Center of Photosynthetic Bacteria

The temperature dependence of the sequential coupling of proton transfer to the second interquinone electron transfer is studied in the reaction center proteins of photosynthetic bacteria modified by different mutations and treatment by divalent cations. The Eyring plots of kinetics were evaluated by the Marcus theory of electron and proton transfer. In mutants of electron transfer limitation (including the wild type), the observed thermodynamic parameters had to be corrected for those of the fast proton pre-equilibrium. The electron transfer is nonadiabatic with transmission coefficient 6 × 10^-4, and the reorganization energy amounts to 1.2 eV. If the proton transfer is the rate limiting step, the reorganization energy and the works terms fall in the range of 200-500 meV, depending on the site of damage in the proton transfer chain. The product term is 100-150 meV larger than the reactant term. While the electron transfer mutants have a low free energy of activation (∼200 meV), the proton transfer variants show significantly elevated levels of the free energy barrier (∼500 meV). The second electron transfer in the bacterial reaction center can serve as a model system of coupled electron and proton transfer in other proteins or ion channels.

Tribute in memory of Jacques Breton (1942-2018)

Jacques Breton spent his 39 years of professional life at Saclay, a center of the French Atomic Energy Commission. He studied photosynthesis with various advanced biophysical tools, often developed by himself and his numerous coworkers, obtaining a large number of new information on the structure and the functioning of antenna and of reaction centers of plants and bacteria: excitation migration in the antenna, orientation of molecules, rate of primary reactions, binding of pigments and electron transfer cofactors. Although it is much too short to illustrate his impressive work, we hope that this contribution will help maintaining the souvenir of Jacques Breton as an active and enthusiastic person, full of qualities, devoted to research and to his family as well. We include personal comments from N. E. Geacintov, A. Dobek, W. Leibl, M. Vos and W. W. Parson.

Chemical rescue of H+ delivery in proton transfer mutants of reaction center of photosynthetic bacteria

In the native and most mutant reaction centers of bacterial photosynthesis, the electron transfer is coupled to proton transfer and is rate limiting for the second reduction of Q_B^- → Q_BH₂. In the presence of divalent metal ions (e.g. Cd²⁺) or in some ("proton transfer") mutants (L210DN/M17DN or L213DN), the proton delivery to Q_B^- is made rate limiting and the properties of the proton pathway can be directly examined. We found that small weak acids and buffers in large concentrations (up to 1 M) were able to rescue the severely impaired proton transfer capability differently depending on the location of the defects: lesions at the protein surface (proton gate H126H/H128H + Cd²⁺), beneath the surface (M17DN + Cd²⁺, L210DN/M17DN) or deep inside the protein (L213DN) could be completely, partially or to very small extent recovered, respectively. Small zwitterionic acids (azide/hydrazoic acid) and buffers (tricine) proved to be highly effective rescuers consistent with their enhanced binding affinity and access to any of the proton acceptors (including Q_B^- itself) in the pathway. As a consequence, back titration of the protons at L212Glu could be observed as a pH-dependence of the rate constant of the charge recombination in the presence of azide or formate. Model calculations support the collective influence of the acid cluster on the change of the protonation states upon extension of the cluster with the bound small acid. In proton transfer mutants, the rescuing agents decreased the free energy of activation together with their enthalpic and entropic components. This is in agreement with the hypothesis that they function as protein-penetrating protonophores delivering protons into the chain and select dominating paths out of many alternate routes. We estimate that the proton delivery will be accelerated in one pathway out of 100-200 alternate pathways. The implications for design of the chemical recovery of impaired intra-protein proton transfer pathways in proton transfer mutants are discussed.

Time-resolved infrared spectroscopy in the study of photosynthetic systems

Time-resolved (TR) infrared (IR) spectroscopy in the nanosecond to second timescale has been extensively used, in the last 30 years, in the study of photosynthetic systems. Interesting results have also been obtained at lower time resolution (minutes or even hours). In this review, we first describe the used techniques-dispersive IR, laser diode IR, rapid-scan Fourier transform (FT)IR, step-scan FTIR-underlying the advantages and disadvantages of each of them. Then, the main TR-IR results obtained so far in the investigation of photosynthetic reactions (in reaction centers, in light-harvesting systems, but also in entire membranes or even in living organisms) are presented. Finally, after the general conclusions, the perspectives in the field of TR-IR applied to photosynthesis are described.

Identifying involvement of Lys251/Asp252 pair in electron transfer and associated proton transfer at the quinone reduction site of Rhodobacter capsulatus cytochrome bc1

Describing dynamics of proton transfers in proteins is challenging, but crucial for understanding processes which use them for biological functions. In cytochrome bc1, one of the key enzymes of respiration or photosynthesis, proton transfers engage in oxidation of quinol (QH2) and reduction of quinone (Q) taking place at two distinct catalytic sites. Here we evaluated by site-directed mutagenesis the contribution of Lys251/Asp252 pair (bacterial numbering) in electron transfers and associated with it proton uptake to the quinone reduction site (Qi site). We showed that the absence of protonable group at position 251 or 252 significantly changes the equilibrium levels of electronic reactions including the Qi-site mediated oxidation of heme bH, reverse reduction of heme bH by quinol and heme bH/Qi semiquinone equilibrium. This implicates the role of H-bonding network in binding of quinone/semiquinone and defining thermodynamic properties of Q/SQ/QH2 triad. The Lys251/Asp252 proton path is disabled only when both protonable groups are removed. With just one protonable residue from this pair, the entrance of protons to the catalytic site is sustained, albeit at lower rates, indicating that protons can travel through parallel routes, possibly involving water molecules. This shows that proton paths display engineering tolerance for change as long as all the elements available for functional cooperation secure efficient proton delivery to the catalytic site.

Dehydration affects the electronic structure of the primary electron donor in bacterial photosynthetic reaction centers: evidence from visible-NIR and light-induced difference FTIR spectroscopy

The photosynthetic reaction center (RC) is a membrane pigment-protein complex that catalyzes the initial charge separation reactions of photosynthesis. Following photoexcitation, the RC undergoes conformational relaxations which stabilize the charge-separated state. Dehydration of the complex inhibits its conformational dynamics, providing a useful tool to gain insights into the relaxational processes. We analyzed the effects of dehydration on the electronic structure of the primary electron donor P, as probed by visible-NIR and light-induced FTIR difference spectroscopy, in RC films equilibrated at different relative humidities r. Previous FTIR and ENDOR spectroscopic studies revealed that P, an excitonically coupled dimer of bacteriochlorophylls, can be switched between two conformations, P866 and P850, which differ in the extent of delocalization of the unpaired electron between the two bacteriochlorophyll moieties (PL and PM) of the photo-oxidized radical P(+). We found that dehydration (at r = 11%) shifts the optical Qy band of P from 866 to 850-845 nm, a large part of the effect occurring already at r = 76%. Such a dehydration weakens light-induced difference FTIR marker bands, which probe the delocalization of charge distribution within the P(+) dimer (the electronic band of P(+) at 2700 cm(-1), and the associated phase-phonon vibrational modes at around 1300, 1480, and 1550 cm(-1)). From the analysis of the P(+) keto C[double bond, length as m-dash]O bands at 1703 and 1713-15 cm(-1), we inferred that dehydration induces a stronger localization of the unpaired electron on PL(+). The observed charge redistribution is discussed in relation to the dielectric relaxation of the photoexcited RC on a long (10(2) s) time scale.

Photosynthetic diode: electron transport rectification by wetting the quinone cofactor

We report 11 μs of molecular dynamics simulations of the electron-transfer reaction between primary and secondary quinone cofactors in the bacterial reaction center. The main question addressed here is the mechanistic reason for unidirectional electron transfer between chemically identical cofactors. We find that electron is trapped at the secondary quinone by wetting of the protein pocket following electron transfer on the time-scale shorter than the backward transition. This mechanism provides effective rectification of the electron transport, making the reaction center a molecular diode operating by cyclic charge-induced electrowetting.

Hydrogen bond network around the semiquinone of the secondary quinone acceptor Q(B) in bacterial photosynthetic reaction centers

By utilizing a combined pulsed EPR and DFT approach, the high-resolution structure of the QB site semiquinone (SQB) was determined. The development of such a technique is crucial toward an understanding of protein-bound semiquinones on the structural level, as (i) membrane protein crystallography typically results in low resolution structures, and (ii) obtaining protein crystals in the semiquinone form is rarely feasible. The SQB hydrogen bond network was investigated with Q- (∼34 GHz) and X-band (∼9.7 GHz) pulsed EPR spectroscopy on fully deuterated reactions centers from Rhodobacter sphaeroides. Simulations in the SQB g-tensor reference frame provided the principal values and directions of the H-bond proton hyperfine tensors. Three protons were detected, one with an anisotropic tensor component, T = 4.6 MHz, assigned to the histidine NδH of His-L190, and two others with similar anisotropic constants T = 3.2 and 3.0 MHz assigned to the peptide NpH of Gly-L225 and Ile-L224, respectively. Despite the strong similarity in the peptide couplings, all hyperfine tensors were resolved in the Q-band ENDOR spectra. The Euler angles describing the series of rotations that bring the hyperfine tensors into the SQB g-tensor reference frame were obtained by least-squares fitting of the spectral simulations to the ENDOR data. These Euler angles show the locations of the hydrogen bonded protons with respect to the semiquinone. Our geometry optimized model of SQB used in previous DFT work is in strong agreement with the angular constraints from the spectral simulations, providing the foundation for future joint pulsed EPR and DFT semiquinone structural determinations in other proteins.

Stigmatellin probes the electrostatic potential in the QB site of the photosynthetic reaction center

The electrostatic potential in the secondary quinone (QB) binding site of the reaction center (RC) of the photosynthetic bacterium Rhodobacter sphaeroides determines the rate and free energy change (driving force) of electron transfer to QB. It is controlled by the ionization states of residues in a strongly interacting cluster around the QB site. Reduction of the QB induces change of the ionization states of residues and binding of protons from the bulk. Stigmatellin, an inhibitor of the mitochondrial and photosynthetic respiratory chain, has been proven to be a unique voltage probe of the QB binding pocket. It binds to the QB site with high affinity, and the pK value of its phenolic group monitors the local electrostatic potential with high sensitivity. Investigations with different types of detergent as a model system of isolated RC revealed that the pK of stigmatellin was controlled overwhelmingly by electrostatic and slightly by hydrophobic interactions. Measurements showed a high pK value (>11) of stigmatellin in the QB pocket of the dark-state wild-type RC, indicating substantial negative potential. When the local electrostatics of the QB site was modulated by a single mutation, L213Asp → Ala, or double mutations, L213Asp-L212Glu → Ala-Ala (AA), the pK of stigmatellin dropped to 7.5 and 7.4, respectively, which corresponds to a >210 mV increase in the electrostatic potential relative to the wild-type RC. This significant pK drop (ΔpK > 3.5) decreased dramatically to (ΔpK > 0.75) in the RC of the compensatory mutant (AA+M44Asn → AA+M44Asp). Our results indicate that the L213Asp is the most important actor in the control of the electrostatic potential in the QB site of the dark-state wild-type RC, in good accordance with conclusions of former studies using theoretical calculations or light-induced charge recombination assay.

FTIR studies of metal ligands, networks of hydrogen bonds, and water molecules near the active site Mn₄CaO₅ cluster in Photosystem II

The photosynthetic conversion of water to molecular oxygen is catalyzed by the Mn₄CaO₅ cluster in Photosystem II and provides nearly our entire supply of atmospheric oxygen. The Mn₄CaO₅ cluster accumulates oxidizing equivalents in response to light-driven photochemical events within Photosystem II and then oxidizes two molecules of water to oxygen. The Mn₄CaO₅ cluster converts water to oxygen much more efficiently than any synthetic catalyst because its protein environment carefully controls the cluster's reactivity at each step in its catalytic cycle. This control is achieved by precise choreography of the proton and electron transfer reactions associated with water oxidation and by careful management of substrate (water) access and proton egress. This review describes the FTIR studies undertaken over the past two decades to identify the amino acid residues that are responsible for this control and to determine the role of each. In particular, this review describes the FTIR studies undertaken to characterize the influence of the cluster's metal ligands on its activity, to delineate the proton egress pathways that link the Mn₄CaO₅ cluster with the thylakoid lumen, and to characterize the influence of specific residues on the water molecules that serve as substrate or as participants in the networks of hydrogen bonds that make up the water access and proton egress pathways. This information will improve our understanding of water oxidation by the Mn₄CaO₅ catalyst in Photosystem II and will provide insight into the design of new generations of synthetic catalysts that convert sunlight into useful forms of storable energy. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.

Conformational differences between the methoxy groups of QA and QB site ubisemiquinones in bacterial reaction centers: a key role for methoxy group orientation in modulating ubiquinone redox potential

Ubiquinone is an almost universal, membrane-associated redox mediator. Its ability to accept either one or two electrons allows it to function in critical roles in biological electron transport. The redox properties of ubiquinone in vivo are determined by its environment in the binding sites of proteins and by the dihedral angle of each methoxy group relative to the ring plane. This is an attribute unique to ubiquinone among natural quinones and could account for its widespread function with many different redox complexes. In this work, we use the photosynthetic reaction center as a model system for understanding the role of methoxy conformations in determining the redox potential of the ubiquinone/semiquinone couple. Despite the abundance of X-ray crystal structures for the reaction center, quinone site resolution has thus far been too low to provide a reliable measure of the methoxy dihedral angles of the primary and secondary quinones, QA and QB. We performed 2D ESEEM (HYSCORE) on isolated reaction centers with ubiquinones (13)C-labeled at the headgroup methyl and methoxy substituents, and have measured the (13)C isotropic and anisotropic components of the hyperfine tensors. Hyperfine couplings were compared to those derived by DFT calculations as a function of methoxy torsional angle allowing estimation of the methoxy dihedral angles for the semiquinones in the QA and QB sites. Based on this analysis, the orientation of the 2-methoxy groups are distinct in the two sites, with QB more out of plane by 20-25°. This corresponds to an ≈50 meV larger electron affinity for the QB quinone, indicating a substantial contribution to the experimental difference in redox potentials (60-75 mV) of the two quinones. The methods developed here can be readily extended to ubiquinone-binding sites in other protein complexes.

Effects of dehydration on light-induced conformational changes in bacterial photosynthetic reaction centers probed by optical and differential FTIR spectroscopy

Following light-induced electron transfer between the primary donor (P) and quinone acceptor (Q(A)) the bacterial photosynthetic reaction center (RC) undergoes conformational relaxations which stabilize the primary charge separated state P(+)Q(A)(-). Dehydration of RCs from Rhodobacter sphaeroides hinders these conformational dynamics, leading to acceleration of P(+)Q(A)(-) recombination kinetics [Malferrari et al., J. Phys. Chem. B 115 (2011) 14732-14750]. To clarify the structural basis of the conformational relaxations and the involvement of bound water molecules, we analyzed light-induced P(+)Q(A)(-)/PQ(A) difference FTIR spectra of RC films at two hydration levels (relative humidity r=76% and r=11%). Dehydration reduced the amplitude of bands in the 3700-3550cm(-1) region, attributed to water molecules hydrogen bonded to the RC, previously proposed to stabilize the charge separation by dielectric screening [Iwata et al., Biochemistry 48 (2009) 1220-1229]. Other features of the FTIR difference spectrum were affected by partial depletion of the hydration shell (r=11%), including contributions from modes of P (9-keto groups), and from NH or OH stretching modes of amino acidic residues, absorbing in the 3550-3150cm(-1) range, a region so far not examined in detail for bacterial RCs. To probe in parallel the effects of dehydration on the RC conformational relaxations, we analyzed by optical absorption spectroscopy the kinetics of P(+)Q(A)(-) recombination following the same photoexcitation used in FTIR measurements (20s continuous illumination). The results suggest a correlation between the observed FTIR spectral changes and the conformational rearrangements which, in the hydrated system, strongly stabilize the P(+)Q(A)(-) charge separated state over the second time scale.

A New Method forD2O/H2OExchange in Infrared Spectroscopy of Proteins

In this paper, we describe a new method to obtain D2O/H2O exchange in photosynthetic reaction centres fromRhodobacter sphaeroides. The method is characterized by: (i) a very high efficiency of the isotopic replacement; (ii) an extremely low amount of D2O needed; (iii) the short time required for dehydration and D2O rehydration; (iv) the possibility of controlling concomitantly the hydration state of the sample. The proposed method can be applied to other proteins.

Charge separation in photosystem II: a comparative and evolutionary overview

Our current understanding of the PSII reaction centre owes a great deal to comparisons to the simpler and better understood, purple bacterial reaction centre. Here we provide an overview of the similarities with a focus on charge separation and the electron acceptors. We go on to discuss some of the main differences between the two kinds of reaction centres that have been highlighted by the improving knowledge of PSII. We attempt to relate these differences to functional requirements of water splitting. Some are directly associated with that function, e.g. high oxidation potentials, while others are associated with regulation and protection against photodamage. The protective and regulatory functions are associated with the harsh chemistry performed during its normal function but also with requirements of the enzyme while it is undergoing assembly and repair. Key aspects of PSII reaction centre evolution are also addressed. This article is part of a Special Issue entitled: Photosystem II.

Light-induced quinone reduction in photosystem II

The photosystem II core complex is the water:plastoquinone oxidoreductase of oxygenic photosynthesis situated in the thylakoid membrane of cyanobacteria, algae and plants. It catalyzes the light-induced transfer of electrons from water to plastoquinone accompanied by the net transport of protons from the cytoplasm (stroma) to the lumen, the production of molecular oxygen and the release of plastoquinol into the membrane phase. In this review, we outline our present knowledge about the "acceptor side" of the photosystem II core complex covering the reaction center with focus on the primary (Q(A)) and secondary (Q(B)) quinones situated around the non-heme iron with bound (bi)carbonate and a comparison with the reaction center of purple bacteria. Related topics addressed are quinone diffusion channels for plastoquinone/plastoquinol exchange, the newly discovered third quinone Q(C), the relevance of lipids, the interactions of quinones with the still enigmatic cytochrome b559 and the role of Q(A) in photoinhibition and photoprotection mechanisms. This article is part of a Special Issue entitled: Photosystem II.

Carboxylate shifts steer interquinone electron transfer in photosynthesis

Understanding the mechanisms of electron transfer (ET) in photosynthetic reaction centers (RCs) may inspire novel catalysts for sunlight-driven fuel production. The electron exit pathway of type II RCs comprises two quinone molecules working in series and in between a non-heme iron atom with a carboxyl ligand (bicarbonate in photosystem II (PSII), glutamate in bacterial RCs). For decades, the functional role of the iron has remained enigmatic. We tracked the iron site using microsecond-resolution x-ray absorption spectroscopy after laser-flash excitation of PSII. After formation of the reduced primary quinone, Q(A)(-), the x-ray spectral changes revealed a transition (t½ ≈ 150 μs) from a bidentate to a monodentate coordination of the bicarbonate at the Fe(II) (carboxylate shift), which reverted concomitantly with the slower ET to the secondary quinone Q(B). A redox change of the iron during the ET was excluded. Density-functional theory calculations corroborated the carboxylate shift both in PSII and bacterial RCs and disclosed underlying changes in electronic configuration. We propose that the iron-carboxyl complex facilitates the first interquinone ET by optimizing charge distribution and hydrogen bonding within the Q(A)FeQ(B) triad for high yield Q(B) reduction. Formation of a specific priming intermediate by nuclear rearrangements, setting the stage for subsequent ET, may be a common motif in reactions of biological redox cofactors.

Interaction between Na+ ion and carboxylates of the PomA-PomB stator unit studied by ATR-FTIR spectroscopy

Bacterial flagellar motors are molecular machines powered by the electrochemical potential gradient of specific ions across the membrane. The PomA-PomB stator complex of Vibrio alginolyticus couples Na(+) influx to torque generation in this supramolecular motor, but little is known about how Na(+) associates with the PomA-PomB complex in the energy conversion process. Here, by means of attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy, we directly observed binding of Na(+) to carboxylates in the PomA-PomB complex, including the functionally essential residue Asp24. The Na(+) affinity of Asp24 is estimated to be approximately 85 mM, close to the apparent K(m) value from the swimming motility of the cells (78 mM). At least two other carboxylates are shown to be capable of interacting with Na(+), but with somewhat lower affinities. We conclude that Asp24 and at least two other carboxylates constitute Na(+) interaction sites in the PomA-PomB complex. This work reveals features of the Na(+) pathway in the PomA-PomB Na(+) channel by using vibrational spectroscopy.

Fourier transform infrared (FTIR) spectroscopy

Fourier transform infrared (FTIR) spectroscopy probes the vibrational properties of amino acids and cofactors, which are sensitive to minute structural changes. The lack of specificity of this technique, on the one hand, permits us to probe directly the vibrational properties of almost all the cofactors, amino acid side chains, and of water molecules. On the other hand, we can use reaction-induced FTIR difference spectroscopy to select vibrations corresponding to single chemical groups involved in a specific reaction. Various strategies are used to identify the IR signatures of each residue of interest in the resulting reaction-induced FTIR difference spectra. (Specific) Isotope labeling, site-directed mutagenesis, hydrogen/deuterium exchange are often used to identify the chemical groups. Studies on model compounds and the increasing use of theoretical chemistry for normal modes calculations allow us to interpret the IR frequencies in terms of specific structural characteristics of the chemical group or molecule of interest. This review presents basics of FTIR spectroscopy technique and provides specific important structural and functional information obtained from the analysis of the data from the photosystems, using this method.

M234Glu is a component of the proton sponge in the reaction center from photosynthetic bacteria

Bacterial reaction centers use light energy to couple the uptake of protons to the successive semi-reduction of two quinones, namely Q(A) and Q(B). These molecules are situated symmetrically in regard to a non-heme iron atom. Four histidines and one glutamic acid, M234Glu, constitute the five ligands of this atom. By flash-induced absorption spectroscopy and delayed fluorescence we have studied in the M234EH and M234EL variants the role played by this acidic residue on the energetic balance between the two quinones as well as in proton uptake. Delayed fluorescence from the P(+)Q(A)(-) state (P is the primary electron donor) and temperature dependence of the rate of P(+)Q(A)(-) charge recombination that are in good agreement show that in the two RC variants, both Q(A)(-) and Q(B)(-) are destabilized by about the same free energy amount: respectively approximately 100 +/- 5 meV and 90 +/- 5 meV for the M234EH and M234EL variants, as compared to the WT. Importantly, in the M234EH and M234EL variants we observe a collapse of the high pH band (present in the wild-type reaction center) of the proton uptake amplitudes associated with formation of Q(A)(-) and Q(B)(-). This band has recently been shown to be a signature of a collective behaviour of an extended, multi-entry, proton uptake network. M234Glu seems to play a central role in the proton sponge-like system formed by the RC protein.

Identification of FTIR bands due to internal water molecules around the quinone binding sites in the reaction center from Rhodobacter sphaeroides

The bacterial reaction center (RC) is a membrane protein complex that performs photosynthetic electron transfer from a bacteriochlorophyll dimer to quinone acceptors Q(A) and Q(B). Q(B) accepts electrons from the primary quinone, Q(A), in two sequential electron transfer reactions coupled to uptake of a proton from solution. It has been suggested that water molecules along the proton uptake pathway are protonated upon quinone reduction on the basis of FTIR difference spectra [Breton, J., and Nabedryk, E. (1998) Photosynth. Res. 55, 301-307]. We examined the possible involvement of water molecules in the photoreaction processes by studying (18)O water isotope effects on FTIR difference spectra resulting from formation of Q(A)(-) and Q(B)(-). Continuum bands in D(2)O due to Q(B)(-) formation in the 2300-1800 cm(-1) region did not show spectral shifts by (18)O water in the wild-type (WT) RC, suggesting that these bands do not originate from (protonated) water. In contrast, the Q(B)(-)/Q(B) spectrum of the EQ-L212 mutant RC showed a spectral shift of a band near 2100 cm(-1) due to (18)O water substitution, consistent with protonation of internal water. FTIR shifts due to (18)O water were also observed following formation of Q(A)(-) and Q(B)(-) in the spectral region of 3700-3500 cm(-1) characteristic of weakly hydrogen bonded water. The water responsible for the Q(B)(-) change was localized near Glu-L212 by spectral shifts in mutant RCs. The weakly hydrogen bonded water perturbed by quinone reduction may play a role in stabilizing the charge-separated state.