BBA - Bioenergetics (v.1847, #1)

PUB (iii-iv).

Ultrafast infrared spectroscopy in photosynthesis by Mariangela Di Donato; Marie Louise Groot (2-11).
In recent years visible pump/mid-infrared (IR) probe spectroscopy has established itself as a key technology to unravel structure–function relationships underlying the photo-dynamics of complex molecular systems. In this contribution we review the most important applications of mid-infrared absorption difference spectroscopy with sub-picosecond time-resolution to photosynthetic complexes. Considering several examples, such as energy transfer in photosynthetic antennas and electron transfer in reaction centers and even more intact structures, we show that the acquisition of ultrafast time resolved mid-IR spectra has led to new insights into the photo-dynamics of the considered systems and allows establishing a direct link between dynamics and structure, further strengthened by the possibility of investigating the protein response signal to the energy or electron transfer processes. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
Keywords: Ultrafast infrared spectroscopy; Photosynthesis; Reaction center; Energy transfer; Electron transfer; Review;

Resonance Raman spectroscopy may yield precise information on the conformation of, and the interactions assumed by, the chromophores involved in the first steps of the photosynthetic process. Selectivity is achieved via resonance with the absorption transition of the chromophore of interest. Fluorescence line-narrowing spectroscopy is a complementary technique, in that it provides the same level of information (structure, conformation, interactions), but in this case for the emitting pigment(s) only (whether isolated or in an ensemble of interacting chromophores). The selectivity provided by these vibrational techniques allows for the analysis of pigment molecules not only when they are isolated in solvents, but also when embedded in soluble or membrane proteins and even, as shown recently, in vivo. They can be used, for instance, to relate the electronic properties of these pigment molecules to their structure and/or the physical properties of their environment. These techniques are even able to follow subtle changes in chromophore conformation associated with regulatory processes. After a short introduction to the physical principles that govern resonance Raman and fluorescence line-narrowing spectroscopies, the information content of the vibrational spectra of chlorophyll and carotenoid molecules is described in this article, together with the experiments which helped in determining which structural parameter(s) each vibrational band is sensitive to. A selection of applications is then presented, in order to illustrate how these techniques have been used in the field of photosynthesis, and what type of information has been obtained. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
Keywords: Photosynthesis; Light-harvesting; Reaction center; Carotenoid; Chlorophyll;

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.
Keywords: FTIR; Photosynthesis; Water oxidation; Oxygen evolving complex; Mn4CaO5 cluster; Hydrogen bond network;

Photosynthetic water oxidation, which provides the electrons necessary for CO2 reduction and releases O2 and protons, is performed at the Mn4CaO5 cluster in photosystem II (PSII). In this review, studies that assessed the mechanism of water oxidation using infrared spectroscopy are summarized focusing on electron and proton transfer dynamics. Structural changes in proteins and water molecules between intermediates known as S i states (i  = 0–3) were detected using flash-induced Fourier transform infrared (FTIR) difference spectroscopy. Electron flow in PSII and proton release from substrate water were monitored using the infrared changes in ferricyanide as an exogenous electron acceptor and Mes buffer as a proton acceptor. Time-resolved infrared (TRIR) spectroscopy provided information on the dynamics of proton-coupled electron transfer during the S-state transitions. In particular, a drastic proton movement during the lag phase (~ 200 μs) before electron transfer in the S3  → S0 transition was detected directly by monitoring the infrared absorption of a polarizable proton in a hydrogen bond network. Furthermore, the proton release pathways in the PSII proteins were analyzed by FTIR difference measurements in combination with site-directed mutagenesis, isotopic substitutions, and quantum chemical calculations. Therefore, infrared spectroscopy is a powerful tool for understanding the molecular mechanism of photosynthetic water oxidation. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
Keywords: FTIR; Time-resolved infrared spectroscopy; Photosynthesis; Water oxidation; Oxygen evolution; Proton transfer;

In bioenergetic reactions, electrons are transferred long distances via a hopping mechanism. In photosynthesis and DNA synthesis, the aromatic amino acid residue, tyrosine, functions as an intermediate that is transiently oxidized and reduced during long distance electron transfer. At physiological pH values, oxidation of tyrosine is associated with a deprotonation of the phenolic oxygen, giving rise to a proton coupled electron transfer (PCET) reaction. Tyrosine-based PCET reactions are important in photosystem II, which carries out the light-induced oxidation of water, and in ribonucleotide reductase, which reduces ribonucleotides to form deoxynucleotides. Photosystem II contains two redox-active tyrosines, YD (Y160 in the D2 polypeptide) and YZ (Y161 in the D1 polypeptide). YD forms a light-induced stable radical, while YZ functions as an essential charge relay, oxidizing the catalytic Mn4CaO5 cluster on each of four photo-oxidation reactions. In Escherichia coli class 1a RNR, the β2 subunit contains the radical initiator, Y122O •, which is reversibly reduced and oxidized in long range electron transfer with the α2 subunit. In the isolated E. coli β2 subunit, Y122O • is a stable radical, but Y122O • is activated for rapid PCET in an α2β2 substrate/effector complex. Recent results concerning the structure and function of YD, YZ, and Y122 are reviewed here. Comparison is made to recent results derived from bioengineered proteins and biomimetic compounds, in which tyrosine-based charge transfer mechanisms have been investigated. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.Display Omitted
Keywords: Ribonucleotide reductase; Azurin; Photosystem II; EPR spectroscopy; RIFT-IR spectroscopy; DNA synthesis;

Vibrational spectroscopy of photosystem I by Gary Hastings (55-68).
Fourier transform infrared difference spectroscopy (FTIR DS) has been widely used to study the structural details of electron transfer cofactors (and their binding sites) in many types of photosynthetic protein complexes. This review focuses in particular on work that has been done to investigate the A1 cofactor in photosystem I photosynthetic reaction centers. A review of this subject area last appeared in 2006 [1], so only work undertaken since then will be covered here.Following light excitation of intact photosystem I particles the P700+A1 secondary radical pair state is formed within 100 ps. This state decays within 300 ns at room temperature, or 300 μs at 77 K. Given the short-lived nature of this state, it is not easily studied using “static” photo-accumulation FTIR difference techniques at either temperature. Time-resolved techniques are required. This article focuses on the use of time-resolved step-scan FTIR DS for the study of the P700+A1 state in intact photosystem I. Up until now, only our group has undertaken studies in this area. So, in this article, recent work undertaken in our lab is described, where we have used low-temperature (77 K), microsecond time-resolved step-scan FTIR DS to study the P700+A1 state in photosystem I.In photosystem I a phylloquinone molecule occupies the A1 binding site. However, different quinones can be incorporated into the A1 binding site, and here work is described for photosystem I particles with plastoquinone-9, 2-phytyl naphthoquinone and 2-methyl naphthoquinone incorporated into the A1 binding site. Studies in which 18O isotope labeled phylloquinone has been incorporated into the A1 binding site are also discussed.To fully characterize PSI particles with different quinones incorporated into the A1 binding site nanosecond to millisecond visible absorption spectroscopy has been shown to be of considerable value, especially so when undertaken using identical samples under identical conditions to that used in time-resolved step-scan FTIR measurements. In this article the latest work that has been undertaken using both visible and infrared time resolved spectroscopies on the same sample will be described.Finally, vibrational spectroscopic data that has been obtained for phylloquinone in the A1 binding site in photosystem I is compared to corresponding data for ubiquinone in the QA binding site in purple bacterial reaction centers. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.Display Omitted
Keywords: Photosynthesis; Photosystem I; FTIR; Time-resolved step-scan; A1; Normal mode;

Ultrafast time-resolved vibrational spectroscopies of carotenoids in photosynthesis by Hideki Hashimoto; Mitsuru Sugisaki; Masayuki Yoshizawa (69-78).
This review discusses the application of time-resolved vibrational spectroscopies to the studies of carotenoids in photosynthesis. The focus is on the ultrafast time regime and the study of photophysics and photochemistry of carotenoids by femtosecond time-resolved stimulated Raman and four-wave mixing spectroscopies. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.Display Omitted
Keywords: Carotenoid; Photosynthesis; Time-resolved stimulated Raman spectroscopy; Coherent spectroscopy; Four-wave mixing spectroscopy;

The catalytic site of heme–copper oxidases encompasses two close-lying ligand binding sites: the heme, where oxygen is bound and reduced and the CuB atom, which acts as ligand entry and release port. Diatomic gaseous ligands with a dipole moment, such as the signaling molecules carbon monoxide (CO) and nitric oxide (NO), carry clear infrared spectroscopic signatures in the different states that allow characterization of the dynamics of ligand transfer within, into and out of the active site using time-resolved infrared spectroscopy. We review the nature and diversity of these processes that have in particular been characterized with CO as ligand and which take place on time scales ranging from femtoseconds to milliseconds. These studies have advanced our understanding of the functional ligand pathways and reactivity in enzymes and more globally represent intriguing model systems for mechanisms of ligand motion in a confined protein environment. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
Keywords: Ligand dynamics; Cytochrome c oxidases; Heme proteins; Binuclear center; Time-resolved spectroscopy;

Recent progress in studies on the proton-pumping and O2 reduction mechanisms of cytochrome c oxidase (CcO) elucidated by infrared (IR) and resonance Raman (rR) spectroscopy, is reviewed. CcO is the terminal enzyme of the respiratory chain and its O2 reduction reaction is coupled with H+ pumping activity across the inner mitochondrial membrane. The former is catalyzed by heme a 3 and its mechanism has been determined using a rR technique, while the latter used the protein moiety and has been investigated with an IR technique. The number of H+ relative to e transferred in the reaction is 1:1, and their coupling is presumably performed by heme a and nearby residues. To perform this function, different parts of the protein need to cooperate with each other spontaneously and sequentially. It is the purpose of this article to describe the structural details on the coupling on the basis of the vibrational spectra of certain specified residues and chromophores involved in the reaction. Recent developments in time-resolved IR and Raman technology concomitant with protein manipulation methods have yielded profound insights into such structural changes. In particular, the new IR techniques that yielded the breakthrough are reviewed and assessed in detail. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
Keywords: Cytochrome c oxidase; Proton-pumping mechanism; Time-resolved infrared and Raman spectroscopy;

Proton translocation in cytochrome c oxidase: Insights from proton exchange kinetics and vibrational spectroscopy by Izumi Ishigami; Masahide Hikita; Tsuyoshi Egawa; Syun-Ru Yeh; Denis L. Rousseau (98-108).
Cytochrome c oxidase is the terminal enzyme in the electron transfer chain. It reduces oxygen to water and harnesses the released energy to translocate protons across the inner mitochondrial membrane. The mechanism by which the oxygen chemistry is coupled to proton translocation is not yet resolved owing to the difficulty of monitoring dynamic proton transfer events. Here we summarize several postulated mechanisms for proton translocation, which have been supported by a variety of vibrational spectroscopic studies. We recently proposed a proton translocation model involving proton accessibility to the regions near the propionate groups of the heme a and heme a 3 redox centers of the enzyme based by hydrogen/deuterium (H/D) exchange Raman scattering studies (Egawa et al., PLoS ONE 2013). To advance our understanding of this model and to refine the proton accessibility to the hemes, the H/D exchange dependence of the heme propionate group vibrational modes on temperature and pH was measured. The H/D exchange detected at the propionate groups of heme a 3 takes place within a few seconds under all conditions. In contrast, that detected at the heme a propionates occurs in the oxidized but not the reduced enzyme and the H/D exchange is pH-dependent with a pKa of ~ 8.0 (faster at high pH). Analysis of the thermodynamic parameters revealed that, as the pH is varied, entropy/enthalpy compensation held the free energy of activation in a narrow range. The redox dependence of the possible proton pathways to the heme groups is discussed. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
Keywords: Raman spectroscopy; Proton translocation; Cytochrome oxidase; Vibrational spectroscopy; Heme;

The pathway of O2 to the active site in heme–copper oxidases by Ólöf Einarsdóttir; William McDonald; Chie Funatogawa; Istvan Szundi; William H. Woodruff; R. Brian Dyer (109-118).
The route of O2 to and from the high-spin heme in heme–copper oxidases has generally been believed to emulate that of carbon monoxide (CO). Time-resolved and stationary infrared experiments in our laboratories of the fully reduced CO-bound enzymes, as well as transient optical absorption saturation kinetics studies as a function of CO pressure, have provided strong support for CO binding to CuB + on the pathway to and from the high-spin heme. The presence of CO on CuB + suggests that O2 binding may be compromised in CO flow-flash experiments. Time-resolved optical absorption studies show that the rate of O2 and NO binding in the bovine enzyme (1 × 108  M− 1  s− 1) is unaffected by the presence of CO, which is consistent with the rapid dissociation (t1/2 = 1.5 μs) of CO from CuB +. In contrast, in Thermus thermophilus (Tt) cytochrome ba 3 the O2 and NO binding to heme a 3 slows by an order of magnitude in the presence of CO (from 1 × 109 to 1 × 108  M− 1  s− 1), but is still considerably faster (~ 10 μs at 1 atm O2) than the CO off-rate from CuB in the absence of O2 (milliseconds). These results show that traditional CO flow-flash experiments do not give accurate results for the physiological binding of O2 and NO in Tt ba 3, namely, in the absence of CO. They also raise the question whether in CO flow-flash experiments on Tt ba 3 the presence of CO on CuB + impedes the binding of O2 to CuB + or, if O2 does not bind to CuB + prior to heme a 3, whether the CuB +–CO complex sterically restricts access of O2 to the heme. Both possibilities are discussed, and we argue that O2 binds directly to heme a 3 in Tt ba 3, causing CO to dissociate from CuB + in a concerted manner through steric and/or electronic effects. This would allow CuB + to function as an electron donor during the fast (5 μs) breaking of the O―O bond. These results suggest that the binding of CO to CuB + on the path to and from heme a 3 may not be applicable to O2 and NO in all heme-copper oxidases. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
Keywords: Time-resolved infrared spectroscopy; Time-resolved infrared linear dichroism; Thermus thermophilus ba 3; Photolabile O2 and NO complex; CO photodissociation and recombination dynamics;

Cytochrome c oxidase (CcO) catalyzes the four electron reduction of molecular oxygen to water while avoiding the formation of toxic peroxide; a quality that is of high relevance for the development of oxygen-reducing catalysts. Resonance Raman spectroscopy has been used since many years as a technique to identify electron transfer pathways in cytochrome c oxidase and to identify the key intermediates in the catalytic cycle. This information can be compared to artificial systems such as modified heme–copper enzymes, molecular heme–copper catalysts or CcO/electrode complexes in order to shed light into the reaction mechanism of these non-natural systems. Understanding the structural commonalities and differences of CcO with its non-natural analogs is of great value for designing efficient oxygen-reducing catalysts. In this review therefore Raman spectroscopic measurements on artificial heme–copper enzymes and model complexes are summarized and compared to the natural enzyme cytochrome c oxidase. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.Display Omitted
Keywords: Cytochrome c oxidase; Resonance Raman; Surface enhanced Raman spectroscopy; Oxo intermediate; Biomimetic complex; Oxygen reduction;

In bioenergetic systems quinones play a central part in the coupling of electron and proton transfer. The specific function of each quinone binding site is based on the protein–quinone interaction that can be described by means of reaction induced FTIR difference spectroscopy, induced for example by light or electrochemically. The identification of sites in enzymes from the respiratory chain is presented together with the analysis of the accommodation of different types of quinones to the same enzyme and the possibility to monitor the interaction with inhibitors. Reaction induced FTIR difference spectroscopy is shown to give an essential information on the general geometry of quinone binding sites, the conformation of the ring and of the substituents as well as essential structural information on the identity of the amino-acid residues lining this site. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
Keywords: Quinone; FTIR spectroscopy; Electrochemistry; bd oxidase; Quinol oxidase; bc 1 complex;

Infrared spectroscopic studies on the V-ATPase by Hideki Kandori; Yuji Furutani; Takeshi Murata (134-141).
V-ATPase is an ATP-driven rotary motor that vectorially transports ions. Together with F-ATPase, a homologous protein, several models on the ion transport have been proposed, but their molecular mechanisms are yet unknown. V-ATPase from Enterococcus hirae forms a large supramolecular protein complex (total molecular weight: ~ 700,000) and physiologically transports Na+ and Li+ across a hydrophobic lipid bilayer. Stabilization of these cations in the binding site has been discussed on the basis of X-ray crystal structures of a membrane-embedded domain, the K-ring (Na+ and Li+ bound forms). Sodium or lithium ion binding-induced difference FTIR spectra of the intact E. hirae V-ATPase have been measured in aqueous solution at physiological temperature. The results suggest that sodium or lithium ion binding induces the deprotonation of Glu139, a hydrogen-bonding change in the tyrosine residue and rigid α-helical structures. Identical difference FTIR spectra between the entire V-ATPase complex and K-ring strongly suggest that protein interaction with the I subunit does not cause large structural changes in the K-ring. This result supports the previously proposed Na+ transport mechanism by V-ATPase stating that a flip-flop movement of a carboxylate group of Glu139 without large conformational changes in the K-ring accelerates the replacement of a Na+ ion in the binding site. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
Keywords: V1/Vo-ATPase; ATR-FTIR spectroscopy; X-ray crystallography; Sodium binding; Protonation; Conformation change;