Low-frequency fourier transform infrared spectroscopy of the oxygen-evolving and quinone acceptor complexes in photosystem II

Nanosecond time-resolved infrared spectroscopy for the study of electron transfer in photosystem I

Microsecond time-resolved step-scan FTIR difference spectroscopy was used to study photosystem I (PSI) from Thermosynechococcus vestitus BP-1 (T. vestitus, formerly known as T. elongatus) at 77 K. In addition, photoaccumulated (P700+-P700) FTIR difference spectra were obtained at both 77 and 293 K. The FTIR difference spectra are presented here for the first time. To extend upon these FTIR studies nanosecond time-resolved infrared difference spectroscopy was also used to study PSI from T. vestitus at 296 K. Nanosecond infrared spectroscopy has never been used to study PSI samples at physiological temperatures, and here it is shown that such an approach has great value as it allows a direct probe of electron transfer down both branches in PSI. In PSI at 296 K, the infrared flash-induced absorption changes indicate electron transfer down the B- and A-branches is characterized by time constants of 33 and 364 ns, respectively, in good agreement with visible spectroscopy studies. These time constants are associated with forward electron transfer from A1- to FX on the B- and A-branches, respectively. At several infrared wavelengths flash-induced absorption changes at 296 K recover in tens to hundreds of milliseconds. The dominant decay phase is characterized by a lifetime of 128 ms. These millisecond changes are assigned to radical pair recombination reactions, with the changes being associated primarily with P700+ rereduction. This conclusion follows from the observation that the millisecond infrared spectrum is very similar to the photoaccumulated (P700+-P700) FTIR difference spectrum.

Structural Reorganization of a Synthetic Mimic of the Oxygen-Evolving Center in Multiple Redox Transitions Revealed by Electrochemical FTIR Spectra

In photosynthesis, the protein-bound natural oxygen-evolving center (OEC) undergoes multiple oxidation-state transitions in the light-driven water splitting reactions with a stepwise change in the oxidation potential. Because the protein is vulnerable to electrochemical oxidation, the multiple oxidation/reduction-state transitions can hardly be achieved by electrochemical oxidation with a continuous change in the oxidation potential. An OEC mimic that can undergo four redox transitions has been synthesized (Zhang, C., Science, 2015, 348, 690-693). Here we report an electrochemical FTIR spectroscopic study of this synthetic complex at its multiple oxidation states in the low-frequency region for Mn-O bonds. Compared with those of the native OEC induced by pulsed laser flashes, our results also show the existence of two structural isomers in the S₂ state, with the closed cubane conformer being more stable than the open cubane conformer, in contrast to that of the native OEC in which the open form is more stable.

Highly Sensitive Low-Frequency Time-Domain Raman Spectroscopy via Fluorescence Encoding

Fluorescence-encoded vibrational spectroscopy has become increasingly more popular by virtue of its high chemical specificity and sensitivity. However, current fluorescence-encoded vibrational spectroscopy methods lack sensitivity in the low-frequency region, which if addressed could further enhance their capabilities. Here, we present a method for highly sensitive low-frequency fluorescence-encoded vibrational spectroscopy, termed fluorescence-encoded time-domain coherent Raman spectroscopy (FLETCHERS). By first exciting molecules into vibrationally excited states and then promoting the vibrating molecules to electronic states at varying times, the molecular vibrations can be encoded onto the emitted time-domain fluorescence intensity. We demonstrate the sensitive low-frequency detection capability of FLETCHERS by measuring vibrational spectra in the lower fingerprint region of rhodamine 800 solutions as dilute as 250 nM, which is ∼1000 times more sensitive than conventional vibrational spectroscopy. These results, along with further improvement of the method, open up the prospect of performing single-molecule vibrational spectroscopy in the low-frequency region.

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.

Warwick Hillier: a tribute

Warwick Hillier (October 18, 1967-January 10, 2014) made seminal contributions to our understanding of photosynthetic water oxidation employing membrane inlet mass spectrometry and FTIR spectroscopy. This article offers a collection of historical perspectives on the scientific impact of Warwick Hillier's work and tributes to the personal impact his life and ideas had on his collaborators and colleagues.

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.

FTIR evidence that the PsbP extrinsic protein induces protein conformational changes around the oxygen-evolving Mn cluster in photosystem II

Extrinsic proteins of photosystem II (PSII) regulate the oxygen-evolving reaction performed at the Mn cluster by controlling the binding properties of the indispensable cofactors Ca(2+) and Cl(-). However, the molecular mechanism underlying this regulation is not yet understood. We have investigated the structural couplings of the extrinsic proteins PsbO, PsbP, and PsbQ of higher plants with the Mn cluster using Fourier transform infrared (FTIR) spectroscopy. Light-induced FTIR difference spectra upon the S(1) --> S(2) transition were measured using spinach PSII membranes, and the effects of the selective depletion of extrinsic proteins were examined. Depletion of the PsbP and PsbQ proteins by NaCl washing revealed clear changes in the amide I bands with no appreciable changes in the bands of carboxylate and imidazole groups, whereas the depletion of all three proteins by CaCl(2) washing did not cause further changes. The original amide I features were recovered by reconstitution of the NaCl-washed PSII with PsbP, and the same recovery was observed with (13)C-labeled PsbP. These results indicate that the PsbP protein, but not PsbQ and PsbO, affects the protein conformation around the Mn cluster in the intrinsic proteins without changing the ligand structure. Reconstitution with Delta15-PabP, in which the 15 N-terminal residues were truncated, did not restore the amide I bands, indicating that the interaction of the N-terminal region induces the conformational changes. This observation correlates well with a previous finding that Delta15-PabP did not restore the Ca(2+) and Cl(-) retention ability upon rebinding to PSII [Ifuku, K., et al. (2005) Photosynth. Res. 84, 251-255]. Therefore, the evidence strongly suggests that protein conformational changes around the Mn cluster induced by PsbP through its N-terminal region affect the binding properties of Ca(2+) and Cl(-) and enhance their retention.

Drastic changes in the ligand structure of the oxygen-evolving Mn cluster upon Ca2+ depletion as revealed by FTIR difference spectroscopy

A Fourier transform infrared (FTIR) difference spectrum of the oxygen-evolving Mn cluster upon the S(1)-to-S(2) transition was obtained with Ca(2+)-depleted photosystem II (PSII) membranes to investigate the structural relevance of Ca(2+) to the Mn cluster. Previously, Noguchi et al. [Biochim. Biophys. Acta 1228 (1995) 189] observed drastic changes in the carboxylate stretching region of the S(2)/S(1) FTIR spectrum upon Ca(2+) depletion, whereas Kimura and co-workers [Biochemistry 40 (2001) 14061; ibid. 41 (2002) 5844] later claimed that these changes were not ascribed to Ca(2+) depletion itself but caused by the interaction of EDTA to the Mn cluster and/or binding of K(+) at the Ca(2+) site. In the present study, the preparation of the Ca(2+)-depleted PSII sample and its FTIR measurement were performed in the absence of EDTA and K(+). The obtained S(2)/S(1) spectrum exhibited the loss of carboxylate bands at 1587/1562 and 1364/1403 cm(-1) and diminished amide I intensities, which were identical to the previous observations in the presence of EDTA and K(+). This result indicates that the drastic FTIR changes are a pure effect of Ca(2+) depletion, and provides solid evidence for the general view that Ca(2+) is strongly coupled with the Mn cluster.

X-ray absorption and molecular dynamics study of cation binding sites in the purple membrane

The present work describes the results of a study aimed at identifying candidate cation binding sites on the extracellular region of bacteriorhodopsin, including a site near the retinal pocket. The approach used is a combined effort involving computational chemistry methods (computation of cation affinity maps and molecular dynamics) together with the Extended X-Ray Absorption Fine Structure (EXAFS) technique to obtain relevant information about the local structure of the protein in the neighborhood of Mn(2+) ions in different affinity binding sites. The results permit the identification of a high-affinity binding site where the ion is coordinated simultaneously to Asp212(-) and Asp85(-). Comparison of EXAFS data of the wild type protein with the quadruple mutant E9Q/E74Q/E194Q/E204Q at pH 7.0 and 10.0 demonstrate that extracellular glutamic acid residues are involved in cation binding.

Light-induced FTIR difference spectroscopy as a powerful tool toward understanding the molecular mechanism of photosynthetic oxygen evolution

The molecular mechanism of photosynthetic oxygen evolution remains a mystery in photosynthesis research. Although recent X-ray crystallographic studies of the photosystem II core complex at 3.0-3.5 A resolutions have revealed the structure of the oxygen-evolving center (OEC), with approximate positions of the Mn and Ca ions and the amino acid ligands, elucidation of its detailed structure and the reactions during the S-state cycle awaits further spectroscopic investigations. Light-induced Fourier transform infrared (FTIR) difference spectroscopy was first applied to the OEC in 1992 as detection of its structural changes upon the S(1)-->S(2) transition, and spectra during the S-state cycle induced by consecutive flashes were reported in 2001. These FTIR spectra provide extensive structural information on the amino acid side groups, polypeptide chains, metal core, and water molecules, which constitute the OEC and are involved in its reaction. FTIR spectroscopy is thus becoming a powerful tool in investigating the reaction mechanism of photosynthetic oxygen evolution. In this mini-review, the measurement method of light-induced FTIR spectra of OEC is introduced and the results obtained thus far using this technique are summarized.

Vibrational spectroscopy to study the properties of redox-active tyrosines in photosystem II and other proteins

Tyrosine radicals play catalytic roles in essential metalloenzymes. Their properties--midpoint potential, stability...--or environment varies considerably from one enzyme to the other. To understand the origin of these properties, the redox tyrosines are studied by a number of spectroscopic techniques, including Fourier transform infrared (FTIR) and resonance Raman (RR) spectroscopy. An increasing number of vibrational data are reported for the (modified-) redox active tyrosines in ribonucleotide reductases, photosystem II, heme catalase and peroxidases, galactose and glyoxal oxidases, and cytochrome oxidase. The spectral markers for the tyrosinyl radicals have been recorded on models of (substituted) phenoxyl radicals, free or coordinated to metals. We review these vibrational data and present the correlations existing between the vibrational modes of the radicals and their properties and interactions formed with their environment: we present that the nu7a(C-O) mode of the radical, observed both by RR and FTIR spectroscopy at 1480-1515 cm(-1), is a sensitive marker of the hydrogen bonding status of (substituted)-phenoxyl and Tyr*, while the nu8a(C-C) mode may probe coordination of the Tyr* to a metal. For photosystem II, the information obtained by light-induced FTIR difference spectroscopy for the two redox tyrosines TyrD and TyrZ and their hydrogen bonding partners is discussed in comparison with those obtained by other spectroscopic methods.

Impact of Replacement of D1 C-terminal Alanine with Glycine on Structure and Function of Photosynthetic Oxygen-evolving Complex

The C-terminal alanine 344 (Ala-344) in the D1 protein of photosystem II is conserved in all of the organisms performing oxygenic photosynthesis. A free alpha-COO(-) of Ala-344 has been proposed to be responsible for ligating the Mn cluster. Here, we constructed a mutant having D1 in which D1-Ala-344 was replaced with glycine (Gly) in cyanobacterium Synechocystis sp. PCC 6803. The effects of this minimal change in the side group from methyl to hydrogen on the properties of the oxygen-evolving complex were comprehensively investigated using purified core particles. The mutant grew photoautotrophically, and little change was observed in the protein composition of the oxygen-evolving core particles. The Gly-substituted oxygen-evolving complex showed small but normal S(2) multiline and enhanced g = 4.1 electron spin resonance signals and S(2)-state thermoluminescence bands with slightly elevated peak temperature. The Gly substitution resulted in distinct but relatively small changes in a few bands arising from the putative carboxylate ligand for the Mn cluster in the mid-frequency (1800-1000 cm(-1)) S(2)/S(1) Fourier transform infrared difference spectrum. In contrast, the low frequency (670-350 cm(-1)) S(2)/S(1) Fourier transform infrared difference spectrum was markedly changed by the substitution. The results indicate that the internal structure of the Mn cluster and/or the interaction between the Mn cluster and its ligand are considerably altered by a simple change in the side group, from methyl to hydrogen, at the C-terminal of the D1 protein.

FTIR spectroscopy shows structural similarities between photosystems II from cyanobacteria and spinach

Photosystem II (PSII), an essential component of oxygenic photosynthesis, is a membrane-bound pigment protein complex found in green plants and cyanobacteria. Whereas the molecular structure of cyanobacterial PSII has been resolved with at least medium resolution [Zouni, A., Witt, H.-T., Kern, J., Fromme, P., Krauss, N., Saenger, W. & Orth, P. (2001) Nature (London) 409, 739-743; Kamiya, N. & Shen, J.R. (2003) Proc. Natl Acad. Sci. USA 100, 98-103], the structure of higher plant PSII is only known at low resolution. Therefore Fourier transform infrared (FTIR) difference spectroscopy was used to compare PSII from both Thermosynechococcus elongatus and Synechocystis PCC6803 core complexes with PSII-enriched membranes from spinach (BBY). FTIR difference spectra of T. elongatus core complexes are presented for several different intermediates. As the FTIR difference spectra show close similarities among the three species, the structural arrangement of cofactors in PSII and their interactions with the protein microenvironment during photosynthetic charge separation must be very similar in higher plant PSII and cyanobacterial PSII. A structural model of higher plant PSII can therefore be predicted from the structure of cyanobacterial PSII.

Raman spectra and normal coordinate analyses of low-frequency vibrations of oxo-bridged manganese complexes

The active sites of certain metalloenzymes involved in oxygen metabolism, such as manganese catalase and the oxygen-evolving complex of photosystem II, contain micro -oxo-bridged Mn clusters with ligands that include H(2)O and micro (1,3)-carboxylato bridges provided by protein side chains. In order to understand better the vibrational spectra of such clusters, the low-frequency resonance Raman spectra of a series of structurally characterized Mn-oxo model complexes were examined. The series includes complexes of the type [Mn(2)(O)(OAc)(2)(bpy)(2)(L)(2)] and [Mn(2)(O)(2)(OAc)(bpy)(2)(L)(2)], where bpy=2,2'-bipyridine, OAc=acetate and L=H(2)O or Cl(-). Complexes containing the isotopomers OAc- d(3) and D(2)O, as well as those containing both isotopomers, were also examined. Normal coordinate analyses (NCA) were performed on the various complexes using theGF matrix method. Selected vibrational modes in the 200-600 cm(-1) region were assigned based on the spectra and NCA, which identify vibrational modes arising from the metal-ligand bonds. These results will be useful in interpreting the vibrational spectra obtained from metalloproteins containing Mn-oxo complexes in their active sites.

Amino acid residues involved in the coordination and assembly of the manganese cluster of photosystem II. Proton-coupled electron transport of the redox-active tyrosines and its relationship to water oxidation

The combination of site-directed mutagenesis, isotopic labeling, new magnetic resonance techniques and optical spectroscopic methods have provided new insights into cofactor coordination and into the mechanism of electron transport and proton-coupled electron transport in photosystem II. Site-directed mutations in the D1 polypeptide of this photosystem have implicated a number of histidine and carboxylate residues in the coordination and assembly of the manganese cluster, responsible for photosynthetic water oxidation. Many of these are located in the carboxy-terminal region of this polypeptide close to the processing site involved in its maturation. This maturation is a required precondition for cluster assembly. Recent proposals for the mechanism of water oxidation have directly implicated redox-active tyrosine Y(Z) in this mechanism and have emphasized the importance of the coupling of proton and electron transfer in the reduction of Y(Z)(radical) by the Mn cluster. The interaction of both homologous redox-active tyrosines Y(Z) and Y(D) with their respective homologous proton acceptors is discussed in an effort to better understand the significance of such coupling.

Vibrational spectroscopy of the oxygen-evolving complex and of manganese model compounds

A number of molecularly specific models for the oxygen-evolving complex in photosystem II (PSII) and of manganese-substrate water intermediates that may occur in this process have been proposed recently. We summarize this work briefly. Fourier transform infrared techniques have emerged as fruitful tools to study the molecular structures of Y(Z) and the manganese complex. We discuss recent work in which mid-IR (1000-2000 cm(-1)) methods have been used in this effort. The low-frequency IR region (<1000 cm(-1)) has been more difficult to access for technical reasons, but good progress has been made in overcoming these obstacles. We update recent low-frequency work on PSII and then present a detailed summary of relevant manganese model compounds that will be of importance in understanding the emerging biological data.

Amino acid residues that modulate the properties of tyrosine Y(Z) and the manganese cluster in the water oxidizing complex of photosystem II

The catalytic site for photosynthetic water oxidation is embedded in a protein matrix consisting of nearly 30 different polypeptides. Residues from several of these polypeptides modulate the properties of the tetrameric Mn cluster and the redox-active tyrosine residue, Y(Z), that are located at the catalytic site. However, most or all of the residues that interact directly with Y(Z) and the Mn cluster appear to be contributed by the D1 polypeptide. This review summarizes our knowledge of the environments of Y(Z) and the Mn cluster as obtained from the introduction of site-directed, deletion, and other mutations into the photosystem II polypeptides of the cyanobacterium Synechocystis sp. PCC 6803 and the green alga Chlamydomonas reinhardtii.

Mechanism of photosynthetic water oxidation: combining biophysical studies of photosystem II with inorganic model chemistry

A mechanism for photosynthetic water oxidation is proposed based on a structural model of the oxygen-evolving complex (OEC) and its placement into the modeled structure of the D1/D2 core of photosystem II. The structural model of the OEC satisfies many of the geometrical constraints imposed by spectroscopic and biophysical results. The model includes the tetranuclear manganese cluster, calcium, chloride, tyrosine Z, H190, D170, H332 and H337 of the D1 polypeptide and is patterned after the reversible O2-binding diferric site in oxyhemerythrin. The mechanism for water oxidation readily follows from the structural model. Concerted proton-coupled electron transfer in the S2-->S3 and S3-->S4 transitions forms a terminal Mn(V)=O moiety. Nucleophilic attack on this electron-deficient Mn(V)=O by a calcium-bound water molecule results in a Mn(III)-OOH species, similar to the ferric hydroperoxide in oxyhemerythrin. Dioxygen is released in a manner analogous to that in oxyhemerythrin, concomitant with reduction of manganese and protonation of a mu-oxo bridge.

Vibrational spectroscopy as a tool for probing protein function

Vibrational spectroscopy has become increasingly important as a tool for understanding the mechanisms of photosystem II, phytochrome and terminal oxidases. More general enzymatic or receptor systems have been studied, opening a new field of applications. Femtosecond infrared pump/probe studies of the important amide-I band seem to provide a basis for its molecular and structural interpretation.

Light-induced FTIR difference spectroscopy of the S(2)-to-S(3) state transition of the oxygen-evolving complex in Photosystem II

We have applied flash-induced FTIR spectroscopy to study structural changes upon the S(2)-to-S(3) state transition of the oxygen-evolving complex (OEC) in Photosystem II (PSII). We found that several modes in the difference IR spectrum are associated with bond rearrangements induced by the second laser flash. Most of these IR modes are absent in spectra of S(2)/S(1), of the acceptor-side non-heme ion, of Yradical(D)/Y(D) and of S(3)'/S(2)' from Ca-depleted PSII preparations. Our results suggest that these IR modes most likely originate from structural changes in the oxygen-evolving complex itself upon the S(2)-to-S(3) state transition in PSII.

Deprotonation of the 33-kDa, extrinsic, manganese-stabilizing subunit accompanies photooxidation of manganese in photosystem II

Photosystem II catalyzes photosynthetic water oxidation. The oxidation of water to molecular oxygen requires four sequential oxidations; the sequentially oxidized forms of the catalytic site are called the S states. An extrinsic subunit, the manganese-stabilizing protein (MSP), promotes the efficient turnover of the S states. MSP can be removed and rebound to the reaction center; removal and reconstitution is associated with a decrease in and then a restoration of enzymatic activity. We have isotopically edited MSP by uniform (13)C labeling of the Escherichia coli-expressed protein and have obtained the Fourier transform infrared spectrum associated with the S(1) to S(2) transition in the presence either of reconstituted (12)C or (13)C MSP. (13)C labeling of MSP is shown to cause 30-60 cm(-1) shifts in a subset of vibrational lines. The derived, isotope-edited vibrational spectrum is consistent with a deprotonation of glutamic/aspartic acid residues on MSP during the S(1) to S(2) transition; the base, which accepts this proton(s), is not located on MSP. This finding suggests that this subunit plays a role as a stabilizer of a charged transition state and, perhaps, as a general acid/base catalyst of oxygen evolution. These results provide a molecular explanation for known MSP effects on oxygen evolution.