A reaction-induced FT-IR study of cyanobacterial photosystem I

Detection of Catalytically Linked Conformational Changes in Wild-Type Class Ia Ribonucleotide Reductase Using Reaction-Induced FTIR Spectroscopy

The enzyme, ribonucleotide reductase (RNR), is essential for DNA synthesis in all cells. The class Ia Escherichia coli RNR consists of two dimeric subunits, α₂ and β₂, which form an active but unstable heterodimer of dimers, α₂β₂. The structure of the wild-type form of the enzyme has been challenging to study due to the instability of the catalytic complex. A long-range proton-coupled electron-transfer (PCET) pathway facilitates radical migration from the Y122 radical-diiron cofactor in the β subunit to an active site cysteine, C439, in the α subunit to initiate the RNR chemistry. The PCET reactions and active site chemistry are spectroscopically masked by a rate-limiting, conformational gate. Here, we present a reaction-induced Fourier transform infrared (RIFTIR) spectroscopic method to monitor the mechanism of the active, wild-type RNR α₂β₂ complex. This method is employed to obtain new information about conformational changes accompanying RNR catalysis, including the role of carboxylate interactions, deprotonation, and oxidation of active site cysteines, and a detailed description of reversible secondary structural changes. Labeling of tyrosine revealed a conformationally active tyrosine in the β subunit, assigned to Y356β, which is part of the intersubunit PCET pathway. New insights into the roles of the inhibitors, azidoUDP and dATP, and the sensitivity of RIFTIR spectroscopy to detect subtle conformational motions arising from protein allostery are also presented.

Thermostability of photosystem I trimers and monomers from the cyanobacterium Thermosynechococcus elongatus

The performance of solar energy conversion into alternative energy sources in artificial systems highly depends on the thermostability of photosystem I (PSI) complexes Terasaki et al. (2007), Iwuchukwu et al. (2010), Kothe et al. (2013) . To assess the thermostability of PSI complexes from the thermophilic cyanobacterium Thermosynechococcus elongatus heating induced perturbations on the level of secondary structure of the proteins were studied. Changes were monitored by Fourier transform infrared (FT-IR) spectra in the mid-IR region upon slow heating (1°C per minute) of samples in D₂O phosphate buffer (pD 7.4) from 20°C to 100°C. These spectra showed distinct changes in the Amide I region of PSI complexes as a function of the rising temperature. Absorbance at the Amide I maximum of PSI monomers (centered around 1653cm^-1), gradually dropped in two temperature intervals, i.e. 60-75 and 80-90°C. In contrast, absorbance at the Amide I maximum of PSI trimers (around 1656cm^-1) dropped only in one temperature interval 80-95°C. The thermal profile of the spectral shift of α-helices bands in the region 1656-1642cm^-1 confirms the same two temperature intervals for PSI monomers and only one interval for trimers. Apparently, the observed absorbance changes at the Amide I maximum during heating of PSI monomers and trimers are caused by deformation and unfolding of α-helices. The absence of absorbance changes in the interval of 20-65°C in PSI trimers is probably caused by a greater stability of protein secondary structure as compared to that in monomers. Upon heating above 80°C a large part of α-helices both in trimers and monomers converts to unordered and aggregated structures. Spectral changes of PSI trimers and monomers heated up to 100°C are irreversible due to protein denaturation and non-specific aggregation of complexes leading to new absorption bands at 1618-1620cm^-1. We propose that monomers shield the denaturation sensitive sides at the monomer/monomer interface within a trimer, making the oligomeric structure more stable against thermal stress.

Synthesis and characterization of chlorophyll a enol derivatives: Chlorophyll a tert-butyldimethylsilyl-enol ether and 131-deoxo-131, 132-didehydro-chlorophyll a

Using the sterically hindered base, 1,8-diazabicyclo[5.4.0]undec-7-ene, for enolization and tert-butyldimethylsilyl-trifluoromethanesulfonate for silylation, chlorophyll (Chl) [Formula: see text] produced after 15 min at 0 [Formula: see text]C in deaerated pyridine solution under argon, after work-up and chromatographic purification on a sucrose column, tert-butyldimethylsilyl-enol ether of Chl [Formula: see text] in a yield of 77%. The 131-deoxo-131,132-didehydro-chlorophyll [Formula: see text], was obtained in a yield of 23% through a reaction sequence, where Chl [Formula: see text] was first reduced with sodium borohydride to 13[Formula: see text]-hydroxy-Chl [Formula: see text], which via demetalation yielded 13[Formula: see text]-hydroxypheophytin [Formula: see text]. In the presence of the sterically hindered base, 1,8-bis(dimethylamino)naphthalene, trifluoroacetylimidazole dehydrated 13[Formula: see text]-hydroxypheophytin [Formula: see text] to 131-deoxo-131,132-didehydro-pheophytin [Formula: see text], which after metalation yielded 131-deoxo-131,132-didehydro-Chl [Formula: see text]. Using 1,8-bis(dimethylamino)naphthalene and trifluoroacetylimidazole, the straight conversion of 13[Formula: see text]-hydroxy-Chl [Formula: see text] to 131-deoxo-131,132-didehydro-Chl [Formula: see text] was found unsuccessful. The major products were characterized by electronic absorption spectra (UV-vis) and practically completely assigned 1H and [Formula: see text]C NMR spectra. Some intermediates of the syntheses were also characterized by ESI-TOF mass spectra. Compared with Chl [Formula: see text], the macrocyclic ring-current in the synthesized Chl [Formula: see text] enol derivatives was found weakened by the expansion of the [Formula: see text]-system to include the isocyclic ring E. Nevertheless, these enol derivatives were still considered to be diamagnetic and aromatic. The possibility of the functional role of the enol derivatives of chlorophyll in photosynthesis is discussed.

Mapping of the local environmental changes in proteins by cysteine scanning

Protein conformational changes, which regulate the activity of proteins, are induced by the alternation of intramolecular interactions. Therefore, the detection of the local environmental changes around the key amino acid residues is essential to understand the activation mechanisms of functional proteins. Here we developed the methods to scan the local environmental changes using the vibrational band of cysteine S-H group. We validated the sensitivity of this method using bathorhodopsin, a photoproduct of rhodopsin trapped at liquid nitrogen temperature, which undergoes little conformational changes from the dark state as shown by the X-ray crystallography. The cysteine residues were individually introduced into 15 positions of Helix III, which contains several key amino acid residues for the light-induced conformational changes of rhodopsin. The shifts of S-H stretching modes of these cysteine residues and native cysteine residues upon the formation of bathorhodopsin were measured by Fourier transform infrared spectroscopy. While most of cysteine residues demonstrated no shift of S-H stretching mode, cysteine residues introduced at positions 117, 118, and 122, which are in the vicinity of the chromophore, demonstrated the significant changes. The current results are consistent with the crystal structure of bathorhodopsin, implying that the cysteine scanning is sensitive enough to detect the tiny conformational changes.

Metal nanoparticle plasmon-enhanced light-harvesting in a photosystem I thin film

Silver metal nanoparticle (NP) enhanced fluorescence is investigated in thin films of cyanobacterial Photosystem I trimer complexes (PSI) by correlating confocal laser scanning microscopy, dark-field imaging, and fluorescence lifetime measurements. PSI represents an interesting light-harvesting complex with a 20 nm diameter that is not uniformly contained within the surface-localized plasmon field of the NPs. With weak far-field illumination, 5- to 20-fold fluorescence enhancement is observed for PSI complexes adjacent to NPs, arising from efficient nanoparticle light collection and subsequent localized, surface plasmon excitation of PSI. Enhanced PSI fluorescence is detected most prominently near "rafts" of aggregated NPs that more completely fill the confocal field of view. These results demonstrate opportunities to probe energy transfer within photosynthetic complexes using plasmonic excitation and to design nanostructures for optimizing artificial light-harvesting systems.

Fourier transform infrared spectroscopy of special pair bacteriochlorophylls in homodimeric reaction centers of heliobacteria and green sulfur bacteria

Heliobacteria and green sulfur bacteria have type I homodimeric reaction centers analogous to photosystem I. One remaining question regarding these homodimeric reaction centers is whether the structures and electron transfer reactions are truly symmetric or not. This question is relevant to the origin of the heterodimeric reaction centers, such as photosystem I and type II reaction centers. In this mini-review, Fourier transform infrared studies on the special pair bacteriochlorophylls, P798 in heliobacteria and P840 in green sulfur bacteria, are summarized. The data are reinterpreted in the light of the X-ray crystallographic structure of photosystem I and the sequence alignments of type I reaction center proteins, and discussed in terms of hydrogen bonding interactions and the symmetry of charge distribution over the dimer.

Tryptophan as a probe of photosystem I electron transfer reactions: a UV resonance Raman study

Photosystem I (PSI) is one of the two membrane-associated reaction centers involved in oxygenic photosynthesis. In photosynthesis, solar energy is converted to chemical energy in the form of a transmembrane charge separation. PSI oxidizes cytochrome c(6) or plastocyanin and reduces ferredoxin. In cyanobacterial PSI, there are 10 tryptophan residues with indole side chains located less than 10 A from the electron transfer cofactors. In this study, we apply pump-probe difference UV resonance Raman (UVRR) spectroscopy to acquire the spectrum of aromatic amino acids in cyanobacterial PSI. This UVRR technique allows the use of the tryptophan vibrational spectrum as a reporter for structural changes, which are linked to PSI electron transfer reactions. Our results show that photo-oxidation of the chlorophyll a/a' heterodimer, P(700), causes shifts in the vibrational frequencies of two or more tryptophan residues. Similar perturbations of tryptophan are observed when P(700) is chemically oxidized. The observed spectral frequencies suggest that the perturbed tryptophan side chains are only weakly or not hydrogen bonded and are located in an environment in which there is steric repulsion. The direction of the spectral shifts is consistent with an oxidation-induced increase in dielectric constant or a change in hydrogen bonding. To explain our results, the perturbation of tryptophan residues must be linked to a PSI conformational change, which is, in turn, driven by P(700) oxidation.

Calculation of the vibrational properties of chlorophyll a in solution

Chlorophyll a (Chl-a) is at the heart of solar energy capture and conversion in plants. Because of this, Chl-a has been the subject of innumerable studies. Recently, we have been able to use quantum mechanical methods to calculate the vibrational properties of neutral and oxidized Chl-a in the gas phase [Wang, R.; Parameswaran, S.; Hastings, G. Vib. Spectrosc. 2007, 44, 357-368]. The calculated vibrational properties do not agree with experiment, however. One factor ignored in our calculations was how solvents could impact the vibrational properties. Here we calculate the vibrational properties of Chl-a and Chl-a+ in several solvents that span a wide range of dielectric constant. The calculated and experimental (Chl-a+-Chl-a) infrared difference spectra now show a remarkable similarity. However, the composition of the calculated vibrational modes are very different from that suggested from experiment. We therefore use our calculated data to make new suggestions as to the origin of the bands in experimental (Chl-a+-Chl-a) FTIR difference spectra. We indicate why bands in experimental spectra may have been misassigned. We also point to other experimental data that support our new band assignments. Assignment of bands in (Chl-a+-Chl-a) FTIR difference spectra were first made nearly 20 years ago. These assignments have formed the basis for evaluating all "cation minus neutral" FTIR difference spectra obtained for all photosynthetic systems since then. All of these experimental FTIR difference spectra should be re-examined in light of our new assignments.

Light-induced dynamics in photosystem I electron transfer

Protein dynamics are likely to play important, regulatory roles in many aspects of photosynthetic electron transfer, but a detailed description of these coupled protein conformational changes has been unavailable. In oxygenic photosynthesis, photosystem I catalyzes the light-driven oxidation of plastocyanin or cytochrome c and the reduction of ferredoxin. A chlorophyll (chl) a/a' heterodimer, P(700), is the secondary electron donor, and the two P(700) chl, are designated P(A) and P(B). We used specific chl isotopic labeling and reaction-induced Fourier-transform infrared spectroscopy to assign chl keto vibrational bands to P(A) and P(B). In the cyanobacterium, Synechocystis sp. PCC 6803, the chl keto carbon was labeled from (13)C-labeled glutamate, and the chl keto oxygen was labeled from (18)O(2). These isotope-based assignments provide new information concerning the structure of P(A)(+), which is found to give rise to two chl keto vibrational bands, with frequencies at 1653 and 1687 cm(-1). In contrast, P(A) gives rise to one chl keto band at 1638 cm(-1). The observation of two P(A)(+) keto frequencies is consistent with a protein relaxation-induced distribution in P(A)(+) hydrogen bonding. These results suggest a light-induced conformational change in photosystem I, which may regulate the oxidation of soluble electron donors and other electron-transfer reactions. This study provides unique information concerning the role of protein dynamics in oxygenic photosynthesis.

Solvent-induced changes in photochemical activity and conformation of photosystem I particles by glycerol

It has been shown that a large number of water molecules coordinate with the pigments and subunits of photosystem I (PSI); however, the function of these water molecules remains to be clarified. In this study, the photosynthetic properties of PSI from spinach were investigated using different spectroscopic and activity measurements under conditions of decreasing water content caused by increasing concentrations of glycerol. The results show that glycerol addition caused pronounced changes in the photochemical activity of PSI particles. At low concentrations (<60%, v/v), glycerol stimulated the rate of oxygen uptake in PSI particles, while higher concentrations of glycerol cause inhibition of PSI activity. The capacity of P700 photooxidation also increased with glycerol concentrations lower than 60%. In contrast, this capacity decreased at higher glycerol concentrations. On the other hand, glycerol addition considerably affected the distribution of the bulk and red antenna chlorophyll (Chl) forms or states, with the population of red-shifted Chl forms augmented with increasing glycerol. In addition, glycerol-treated PSI particles showed a blue shift of the tryptophan fluorescence emission maximum and an increase in their capacity to bind the hydrophobic probe 1-anilino-8-naphthalene sulfonate, indicating a more non-polar environment for tryptophan residues and increased exposure of hydrophobic surfaces.

Electrochromic shift of chlorophyll absorption in photosystem I from Synechocystis sp. PCC 6803: a probe of optical and dielectric properties around the secondary electron acceptor

Nanosecond absorption dynamics at approximately 685 nm after excitation of photosystem I (PS I) from Synechocystis sp. PCC 6803 is consistent with electrochromic shift of absorption bands of the Chl a pigments in the vicinity of the secondary electron acceptor A(1). Based on experimental optical data and structure-based simulations, the effective local dielectric constant has been estimated to be between 3 and 20, which suggests that electron transfer in PS I is accompanied by considerable protein relaxation. Similar effective dielectric constant values have been previously observed for the bacterial photosynthetic reaction center and indicate that protein reorganization leading to effective charge screening may be a necessary structural property of proteins that facilitate the charge transfer function. The data presented here also argue against attributing redmost absorption in PS I to closely spaced antenna chlorophylls (Chls) A38 and A39, and suggest that optical transitions of these Chls, along with that of connecting chlorophyll (A40) lie in the range 680-695 nm.

FTIR difference spectroscopy in combination with isotope labeling for identification of the carbonyl modes of P700 and P700+ in photosystem I

Room temperature, light induced (P700(+)-P700) Fourier transform infrared (FTIR) difference spectra have been obtained using photosystem I (PS I) particles from Synechocystis sp. PCC 6803 that are unlabeled, uniformly (2)H labeled, and uniformly (15)N labeled. Spectra were also obtained for PS I particles that had been extensively washed and incubated in D(2)O. Previously, we have found that extensive washing and incubation of PS I samples in D(2)O does not alter the (P700(+)-P700) FTIR difference spectrum, even with approximately 50% proton exchange. This indicates that the P700 binding site is inaccessible to solvent water. Upon uniform (2)H labeling of PS I, however, the (P700(+)-P700) FTIR difference spectra are considerably altered. From spectra obtained using PS I particles grown in D(2)O and H(2)O, a ((1)H-(2)H) isotope edited double difference spectrum was constructed, and it is shown that all difference bands associated with ester/keto carbonyl modes of the chlorophylls of P700 and P700(+) downshift 4-5/1-3 cm(-1) upon (2)H labeling, respectively. It is also shown that the ester and keto carbonyl modes of the chlorophylls of P700 need not be heterogeneously distributed in frequency. Finally, we find no evidence for the presence of a cysteine mode in our difference spectra. The spectrum obtained using (2)H labeled PS I particles indicates that a negative difference band at 1698 cm(-1) is associated with at least two species. The observed (15)N and (2)H induced band shifts strongly support the idea that the two species are the 13(1) keto carbonyl modes of both chlorophylls of P700. We also show that a negative difference band at approximately 1639 cm(-1) is somewhat modified in intensity, but unaltered in frequency, upon (2)H labeling. This indicates that this band is not associated with a strongly hydrogen bonded keto carbonyl mode of one of the chlorophylls of P700.

Photo-oxidation of P740, the primary electron donor in photosystem I from Acaryochloris marina

Fourier transform infrared spectroscopy (FTIR) difference spectroscopy in combination with deuterium exchange experiments has been used to study the photo-oxidation of P740, the primary electron donor in photosystem I from Acaryochloris marina. Comparison of (P740(+)-P740) and (P700(+)-P700) FTIR difference spectra show that P700 and P740 share many structural similarities. However, there are several distinct differences also: 1), The (P740(+)-P740) FTIR difference spectrum is significantly altered upon proton exchange, considerably more so than the (P700(+)-P700) FTIR difference spectrum. The P740 binding pocket is therefore more accessible than the P700 binding pocket. 2), Broad, "dimer" absorption bands are observed for both P700(+) and P740(+). These bands differ significantly in substructure, however, suggesting differences in the electronic organization of P700(+) and P740(+). 3), Bands are observed at 2727(-) and 2715(-) cm(-1) in the (P740(+)-P740) FTIR difference spectrum, but are absent in the (P700(+)-P700) FTIR difference spectrum. These bands are due to formyl CH modes of chlorophyll d. Therefore, P740 consists of two chlorophyll d molecules. Deuterium-induced modification of the (P740(+)-P740) FTIR difference spectrum indicates that only the highest frequency 13(3) ester carbonyl mode of P740 downshifts, indicating that this ester mode is weakly H-bonded. In contrast, the highest frequency ester carbonyl mode of P700 is free from H-bonding. Deuterium-induced changes in (P740(+)-P740) FTIR difference spectrum could also indicate that one of the chlorophyll d 3(1) carbonyls of P740 is hydrogen bonded.

Methionine changes in bacteriorhodopsin detected by FTIR and cell-free selenomethionine substitution

Bacteriorhodopsin (BR) is an integral membrane protein, which functions as a light-driven proton pump in Halobacterium salinarum. We report evidence that one or more methionine residues undergo a structural change during the BR-->M portion of the BR photocycle. Selenomethionine was incorporated into BR using a cell-free protein translation system containing an amino acid mixture with selenomethionine substituted for methionine. BR-->M FTIR difference spectra recorded for unlabeled and selenomethionine-labeled cell-free expressed BR closely resemble the spectra of in vivo expressed BR. However, reproducible changes occur in two regions near 1,284 and 900 cm(-1) due to selenomethionine incorporation. Isotope labeled tyrosine was also co-incorporated with selenomethionine in order to confirm these assignments. Based on recent x-ray crystallographic studies, likely methionines which give rise to the FTIR difference bands are Met-118 and Met-145, which are located inside the retinal binding pocket and in a position to constrain the motion of retinal during photoisomerization. The assignment of methionine bands in the FTIR difference spectrum of BR provides a means to study methionine-chromophore interaction under physiological conditions. More generally, combining cell-free incorporations of selenomethionine into proteins with FTIR difference spectroscopy provides a useful method for investigating the role of methionines in protein structure and function.