Spectral changes of light-harvesting complex 2 lacking B800 bacteriochlorophyll a under neutral pH conditions.

Exchange of B800 bacteriochlorophyll (BChl) a in light-harvesting complex 2 (LH2) is promising for a better understanding of the mechanism on intracomplex excitation energy transfer of this protein. Structural and spectroscopic properties of LH2 lacking B800 BChl a (B800-depleted LH2), which is an important intermediate protein in the B800 exchange, will be useful to tackle the energy transfer mechanism in LH2 by the B800 exchange strategy. In this study, we report a unique spectral change of B800-depleted LH2, in which the Qy absorption band of B800 BChl a is automatically recovered under neutral pH conditions. This spectral change was facilitated by factors for destabilization of LH2, namely, a detergent, lauryl dimethylamine N-oxide, and an increase in temperature. Spectral analyses in the preparation of an LH2 variant denoted as B800-recovered LH2 indicated that most BChl a that was released by decomposition of part of B800-depleted LH2 was a source of the production of B800-recovered LH2. Characterization of purified B800-recovered LH2 demonstrated that its spectroscopic and structural features was quite similar to those of native LH2. The current results indicate that the recovery of the B800 Qy band of B800-depleted LH2 originates from the combination of decomposition of part of B800-depleted LH2 and in situ reconstitution of BChl a into the B800 binding pockets of residual B800-depleted LH2, resulting in the formation of stable B800-recovered LH2.

Primary charge separation in native and plant pheophytin a-modified reaction centers of Chloroflexus aurantiacus: Ultrafast transient absorption measurements at low temperature.

Ultrafast transient absorption (TA) spectroscopy was used to study electron transfer (ET) at 100 K in native (as isolated) reaction centers (RCs) of the green filamentous photosynthetic bacterium Chloroflexus (Cfl.) aurantiacus. The rise and decay of the 1028 nm anion absorption band of the monomeric bacteriochlorophyll a molecule at the BA binding site were monitored as indicators of the formation and decay of the P+BA- state, respectively (P is the primary electron donor, a dimer of bacteriochlorophyll a molecules). Global analysis of the TA data indicated the presence of at least two populations of the P⁎ excited state, which decay by distinct means, forming the state P+HA- (HA is a photochemically active bacteriopheophytin a molecule). In one population (~65 %), P⁎ decays in ~2 ps with the formation of P+HA- via a short-lived P+BA- intermediate in a two-step ET process P⁎ â†’ P+BA-→ P+HA-. In another population (~35 %), P⁎ decays in ~20 ps to form P+HA- via a superexchange mechanism without producing measurable amounts of P+BA-. Similar TA measurements performed on chemically modified RCs of Cfl. aurantiacus containing plant pheophytin a at the HA binding site also showed the presence of two P⁎ populations (~2 and ~20 ps), with P⁎ decaying through P+BA- only in the ~2 ps population. At 100 K, the quantum yield of primary charge separation in native RCs is determined to be close to unity. The results are discussed in terms of involving a one-step P⁎ â†’ P+HA- superexchange process as an alternative highly efficient ET pathway in Cfl. aurantiacus RCs.

Cryo-EM Structure of the Rhodobacter sphaeroides Light-Harvesting 2 Complex at 2.1 Å.

Light-harvesting 2 (LH2) antenna complexes augment the collection of solar energy in many phototrophic bacteria. Despite its frequent role as a model for such complexes, there has been no three-dimensional (3D) structure available for the LH2 from the purple phototroph Rhodobacter sphaeroides. We used cryo-electron microscopy (cryo-EM) to determine the 2.1 Å resolution structure of this LH2 antenna, which is a cylindrical assembly of nine αß heterodimer subunits, each of which binds three bacteriochlorophyll a (BChl) molecules and one carotenoid. The high resolution of this structure reveals all of the interpigment and pigment-protein interactions that promote the assembly and energy-transfer properties of this complex. Near the cytoplasmic face of the complex there is a ring of nine BChls, which absorb maximally at 800 nm and are designated as B800; each B800 is coordinated by the N-terminal carboxymethionine of LH2-α, part of a network of interactions with nearby residues on both LH2-α and LH2-ß and with the carotenoid. Nine carotenoids, which are spheroidene in the strain we analyzed, snake through the complex, traversing the membrane and interacting with a ring of 18 BChls situated toward the periplasmic side of the complex. Hydrogen bonds with C-terminal aromatic residues modify the absorption of these pigments, which are red-shifted to 850 nm. Overlaps between the macrocycles of the B850 BChls ensure rapid transfer of excitation energy around this ring of pigments, which act as the donors of energy to neighboring LH2 and reaction center light-harvesting 1 (RC-LH1) complexes.

In situ formation of photoactive B-ring reduced chlorophyll isomer in photosynthetic protein LH2.

Natural chlorophylls have a D-ring reduced chlorin π-system; however, no naturally occurring photosynthetically active B-ring reduced chlorins have been reported. Here we report a B-ring reduced chlorin, 17,18-didehydro-bacteriochlorophyll (BChl) a, produced by in situ oxidation of B800 bacteriochlorophyll (BChl) a in a light-harvesting protein LH2 from a purple photosynthetic bacterium Phaeospirillum molischianum. The regioselective oxidation of the B-ring of B800 BChl a is rationalized by its molecular orientation in the protein matrix. The formation of 17,18-didehydro-BChl a produced no change in the local structures and circular arrangement of the LH2 protein. The B-ring reduced 17,18-didehydro-BChl a functions as an energy donor in the LH2 protein. The photoactive B-ring reduced Chl isomer in LH2 will be helpful for understanding the photofunction and evolution of photosynthetic cyclic tetrapyrrole pigments.

Cryo-EM structure of a Ca2+-bound photosynthetic LH1-RC complex containing multiple αß-polypeptides.

The light-harvesting-reaction center complex (LH1-RC) from the purple phototrophic bacterium Thiorhodovibrio strain 970 exhibits an LH1 absorption maximum at 960 nm, the most red-shifted absorption for any bacteriochlorophyll (BChl) a-containing species. Here we present a cryo-EM structure of the strain 970 LH1-RC complex at 2.82 Å resolution. The LH1 forms a closed ring structure composed of sixteen pairs of the αß-polypeptides. Sixteen Ca ions are present in the LH1 C-terminal domain and are coordinated by residues from the αß-polypeptides that are hydrogen-bonded to BChl a. The Ca2+-facilitated hydrogen-bonding network forms the structural basis of the unusual LH1 redshift. The structure also revealed the arrangement of multiple forms of α- and ß-polypeptides in an individual LH1 ring. Such organization indicates a mechanism of interplay between the expression and assembly of the LH1 complex that is regulated through interactions with the RC subunits inside.

Predictive First-Principles Modeling of a Photosynthetic Antenna Protein: The Fenna-Matthews-Olson Complex.

High efficiency of light harvesting in photosynthetic pigment-protein complexes is governed by evolutionary-perfected protein-assisted tuning of individual pigment properties and interpigment interactions. Due to the large number of spectrally overlapping pigments in a typical photosynthetic complex, experimental methods often fail to unambiguously identify individual chromophore properties. Here, we report a first-principles-based modeling protocol capable of predicting properties of pigments in protein environment to a high precision. The technique was applied to successfully uncover electronic properties of the Fenna-Matthews-Olson (FMO) pigment-protein complex. Each of the three subunits of the FMO complex contains eight strongly coupled bacteriochlorophyll a (BChl a) pigments. The excitonic structure of FMO can be described by an electronic Hamiltonian containing excitation (site) energies of BChl a pigments and electronic couplings between them. Several such Hamiltonians have been developed in the past based on the information from various spectroscopic measurements of FMO; however, fine details of the excitonic structure and energy transfer in FMO, especially assignments of short-lived high-energy sites, remain elusive. Utilizing polarizable embedding quantum mechanics/molecular mechanics with the effective fragment potentials, we computed the electronic Hamiltonian of FMO that is in general agreement with previously reported empirical Hamiltonians and quantitatively reproduces experimental absorption and circular dichroism spectra of the FMO protein. The developed computational protocol is sufficiently simple and can be utilized for predictive modeling of other wild-type and mutated photosynthetic pigment-protein complexes.

Carotenoid-to-(bacterio)chlorophyll energy transfer in LH2 antenna complexes from Rba. sphaeroides reconstituted with non-native (bacterio)chlorophylls.

Six variants of the LH2 antenna complex from Rba. sphaeroides, comprising the native B800-B850, B800-free LH2 (B850) and four LH2s with various (bacterio)chlorophylls reconstituted into the B800 site, have been investigated with static and time-resolved optical spectroscopies at room temperature and at 77 K. The study particularly focused on how reconstitution of a non-native (bacterio)chlorophylls affects excitation energy transfer between the naturally bound carotenoid spheroidene and artificially substituted pigments in the B800 site. Results demonstrate there is no apparent trend in the overall energy transfer rate from spheroidene to B850 bacteriochlorophyll a; however, a trend in energy transfer rate from the spheroidene S1 state to Qy of the B800 (bacterio)chlorophylls is noticeable. These outcomes were applied to test the validity of previously proposed energy values of the spheroidene S1 state, supporting a value in the vicinity of 13,400 cm-1 (746 nm).

FMOxFMO: Elucidating Excitonic Interactions in the Fenna-Matthews-Olson Complex with the Fragment Molecular Orbital Method.

In order to study Förster resonance energy transfer (FRET), the fragment molecular orbital (FMO) method is extended to compute electronic couplings between local excitations via the excited state transition density model, enabling efficient calculations of nonlocal excitations in a large molecular system and overcoming the previous limitation of being able to compute only local excitations. The results of these simple but accurate models are validated against full quantum calculations without fragmentation. The developed method is applied to a very important photosynthetic pigment-protein complex, the Fenna-Matthews-Olson complex (FMOc), that is responsible for the energy transfer from a chlorosome to the reaction center in the green sulfur bacteria. Absorption and circular dichroism spectra of FMOc are simulated, and the role of the molecular environment on the excitations is revealed.

A Dual Role for Ca2+ in Expanding the Spectral Diversity and Stability of Light-Harvesting 1 Reaction Center Photocomplexes of Purple Phototrophic Bacteria.

The light-harvesting 1 reaction center (LH1-RC) complex in the purple sulfur bacterium Thiorhodovibrio ( Trv.) strain 970 cells exhibits its LH1 Q y transition at 973 nm, the lowest-energy Q y absorption among purple bacteria containing bacteriochlorophyll a (BChl a). Here we characterize the origin of this extremely red-shifted Q y transition. Growth of Trv. strain 970 did not occur in cultures free of Ca2+, and elemental analysis of Ca2+-grown cells confirmed that purified Trv. strain 970 LH1-RC complexes contained Ca2+. The LH1 Q y band of Trv. strain 970 was blue-shifted from 959 to 875 nm upon Ca2+ depletion, but the original spectral properties were restored upon Ca2+ reconstitution, which also occurs with the thermophilic purple bacterium Thermochromatium ( Tch.) tepidum. The amino acid sequences of the LH1 α- and ß-polypeptides from Trv. strain 970 closely resemble those of Tch. tepidum; however, Ca2+ binding in the Trv. strain 970 LH1-RC occurred more selectively than in Tch. tepidum LH1-RC and with a reduced affinity. Ultraviolet resonance Raman analysis indicated that the number of hydrogen-bonding interactions between BChl a and LH1 proteins of Trv. strain 970 was significantly greater than for Tch. tepidum and that Ca2+ was indispensable for maintaining these bonds. Furthermore, perfusion-induced Fourier transform infrared analyses detected Ca2+-induced conformational changes in the binding site closely related to the unique spectral properties of Trv. strain 970. Collectively, our results reveal an ecological strategy employed by Trv. strain 970 of integrating Ca2+ into its LH1-RC complex to extend its light-harvesting capacity to regions of the near-infrared spectrum unused by other purple bacteria.

Phototrophic purple bacteria as optoacoustic in vivo reporters of macrophage activity.

Τhe morphology, physiology and immunology, of solid tumors exhibit spatial heterogeneity which complicates our understanding of cancer progression and therapy response. Understanding spatial heterogeneity necessitates high resolution in vivo imaging of anatomical and pathophysiological tumor information. We introduce Rhodobacter as bacterial reporter for multispectral optoacoustic (photoacoustic) tomography (MSOT). We show that endogenous bacteriochlorophyll a in Rhodobacter gives rise to strong optoacoustic signals >800 nm away from interfering endogenous absorbers. Importantly, our results suggest that changes in the spectral signature of Rhodobacter which depend on macrophage activity inside the tumor can be used to reveal heterogeneity of the tumor microenvironment. Employing non-invasive high resolution MSOT in longitudinal studies we show spatiotemporal changes of Rhodobacter spectral profiles in mice bearing 4T1 and CT26.WT tumor models. Accessibility of Rhodobacter to genetic modification and thus to sensory and therapeutic functions suggests potential for a theranostic platform organism.

Selective oxidation of B800 bacteriochlorophyll a in photosynthetic light-harvesting protein LH2.

Engineering chlorophyll (Chl) pigments that are bound to photosynthetic light-harvesting proteins is one promising strategy to regulate spectral coverage for photon capture and to improve the photosynthetic efficiency of these proteins. Conversion from the bacteriochlorophyll (BChl) skeleton (7,8,17,18-tetrahydroporphyrin) to the Chl skeleton (17,18-dihydroporphyrin) produces the most drastic change of the spectral range of absorption by light-harvesting proteins. We demonstrated in situ selective oxidation of B800 BChl a in light-harvesting protein LH2 from a purple bacterium Rhodoblastus acidophilus by 2,3-dichloro-5,6-dicyano-1,4-benzoquinone. The newly formed pigment, 3-acetyl Chl a, interacted with the LH2 polypeptides in the same manner as native B800. B850 BChl a was not oxidized in this reaction. CD spectroscopy indicated that the B850 orientation and the content of the α-helices were unchanged by the B800 oxidation. The nonameric circular arrangement of the oxidized LH2 protein was visualized by AFM; its diameter was almost the same as that of native LH2. The in situ oxidation of B800 BChl a in LH2 protein with no structural change will be useful not only for manipulation of the photofunctional properties of photosynthetic pigment-protein complexes but also for understanding the substitution of BChl to Chl pigments in the evolution from bacterial to oxygenic photosynthesis.

Unusual features in the photosynthetic machinery of Halorhodospira halochloris DSM 1059 revealed by complete genome sequencing.

Halorhodospira halochloris is an anaerobic, halophilic, purple photosynthetic bacterium belonging to γ-Proteobacteria. H. halochloris is also characteristic as a thermophilic phototrophic isolate producing bacteriochlorophyll (BChl) b. Here, we report the complete genome sequence of H. halochloris DSM 1059. The genetic arrangement for this bacterium's photosynthetic apparatus is of particular interest; its genome contains two sets of puf operons encoding the reaction center and core light-harvesting 1 (LH1) complexes having almost identical nucleotide sequences (e.g., 98.8-99.9% of nucleotide identities between two sets of pufLM genes, but 100% of deduced amino acid sequence identities). This duplication of photosynthetic genes may provide a glimpse at natural selection in action. The ß-polypeptides of the LH1 complex in purple bacteria usually contain two histidine residues to bind BChl a; however, those of H. halochloris were revealed to have four histidine residues, indicating unusual pigment organization in the LH1 complex of this species. Like in other BChl b-producing phototrophs, the genome of H. halochloris lacks the divinyl reductase genes bciA and bciB. The phylogeny of chlorophyllide a oxidoreductase, which catalyzes committed steps in the synthesis of BChl a and BChl b, indicates that evolution toward BChl b production is convergent. Geranylgeranyl reductase (BchP) of H. halochloris has an insertion region in its primary structure, which could be important for its unusual sequential reduction reactions.

Engineering of B800 bacteriochlorophyll binding site specificity in the Rhodobacter sphaeroides LH2 antenna.

The light-harvesting 2 complex (LH2) of the purple phototrophic bacterium Rhodobacter sphaeroides is a highly efficient, light-harvesting antenna that allows growth under a wide-range of light intensities. In order to expand the spectral range of this antenna complex, we first used a series of competition assays to measure the capacity of the non-native pigments 3-acetyl chlorophyll (Chl) a, Chl d, Chl f or bacteriochlorophyll (BChl) b to replace native BChl a in the B800 binding site of LH2. We then adjusted the B800 site and systematically assessed the binding of non-native pigments. We find that Arg-10 of the LH2 ß polypeptide plays a crucial role in binding specificity, by providing a hydrogen-bond to the 3-acetyl group of native and non-native pigments. Reconstituted LH2 complexes harbouring the series of (B)Chls were examined by transient absorption and steady-state fluorescence spectroscopies. Although slowed 10-fold to ~6 ps, energy transfer from Chl a to B850 BChl a remained highly efficient. We measured faster energy-transfer time constants for Chl d (3.5 ps) and Chl f (2.7 ps), which have red-shifted absorption maxima compared to Chl a. BChl b, red-shifted from the native BChl a, gave extremely rapid (≤0.1 ps) transfer. These results show that modified LH2 complexes, combined with engineered (B)Chl biosynthesis pathways in vivo, have potential for retaining high efficiency whilst acquiring increased spectral range.

Inhibition of bacteriochlorophyll biosynthesis in the purple phototrophic bacteria Rhodospirillumrubrum and Rhodobacter capsulatus grown in the presence of a toxic concentration of selenite.

Background In many works, the chemical composition of bacterially-produced elemental selenium nanoparticles (Se0-nanoparticles) was investigated using electron dispersive X-ray analysis. The results suggest that these particles should be associated with organic compounds. However, a complete analysis of their chemical composition is still missing. Aiming at identifying organic compounds associated with the Se0-nanoparticles produced by the purple phototrophic bacteria Rhodospirillum rubrum and Rhodobacter capsulatus (α group of the proteobacteria), we used MALDI-TOF spectrometry.Results This technic revealed that numerous signals obtained from particles produced by both species of bacteria were from metabolites of the photosynthetic system. Furthermore, not only bacteriochlorophyll a, bacteriopheophytin a, and bacteriopheophorbide a, which are known to accumulate in stationary phase cultures of these bacteria grown phototrophically in the absence of selenite, were identified. The particles were also associated with intermediary metabolites of the bacteriochlorophyll a biosynthesis pathway such as protoporphyrin IX, protoporphyrin IX monomethyl ester, bacteriochlorophyllide a and, most likely, Mg-protoporphyrin IX-monomethyl ester, as well as with oxidation products of the substrates of protochlorophyllide reductase and chlorin reductase.Conclusion Accumulation of intermediary metabolites of the bacteriochlorophyll biosynthesis pathway in these purple phototrophic bacteria was attributed to inhibition of oxygen-sensitive enzymes involved in this pathway. Consistent with this interpretation it has been reported that these bacteria reduce selenite intracellularly, that they contain high levels of glutathione and that the reduction of selenite with glutathione is a very fast reaction accompanied by the production of reactive oxygen species. As many enzymes involved in the biosynthesis of bacteriochlorophyll contain [Fe-S] clusters in their active site, which are known to be degraded in the presence of reactive oxygen species as well as in the presence of molecular oxygen, we concluded that the substrates of these enzymes accumulate in cells during selenite reduction.Association of metabolites of bacteriochlorophyll biosynthesis and degradation with the Se0-nanoparticles produced by Rhodospirillum rubrum and Rhodobacter capsulatus is proposed to result from coating of the nanoparticles with the intracytoplasmic membrane of these bacteria, where the photochemical apparatus is concentrated.

Selective Removal of B800 Bacteriochlorophyll a from Light-Harvesting Complex 2 of the Purple Photosynthetic Bacterium Phaeospirillum molischianum.

The selective removal of B800 bacteriochlorophyll (BChl) a from light-harvesting complex 2 (LH2) in purple photosynthetic bacteria is a clue about elucidation of the mechanism for the transfer of energy from these pigments to B850 BChl a and their roles in the LH2 protein structure. We demonstrated that the kinetics of the removal of B800 BChl a from two representative LH2 proteins derived from Phaeospirillum molischianum and Rhodoblastus acidophilus differed significantly, in contrast to the calculated binding enthalpy. These results may be interpreted as changes in the local structure near B800 BChl a with respect to the geometries of the original crystal structures upon removal of B800 BChl a. Despite the difficulty of removing B800 BChl a from molischianum-LH2, we prepared the molischianum-LH2 protein lacking B800 BChl a by combination of two detergents, n-dodecyl ß-d-maltoside and n-octyl ß-d-glucoside, under acidic conditions. Spectral and atomic force microscopy analyses indicated that the absence of B800 BChl a had little effect on the local structure in the vicinity of B850 BChl a and the circular arrangement in this protein. These results suggest that the hydrophobic domain near B850 BChl a is rigid and plays a major role in the structural formation of molischianum-LH2.

15N photo-CIDNP MAS NMR analysis of reaction centers of Chloracidobacterium thermophilum.

Photochemically induced dynamic nuclear polarization (photo-CIDNP) has been observed in the homodimeric, type-1 photochemical reaction centers (RCs) of the acidobacterium, Chloracidobacterium (Cab.) thermophilum, by 15N magic-angle spinning (MAS) solid-state NMR under continuous white-light illumination. Three light-induced emissive (negative) signals are detected. In the RCs of Cab. thermophilum, three types of (bacterio)chlorophylls have previously been identified: bacteriochlorophyll a (BChl a), chlorophyll a (Chl a), and Zn-bacteriochlorophyll a' (Zn-BChl a') (Tsukatani et al. in J Biol Chem 287:5720-5732, 2012). Based upon experimental and quantum chemical 15N NMR data, we assign the observed signals to a Chl a cofactor. We exclude Zn-BChl because of its measured spectroscopic properties. We conclude that Chl a is the primary electron acceptor, which implies that the primary donor is most likely Zn-BChl a'. Chl a and 81-OH Chl a have been shown to be the primary electron acceptors in green sulfur bacteria and heliobacteria, respectively, and thus a Chl a molecule serves this role in all known homodimeric type-1 RCs.

Nonlinear effect of irradiance on photoheterotrophic activity and growth of the aerobic anoxygenic phototrophic bacterium Dinoroseobacter shibae.

Aerobic anoxygenic photosynthetic bacteria are an important component of marine microbial communities. They produce energy in light using bacteriochlorophyll a containing photosystems. This extra energy provides an advantage over purely heterotrophic bacteria. One of the most intensively studied AAP bacteria is Dinoroseobacter shibae, a member of the environmentally important Roseobacter clade. Light stimulates its growth and metabolism, but the effect of light intensity remains unclear. Here, we show that an increase in biomass along an irradiance gradient followed the exponential rise to the maximum curve, with saturation at about 300 µmol photons m-2 s-1 , without any inhibition at light intensities up to 600 µmol photons m-2 s-1 . The cells adapted to higher irradiance by reducing pigmentation and increasing the electron transfer rate. This additional energy allowed D. shibae to redirect the metabolism of organic carbon sources such as glucose, leucine, glutamate, acetate and pyruvate toward anabolism, resulting in a twofold increase of their assimilation rates. We provide equations that can be feasibly incorporated into the existing model of D. shibae metabolism to further advance our understanding of the role of photoheterotrophy in the ocean.

Energy landscape of the intact and destabilized FMO antennas from C. tepidum and the L122Q mutant: Low temperature spectroscopy and modeling study.

We discuss the excitonic energy landscape of the typically studied wild-type (WT) Fenna-Matthews-Olson (FMO) antenna protein from the green sulfur bacterium Chlorobaculum tepidum (referred to as WTM), which is described as a mixture of intact (WTI) and destabilized (WTD) complexes. Optical spectra of WTM and the L122Q mutant (where leucine 122 near BChl 8 is replaced with glutamine) are compared to WTI FMO. We show that WTM and L122Q samples are mixtures of two subpopulations of proteins, most likely induced by protein conformational changes during the isolation/purification procedures. Absorption, emission, and HB spectra of WTM and L122Q mutant are very similar, in which the low-energy trap (revealed by the nonresonant HB spectra) shifts to higher energies as a function of fluence, supporting a mixture model. No fluence-dependent shift is observed in the WTI FMO trimers. New Hamiltonians are provided for WTI and WTD proteins. Resonant HB spectra show that the internal energy relaxation times in the WTM and L122Q mutant are similar, and depend on excitation frequency. Fast average relaxation times (excited state lifetimes) are observed for burning into the main broad absorption band near 805nm. Burning at longer wavelengths reveals slower total dephasing times. No resonant bleach is observed at λB≤803nm, implying much faster (femtosecond) energy relaxation in this spectral range in agreement with 2D electronic spectroscopy frequency maps.

Reversible Changes in the Structural Features of Photosynthetic Light-Harvesting Complex 2 by Removal and Reconstitution of B800 Bacteriochlorophyll a Pigments.

Light-harvesting complex 2 (LH2) is an integral membrane protein in purple photosynthetic bacteria. This protein possesses two types of bacteriochlorophyll (BChl) a, termed B800 and B850, which exhibit lowest-energy absorption bands (Qy bands) around 800 and 850 nm. These BChl a pigments in the LH2 protein play crucial roles not only in photosynthetic functions but also in folding and maintaining its protein structure. We report herein the reversible structural changes in the LH2 protein derived from a purple photosynthetic bacterium, Rhodoblastus acidophilus, induced by the removal of B800 BChl a (denoted as B800-free LH2) and the reconstitution of exogenous BChl a. Atomic force microscopy observation clearly visualized the nonameric ring structure of the B800-free LH2 with almost the same diameter as the native LH2. Size exclusion chromatography measurements indicated a considerable decrease in the size of the protein induced by the removal of B800 BChl a. The protein size was almost recovered by the insertion of BChl a pigments into the B800 binding sites. The decrease in the LH2 size would mainly originate from the shrinkage of the B800 binding sites perpendicular to the macrocycle of B800 BChl a without deformation of the circular arrangement. The reversible changes in the LH2 structure induced by the removal and reconstitution of B800 BChl a will be helpful for understanding the structural principle and the folding mechanism of photosynthetic pigment-protein complexes.

Constructing an Interpolated Potential Energy Surface of a Large Molecule: A Case Study with Bacteriochlorophyll a Model in the Fenna-Matthews-Olson Complex.

Constructing a reliable potential energy surface (PES) is a key step toward computationally studying the chemical dynamics of any molecular system. The interpolation scheme is a useful tool that can closely follow the accuracy of quantum chemical means at a dramatically reduced computational cost. However, applying interpolation to building a PES of a large molecule is not a straightforward black-box approach, as it frequently encounters practical difficulties associated with its large dimensionality. Here, we present detailed courses of applying interpolation toward building a PES of a large chromophore molecule. We take the example of S0 and S1 electronic states of bacteriochlorophyll a (BChla) molecules in the Fenna-Matthews-Olson light harvesting complex. With a reduced model molecule that bears BChla's main π-conjugated ring, various practical approaches are designed for improving the PES quality in a stable manner and for fine-tuning the final surface such that the surface can be adopted for long time molecular dynamics simulations. Combined with parallel implementation, we show that interpolated mechanics/molecular mechanics (IM/MM) simulations of the entire complex in the nanosecond time scale can be conducted readily without any practical issues. With 1500 interpolation data points for each chromophore unit, the PES error relative to the reference quantum chemical calculation is found to be ∼0.15 eV in the thermally accessible region of the conformational space, together with ∼0.01 eV error in S0 - S1 transition energies. The performance issue related to the use of a large interpolation database within the framework of our parallel routines is also discussed.