Photosystem I at 4 A resolution represents the first structural model of a joint photosynthetic reaction centre and core antenna system

Thermal site energy fluctuations in photosystem I: new insights from MD/QM/MM calculations

Cyanobacterial photosystem I (PSI) is one of the most efficient photosynthetic machineries found in nature. Due to the large scale and complexity of the system, the energy transfer mechanism from the antenna complex to the reaction center is still not fully understood. A central element is the accurate evaluation of the individual chlorophyll excitation energies (site energies). Such an evaluation must include a detailed treatment of site specific environmental influences on structural and electrostatic properties, but also their evolution in the temporal domain, because of the dynamic nature of the energy transfer process. In this work, we calculate the site energies of all 96 chlorophylls in a membrane-embedded model of PSI. The employed hybrid QM/MM approach using the multireference DFT/MRCI method in the QM region allows to obtain accurate site energies under explicit consideration of the natural environment. We identify energy traps and barriers in the antenna complex and discuss their implications for energy transfer to the reaction center. Going beyond previous studies, our model also accounts for the molecular dynamics of the full trimeric PSI complex. Via statistical analysis we show that the thermal fluctuations of single chlorophylls prevent the formation of a single prominent energy funnel within the antenna complex. These findings are also supported by a dipole exciton model. We conclude that energy transfer pathways may form only transiently at physiological temperatures, as thermal fluctuations overcome energy barriers. The set of site energies provided in this work sets the stage for theoretical and experimental studies on the highly efficient energy transfer mechanisms in PSI.

Novel fluorescent self-assembling material with gel properties: ion recognition and energy transfer

A novel fabrication strategy for preparing fluorescent nanomaterials has been proposed based on supramolecular self-assembly complexes and energy transfer. Here a dual acylhydrazone-functionalized molecule (DAF) was designed and synthesized by...

Room temperature XFEL crystallography reveals asymmetry in the vicinity of the two phylloquinones in photosystem I

Photosystem I (PS I) has a symmetric structure with two highly similar branches of pigments at the center that are involved in electron transfer, but shows very different efficiency along the two branches. We have determined the structure of cyanobacterial PS I at room temperature (RT) using femtosecond X-ray pulses from an X-ray free electron laser (XFEL) that shows a clear expansion of the entire protein complex in the direction of the membrane plane, when compared to previous cryogenic structures. This trend was observed by complementary datasets taken at multiple XFEL beamlines. In the RT structure of PS I, we also observe conformational differences between the two branches in the reaction center around the secondary electron acceptors A_1A and A_1B. The π-stacked Phe residues are rotated with a more parallel orientation in the A-branch and an almost perpendicular confirmation in the B-branch, and the symmetry breaking PsaB-Trp673 is tilted and further away from A_1A. These changes increase the asymmetry between the branches and may provide insights into the preferential directionality of electron transfer.

Donor-acceptor conjugates derived from cobalt porphyrin and fullerene via metal-ligand axial coordination: Formation and excited state charge separation

Two types of cobalt porphyrins, viz., meso-tetrakis(tolylporphyrinato)cobalt(II), (TTP)Co (1), and meso-tetrakis(triphenylamino porphyrinato)cobalt(II), [(TPA)4P]Co, (2) were self-assembled via metal-ligand axial coordination of phenyl imidazole functionalized fulleropyrrolidine, ImC[Formula: see text] to form a new series of donor–acceptor constructs. A 1:2 complex formation with ImC[Formula: see text] was established in the case of (TTP)Co while for [(TPA)4P]Co only a 1:1 complex was possible to positively identify. The binding constants [Formula: see text] and [Formula: see text] for step-wise addition of ImC[Formula: see text] to (TTP)Co were found to be 1.07 × 105 and 3.20 × 104 M[Formula: see text], respectively. For [(TPA)4P]Co:ImC[Formula: see text], the measured [Formula: see text] values was found to be 6.48 × 104 M[Formula: see text], slightly smaller than that observed for (TTP)Co. Although both cobalt porphyrins were non-fluorescent, they were able to quench the fluorescence of ImC[Formula: see text] indicating occurrence of excited state events in the supramolecular donor-acceptor complexes. Electrochemistry coupled with spectroelectrochemistry, revealed the formation of cobalt(III) porphyrin cation instead of a cobalt(II) porphyrin radical cation, as the main product, during oxidation of phenyl imidazole coordinated cobalt porphyrin. With the help of computational and electrochemical results, an energy level diagram was constructed to witness excited state photo-events. Competitive energy and electron transfer from excited CoP to coordinated ImC[Formula: see text], and electron transfer from Im1C[Formula: see text]* to cobalt(II) porphyrin resulting into the formation of PCo[Formula: see text]:ImC[Formula: see text] charge separated state was possible to envision from the energy diagram. Finally, using femtosecond transient absorption spectroscopy and data analysis by Glotaran, it was possible to establish sequential occurrence of energy transfer and charge separation processes. The lifetime of the final charge separated state was [Formula: see text] 2 ns. A slightly better charge stabilization was observed in the case of [(TPA)4P]Co:ImC[Formula: see text] due to the presence of electron rich, peripheral triphenylamine substituents on the cobalt porphyrin.

Membrane protein megahertz crystallography at the European XFEL

The world’s first superconducting megahertz repetition rate hard X-ray free-electron laser (XFEL), the European XFEL, began operation in 2017, featuring a unique pulse train structure with 886 ns between pulses. With its rapid pulse rate, the European XFEL may alleviate some of the increasing demand for XFEL beamtime, particularly for membrane protein serial femtosecond crystallography (SFX), leveraging orders-of-magnitude faster data collection. Here, we report the first membrane protein megahertz SFX experiment, where we determined a 2.9 Å-resolution SFX structure of the large membrane protein complex, Photosystem I, a > 1 MDa complex containing 36 protein subunits and 381 cofactors. We address challenges to megahertz SFX for membrane protein complexes, including growth of large quantities of crystals and the large molecular and unit cell size that influence data collection and analysis. The results imply that megahertz crystallography could have an important impact on structure determination of large protein complexes with XFELs.

The European X-ray free-electron laser (EuXFEL) in Hamburg is the first XFEL with a megahertz repetition rate. Here the authors present the 2.9 Å structure of the large membrane protein complex Photosystem I from T. elongatus that was determined at the EuXFEL.

Surface anchored self-assembled reaction centre mimics as photoanodes consisting of a secondary electron donor, aluminium(iii) porphyrin and TiO2 semiconductor

Vertically assembled photoanodes, consisting of aluminum(iii) porphyrin, an electron donor, and semiconductor TiO₂, have been fabricated and their photophysical properties investigated.

Organization of Plant Photosystem II and Photosystem I Supercomplexes

In nature, plants are continuously exposed to varying environmental conditions. They have developed a wide range of adaptive mechanisms, which ensure their survival and maintenance of stable photosynthetic performance. Photosynthesis is delicately regulated at the level of the thylakoid membrane of chloroplasts and the regulatory mechanisms include a reversible formation of a large variety of specific protein-protein complexes, supercomplexes or even larger assemblies known as megacomplexes. Revealing their structures is crucial for better understanding of their function and relevance in photosynthesis. Here we focus our attention on the isolation and a structural characterization of various large protein supercomplexes and megacomplexes, which involve Photosystem II and Photosystem I, the key constituents of photosynthetic apparatus. The photosystems are often attached to other protein complexes in thylakoid membranes such as light harvesting complexes, cytochrome b ₆ f complex, and NAD(P)H dehydrogenase. Structural models of individual supercomplexes and megacomplexes provide essential details of their architecture, which allow us to discuss their function as well as physiological significance.

Insights into the binding behavior of native and non-native cytochromes to photosystem I from Thermosynechococcus elongatus

The binding of photosystem I (PS I) from Thermosynechococcus elongatus to the native cytochrome (cyt) c₆ and cyt c from horse heart (cyt c_HH) was analyzed by oxygen consumption measurements, isothermal titration calorimetry (ITC), and rigid body docking combined with electrostatic computations of binding energies. Although PS I has a higher affinity for cyt c_HH than for cyt c₆, the influence of ionic strength and pH on binding is different in the two cases. ITC and theoretical computations revealed the existence of unspecific binding sites for cyt c_HH besides one specific binding site close to P₇₀₀ Binding to PS I was found to be the same for reduced and oxidized cyt c_HH Based on this information, suitable conditions for cocrystallization of cyt c_HH with PS I were found, resulting in crystals with a PS I:cyt c_HH ratio of 1:1. A crystal structure at 3.4-Å resolution was obtained, but cyt c_HH cannot be identified in the electron density map because of unspecific binding sites and/or high flexibility at the specific binding site. Modeling the binding of cyt c₆ to PS I revealed a specific binding site where the distance and orientation of cyt c₆ relative to P₇₀₀ are comparable with cyt c₂ from purple bacteria relative to P₈₇₀ This work provides new insights into the binding modes of different cytochromes to PS I, thus facilitating steps toward solving the PS I-cyt c costructure and a more detailed understanding of natural electron transport processes.

The Phytol Phosphorylation Pathway Is Essential for the Biosynthesis of Phylloquinone, which Is Required for Photosystem I Stability in Arabidopsis

Phytyl-diphosphate, which provides phytyl moieties as a common substrate in both tocopherol and phylloquinone biosynthesis, derives from de novo isoprenoid biosynthesis or a salvage pathway via phytol phosphorylation. However, very little is known about the role and origin of the phytyl moiety for phylloquinone biosynthesis. Since VTE6, a phytyl-phosphate kinase, is a key enzyme for phytol phosphorylation, we characterized Arabidopsis vte6 mutants to gain insight into the roles of phytyl moieties in phylloquinone biosynthesis and of phylloquinone in photosystem I (PSI) biogenesis. The VTE6 knockout mutants vte6-1 and vte6-2 lacked detectable phylloquinone, whereas the phylloquinone content in the VTE6 knockdown mutant vte6-3 was 90% lower than that in wild-type. In vte6 mutants, PSI function was impaired and accumulation of the PSI complex was defective. The PSI core subunits PsaA/B were efficiently synthesized and assembled into the PSI complex in vte6-3. However, the degradation rate of PSI subunits in the assembled PSI complex was more rapid in vte6-3 than in wild-type. In vte6-3, PSI was more susceptible to high-light damage than in wild-type. Our results provide the first genetic evidence that the phytol phosphorylation pathway is essential for phylloquinone biosynthesis, and that phylloquinone is required for PSI complex stability.

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.

Unexpected capacity for organic carbon assimilation by Thermosynechococcus elongatus, a crucial photosynthetic model organism

Genetic modification of key residues of photosystems is essential to identify functionally crucial processes by spectroscopic and crystallographic investigation; the required protein stability favours use of thermophilic species. The currently unique thermophilic photosynthetic model organism is the cyanobacterial genus Thermosynechococcus. We report the ability of Thermosynechococcus elongatus to assimilate organic carbon, specifically D-fructose. Growth in the presence of a photosynthesis inhibitor opens the door towards crucial amino acid substitutions in photosystems by the rescue of otherwise lethal mutations. Yet depression of batch-culture growth after 7 days implies that additional developments are needed.

Axially assembled photosynthetic reaction center mimics composed of tetrathiafulvalene, aluminum(III) porphyrin and fullerene entities

The distance dependence of sequential electron transfer has been studied in six, vertical, linear supramolecular triads, (TTF-Ph(n)-py → AlPor-Ph(m)-C60, n = 0, 1 and m = 1, 2, 3), constructed using tetrathiafulvalene (TTF), aluminum(III) porphyrin (AlPor) and fullerene (C60) entities. The C60 and TTF units are bound to the Al center on opposite faces of the porphyrin; the C60 through a covalent axial bond using a benzoate spacer, and the TTF through a coordination bond via an appended pyridine. Time-resolved optical and EPR spectroscopic methods and computational studies are used to demonstrate that excitation of the porphyrin leads to step-wise, sequential electron transfer (ET) between TTF and C60, and to study the electron transfer rates and exchange coupling between the components of the triads as a function of the bridge lengths. Femtosecond transient absorption studies show that the rates of charge separation, k(CS) are in the range of 10(9)-10(11) s(-1), depending on the length of the bridges. The lifetimes of the charge-separated state TTF˙(+)-C₆₀˙⁻ obtained from transient absorbance experiments and the singlet lifetimes of the radical pairs obtained by time-resolved EPR are in good agreement with each other and range from 60-130 ns in the triads. The time-resolved EPR data also show that population of the triplet sublevels of the charge-separated state in the presence of a magnetic field leads to much longer lifetimes of >1 μs. The data show that a modest stabilization of the charge separation lifetime occurs in the triads. The attenuation factor β = 0.36 Å(-1) obtained from the exchange coupling values between TTF˙(+) and C₆₀˙⁻ is consistent with values reported in the literature for oligophenylene bridged TTF-C60 conjugates. The singlet charge recombination lifetime shows a much weaker dependence on the distance between the donor and acceptor, suggesting that a simple superexchange model is not sufficient to describe the back reaction.

FRET-capable supramolecular polymers based on a BODIPY-bridged pillar[5]arene dimer with BODIPY guests for mimicking the light-harvesting system of natural photosynthesis

FRET-capable supramolecular polymers based on a pillar[5]arene dimer and BODIPY derivatives were successfully constructed to mimic the photosynthetic light-harvesting system.

Ultrafast charge separation and charge stabilization in axially linked ‘tetrathiafulvalene–aluminum(iii) porphyrin–gold(iii) porphyrin’ reaction center mimics

Sequential electron transfer leading to charge stabilization in newly synthesized vertically aligned ‘tetrathiafulvalene–aluminum(iii) porphyrin–gold(iii) porphyrin’ supramolecular triads is reported.

Long-wavelength chlorophylls in photosystem I of cyanobacteria: origin, localization, and functions

The structural organization of photosystem I (PSI) complexes in cyanobacteria and the origin of the PSI antenna long-wavelength chlorophylls and their role in energy migration, charge separation, and dissipation of excess absorbed energy are discussed. The PSI complex in cyanobacterial membranes is organized preferentially as a trimer with the core antenna enriched with long-wavelength chlorophylls. The contents of long-wavelength chlorophylls and their spectral characteristics in PSI trimers and monomers are species-specific. Chlorophyll aggregates in PSI antenna are potential candidates for the role of the long-wavelength chlorophylls. The red-most chlorophylls in PSI trimers of the cyanobacteria Arthrospira platensis and Thermosynechococcus elongatus can be formed as a result of interaction of pigments peripherally localized on different monomeric complexes within the PSI trimers. Long-wavelength chlorophylls affect weakly energy equilibration within the heterogeneous PSI antenna, but they significantly delay energy trapping by P700. When the reaction center is open, energy absorbed by long-wavelength chlorophylls migrates to P700 at physiological temperatures, causing its oxidation. When the PSI reaction center is closed, the P700 cation radical or P700 triplet state (depending on the P700 redox state and the PSI acceptor side cofactors) efficiently quench the fluorescence of the long-wavelength chlorophylls of PSI and thus protect the complex against photodestruction.

The structure and function of quinones in biological solar energy transduction: a cyclic voltammetry, EPR, and hyperfine sub-level correlation (HYSCORE) spectroscopy study of model naphthoquinones

Quinones function as electron transport cofactors in photosynthesis and cellular respiration. The versatility and functional diversity of quinones is primarily due to the diverse midpoint potentials that are tuned by the substituent effects and interactions with surrounding amino acid residues in the binding site in the protein. In the present study, a library of substituted 1,4-naphthoquinones are analyzed by cyclic voltammetry in both protic and aprotic solvents to determine effects of substituent groups and hydrogen bonds on the midpoint potential. We use continuous-wave electron paramagnetic resonance (EPR) spectroscopy to determine the influence of substituent groups on the electronic properties of the 1,4-naphthoquinone models in an aprotic solvent. The results establish a correlation between the presence of substituent group(s) and the modification of electronic properties and a corresponding shift in the midpoint potential of the naphthoquinone models. Further, we use pulsed EPR spectroscopy to determine the effect of substituent groups on the strength and planarity of the hydrogen bonds of naphthoquinone models in a protic solvent. This study provides support for the tuning of the electronic properties of quinone cofactors by the influence of substituent groups and hydrogen bonding interactions.

A bridging [4Fe-4S] cluster and nucleotide binding are essential for function of the Cfd1-Nbp35 complex as a scaffold in iron-sulfur protein maturation

The essential P-loop NTPases Cfd1 and Nbp35 of the cytosolic iron-sulfur (Fe-S) protein assembly machinery perform a scaffold function for Fe-S cluster synthesis. Both proteins contain a nucleotide binding motif of unknown function and a C-terminal motif with four conserved cysteine residues. The latter motif defines the Mrp/Nbp35 subclass of P-loop NTPases and is suspected to be involved in transient Fe-S cluster binding. To elucidate the function of these two motifs, we first created cysteine mutant proteins of Cfd1 and Nbp35 and investigated the consequences of these mutations by genetic, cell biological, biochemical, and spectroscopic approaches. The two central cysteine residues (CPXC) of the C-terminal motif were found to be crucial for cell viability, protein function, coordination of a labile [4Fe-4S] cluster, and Cfd1-Nbp35 hetero-tetramer formation. Surprisingly, the two proximal cysteine residues were dispensable for all these functions, despite their strict evolutionary conservation. Several lines of evidence suggest that the C-terminal CPXC motifs of Cfd1-Nbp35 coordinate a bridging [4Fe-4S] cluster. Upon mutation of the nucleotide binding motifs Fe-S clusters could no longer be assembled on these proteins unless wild-type copies of Cfd1 and Nbp35 were present in trans. This result indicated that Fe-S cluster loading on these scaffold proteins is a nucleotide-dependent step. We propose that the bridging coordination of the C-terminal Fe-S cluster may be ideal for its facile assembly, labile binding, and efficient transfer to target Fe-S apoproteins, a step facilitated by the cytosolic iron-sulfur (Fe-S) protein assembly proteins Nar1 and Cia1 in vivo.

Toward structure determination using membrane-protein nanocrystals and microcrystals

Membrane proteins are very important for all living cells, being involved in respiration, photosynthesis, cellular uptake and signal transduction, amongst other vital functions. However, less than 300 unique membrane protein structures have been determined to date, often due to difficulties associated with the growth of sufficiently large and well-ordered crystals. This work has been focused on showing the first proof of concept for using membrane protein nanocrystals and microcrystals for high-resolution structure determination. Upon determining that crystals of the membrane protein Photosystem I, which is the largest and most complex membrane protein crystallized to date, exist with only 100 unit cells with sizes of less than 200 nm on an edge, work was done to develop a technique that could exploit the growth of the Photosystem I nanocrystals and microcrystals. Femtosecond X-ray protein nanocrystallography was developed for use at the first high-energy X-ray free electron laser, the LCLS at SLAC National Accelerator Laboratory, in which a liquid jet brought fully-hydrated Photosystem I nanocrystals into the interaction region of the pulsed X-ray source. Diffraction patterns were recorded from millions of individual PSI nanocrystals and data from thousands of different, randomly oriented crystallites were integrated using Monte Carlo integration of the peak intensities. The short pulses (∼70fs) provided by the LCLS allowed the possibility to collect the diffraction data before the onset of radiation damage, exploiting the diffract-before-destroy principle. During the initial experiments at the AMO beamline using 6.9-Å wavelength, Bragg peaks were recorded to 8.5-Å resolution, and an electron-density map was determined that did not show any effects of X-ray-induced radiation damage [94]. Many additional techniques still need to be developed to explore the femtosecond nanocrystallography technique for experimental phasing and time-resolved X-ray crystallography experiments. The first proof-of-principle results for the femtosecond nanocrystallography technique indicate the incredible potential of the technique to offer a new route to the structure determination of membrane proteins.

Red antenna states of Photosystem I trimers from Arthrospira platensis revealed by single-molecule spectroscopy

Single-molecule fluorescence spectroscopy at 1.4K was used to investigate the spectral properties of red (long-wavelength) chlorophylls in trimeric Photosystem I (PSI) complexes from the cyanobacterium Arthrospira platensis. Three distinct red antenna states could be identified in the fluorescence spectra of single PSI trimers from A. platensis in the presence of oxidized P700. Two of them are responsible for broad emission bands centered at 726 and 760nm. These bands are similar to those found in bulk fluorescence spectra measured at cryogenic temperatures. The broad fluorescence bands at ≅726 and ≅760nm belong to individual emitters that are broadened by strong electron-phonon coupling giving rise to a large Stokes-shift of about 20nm and rapid spectral diffusion. An almost perpendicular orientation of the transition dipole moments of F726 and F760 has to be assumed because direct excitation energy transfer does not occur between F726 and F760. For the first time a third red state assigned to the pool absorbing around 708nm could be detected by its zero-phonon lines. The center of the zero-phonon line distribution is found at ≅714nm. The spectral properties of the three red antenna states show a high similarity to the red antenna states found in trimeric PSI of Thermosynechoccocus elongatus. Based on these findings a similar organization of the red antenna states in PSI of these two cyanobacteria is discussed.

Quantum chemical description of absorption properties and excited-state processes in photosynthetic systems

The theoretical description of the initial steps in photosynthesis has gained increasing importance over the past few years. This is caused by more and more structural data becoming available for light-harvesting complexes and reaction centers which form the basis for atomistic calculations and by the progress made in the development of first-principles methods for excited electronic states of large molecules. In this Review, we discuss the advantages and pitfalls of theoretical methods applicable to photosynthetic pigments. Besides methodological aspects of excited-state electronic-structure methods, studies on chlorophyll-type and carotenoid-like molecules are discussed. We also address the concepts of exciton coupling and excitation-energy transfer (EET) and compare the different theoretical methods for the calculation of EET coupling constants. Applications to photosynthetic light-harvesting complexes and reaction centers based on such models are also analyzed.

X-ray diffraction from membrane protein nanocrystals

Membrane proteins constitute > 30% of the proteins in an average cell, and yet the number of currently known structures of unique membrane proteins is < 300. To develop new concepts for membrane protein structure determination, we have explored the serial nanocrystallography method, in which fully hydrated protein nanocrystals are delivered to an x-ray beam within a liquid jet at room temperature. As a model system, we have collected x-ray powder diffraction data from the integral membrane protein Photosystem I, which consists of 36 subunits and 381 cofactors. Data were collected from crystals ranging in size from 100 nm to 2 μm. The results demonstrate that there are membrane protein crystals that contain < 100 unit cells (200 total molecules) and that 3D crystals of membrane proteins, which contain < 200 molecules, may be suitable for structural investigation. Serial nanocrystallography overcomes the problem of x-ray damage, which is currently one of the major limitations for x-ray structure determination of small crystals. By combining serial nanocrystallography with x-ray free-electron laser sources in the future, it may be possible to produce molecular-resolution electron-density maps using membrane protein crystals that contain only a few hundred or thousand unit cells.

Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals

A complete set of structure factors has been extracted from hundreds of thousands of femtosecond single-shot X-ray microdiffraction patterns taken from randomly oriented nanocrystals. The method of Monte Carlo integration over crystallite size and orientation was applied to experimental data from Photosystem I nanocrystals. This arrives at structure factors from many partial reflections without prior knowledge of the particle-size distribution. The data were collected at the Linac Coherent Light Source (the first hard-X-ray laser user facility), to which was fitted a hydrated protein nanocrystal injector jet, according to the method of serial crystallography. The data are single 'still' diffraction snapshots, each from a different nanocrystal with sizes ranging between 100 nm and 2 µm, so the angular width of Bragg peaks was dominated by crystal-size effects. These results were compared with single-crystal data recorded from large crystals of Photosystem I at the Advanced Light Source and the quality of the data was found to be similar. The implications for improving the efficiency of data collection by allowing the use of very small crystals, for radiation-damage reduction and for time-resolved diffraction studies at room temperature are discussed.

Femtosecond protein nanocrystallography-data analysis methods

X-ray diffraction patterns may be obtained from individual submicron protein nanocrystals using a femtosecond pulse from a free-electron X-ray laser. Many "single-shot" patterns are read out every second from a stream of nanocrystals lying in random orientations. The short pulse terminates before significant atomic (or electronic) motion commences, minimizing radiation damage. Simulated patterns for Photosystem I nanocrystals are used to develop a method for recovering structure factors from tens of thousands of snapshot patterns from nanocrystals varying in size, shape and orientation. We determine the number of shots needed for a required accuracy in structure factor measurement and resolution, and investigate the convergence of our Monte-Carlo integration method.

Electronic pathway in reaction centers from Rhodobacter sphaeroides and Chloroflexus aurantiacus

The reaction centers (RC) of Chloroflexus aurantiacus and Rhodobacter sphaeroidesH(M182)L mutant were investigated. Prediction for electron transfer (ET) at very low temperatures was also performed. To describe the kinetics of the C. aurantiacus RCs, the incoherent model of electron transfer was used. It was shown that the asymmetry in electronic coupling parameters must be included to explain the experiments. For the description of R. sphaeroidesH(M182)L mutant RCs, the coherent and incoherent models of electron transfer were used. These two models are discussed with regard to the observed electron transfer kinetics. It seems likely that the electron transfer asymmetry in R. sphaeroides RCs is caused mainly by the asymmetry in the free energy levels of L- and M-side cofactors. In the case of C. aurantiacus RCs, the unidirectionality of the charge separation can be caused mainly by the difference in the electronic coupling parameters in two branches.

Red antenna states of photosystem I from Synechococcus sp. PCC 7002

Absorption, fluorescence and single-molecule spectroscopy at low temperatures were used to elucidate spectral properties, heterogeneities and dynamics of the red-shifted chlorophyll a (Chla) molecules responsible for the fluorescence in photosystem I (PSI) from the cyanobacterium Synechoccocus sp. PCC 7002. The 77 K absorption spectrum indicates the presence of 2-3 red-shifted Chla's absorbing at about 708 nm. The fluorescence emission spectrum is dominated by a broad band at 714 nm. The emission spectra of single PSI complexes show zero-phonon lines (ZPLs) as well as a broad intensity distribution without ZPLs. The spectral region below 710 nm often shows ZPLs, they form a spectral band with a maximum at 698 nm (F698). The region above 710 nm is dominated by broad intensity distributions and the observation of ZPLs is less frequent. The broad distributions are due to the emission of the C708 Chla's and the emission from F698 stems from a Chla species absorbing at the blue side of P700. The properties of these two emissions show a close relation to those of the C708 and C719 pools observed in T. elongatus. Therefore an assignment of F698 and C708 to Chla-species with similarities to C708 and C719 in T. elongatus is proposed.

Atomic-level structural and functional model of a bacterial photosynthetic membrane vesicle

The photosynthetic unit (PSU) of purple photosynthetic bacteria consists of a network of bacteriochlorophyll-protein complexes that absorb solar energy for eventual conversion to ATP. Because of its remarkable simplicity, the PSU can serve as a prototype for studies of cellular organelles. In the purple bacterium Rhodobacter sphaeroides the PSU forms spherical invaginations of the inner membrane, approximately 70 nm in diameter, composed mostly of light-harvesting complexes, LH1 and LH2, and reaction centers (RCs). Atomic force microscopy studies of the intracytoplasmic membrane have revealed the overall spatial organization of the PSU. In the present study these atomic force microscopy data were used to construct three-dimensional models of an entire membrane vesicle at the atomic level by using the known structure of the LH2 complex and a structural model of the dimeric RC-LH1 complex. Two models depict vesicles consisting of 9 or 18 dimeric RC-LH1 complexes and 144 or 101 LH2 complexes, representing a total of 3,879 or 4,464 bacteriochlorophylls, respectively. The in silico reconstructions permit a detailed description of light absorption and electronic excitation migration, including computation of a 50-ps excitation lifetime and a 95% quantum efficiency for one of the model membranes, and demonstration of excitation sharing within the closely packed RC-LH1 dimer arrays.

Assignment of the Qy absorption spectrum of photosystem-I from Thermosynechococcus elongatus based on CAM-B3LYP calculations at the PW91-optimized protein structure

The Qy absorption spectrum of Photosystem-I from Thermosynecochoccus elongatus (formerly Synecochoccus elongatus) is calculated using the CAM-B3LYP density functional and INDO schemes based on a quantum-mechanically refined structure for the entire photosystem obtained using the PW91 density functional. These methods present a priori predictions of the absorption and linear dichroism spectra and include protein electrostatic effects, short range inductive effects, long-range and short-range exciton couplings, and superexchange effects involving aromatic residues and carotenes. CAM-B3LYP is used as it is the only known density functional that correctly describes the Q bands of chlorophylls, all other methods contaminating them with erroneous charge-transfer excitations. A critical feature is found to be the use of fully optimized heavy-atom coordinates, with those obtained from just X-ray crystallography providing a poor description of the electronic properties of the chromophores. The result is a realistic first-principles prediction of the observed absorption band that identifies the nature of the red-shifted chlorophylls as well as the energies of the reaction-center chlorophylls and the exciton couplings acting between them. The "special pair" appears more like a dimer of dimers than a self-contained functional unit, with the exciton couplings between its members and the accessory chlorophylls exceeding the internal coupling.

Three-dimensional crystallization of membrane proteins

Although the examination of the protein data bank reveals an important backlog in the number of three-dimensional structures of membrane proteins, several recent successes are serving as preludes to what will become a very prosperous decade in this field. Systematic investigations of various factors affecting the stability of membrane proteins, as well as their potential to crystallize three dimensionally, have paved the way for such achievements. The importance of the role of detergents both at the level of purification and crystallization is now well established. In addition, the recognition of the protein-detergent complex as the entity to crystallize, as well as the understanding of its physical-chemical properties and discovery of factors affecting these, have permitted the design of better crystallization strategies. As a consequence of the various efforts in the field, new crystallization methods for membrane proteins are being implemented. These have already been successful and are expected to contribute significantly to the future successes. This chapter will review some basic principles in membrane protein crystallization and give an overview of the current state of the art in the field. Some practical guidelines to help the novice approach the problem of membrane protein crystallization from the initial step of protein purification to crystallogenesis will also be given.