Robustness and Optimality of Light Harvesting in Cyanobacterial Photosystem I

Optimization of exciton trapping in energy transfer processes

In this paper, we establish optimal conditions for maximal energy transfer efficiency using solutions for multilevel systems and interpret these analytical solutions with more intuitive kinetic networks resulting from a systematic mapping procedure. The mapping procedure defines an effective hopping rate as the leading order picture and nonlocal kinetic couplings as the quantum correction, hence leading to a rigorous separation of thermal hopping and coherent transfer useful for visualizing pathway connectivity and interference in quantum networks. As a result of these calculations, the dissipative effects of the surrounding environments can be optimized to yield the maximal efficiency, and modulation of the efficiency can be achieved using the cumulative quantum phase along any closed loops. The optimal coupling of the system and its environments is interpreted with the generic mechanisms: (i) balancing localized trapping and delocalized coherence, (ii) reducing the effective detuning via homogeneous line-broadening, (iii) suppressing the destructive interference in nonlinear network configurations, and (iv) controlling phase modulation in closed loop configurations. Though these results are obtained for simple model systems, the physics thus derived provides insights into the working of light harvesting systems, and the approaches thus developed apply to large-scale computation.

What governs the reaction center excitation wavelength of photosystems I and II?

The sun's spectrum harvested through photosynthesis is the primary source of energy for life on earth. Plants, green algae, and cyanobacteria-the major primary producers on earth-utilize reaction centers that operate at wavelengths of 680 and 700 nm. Why were these wavelengths "chosen" in evolution? This study analyzes the efficiency of light conversion into chemical energy as a function of hypothetical reaction center absorption wavelengths given the sun's spectrum and the overpotential cost associated with charge separation. Surprisingly, it is found here that when taking into account the empirical charge separation cost the range 680-720 nm maximizes the conversion efficiency. This suggests the possibility that the wavelengths of photosystem I and II were optimized at some point in their evolution for the maximal utilization of the sun's spectrum.

Self-organized porphyrinic materials

The self-assembly and self-organization of porphyrins and related macrocycles enables the bottom-up fabrication of photonic materials for fundamental studies of the photophysics of these materials and for diverse applications. This rapidly developing field encompasses a broad range of disciplines including molecular design and synthesis, materials formation and characterization, and the design and evaluation of devices. Since the self-assembly of porphyrins by electrostatic interactions in the late 1980s to the present, there has been an ever increasing degree of sophistication in the design of porphyrins that self-assemble into discrete arrays or self-organize into polymeric systems. These strategies exploit ionic interactions, hydrogen bonding, coordination chemistry, and dispersion forces to form supramolecular systems with varying degrees of hierarchical order. This review concentrates on the methods to form supramolecular porphyrinic systems by intermolecular interactions other than coordination chemistry, the characterization and properties of these photonic materials, and the prospects for using these in devices. The review is heuristically organized by the predominant intermolecular interactions used and emphasizes how the organization affects properties and potential performance in devices.

Exciton delocalization and transport in photosystem I of cyanobacteria Synechococcus elongates: simulation study of coherent two-dimensional optical signals

Electronic excitations and the optical properties of the photosynthetic complex PSI are analyzed using an effective exciton model developed by Vaitekonis et al. [Photosynth. Res. 2005, 86, 185]. States of the reaction center, the linker states, the highly delocalized antenna states and the red states are identified and assigned in absorption and circular dichroism spectra by taking into account the spectral distribution of density of exciton states, exciton delocalization length, and participation ratio in the reaction center. Signatures of exciton cooperative dynamics in nonchiral and chirality-induced two-dimensional (2D) photon-echo signals are identified. Nonchiral signals show resonances associated with the red, the reaction center, and the bulk antenna states as well as transport between them. Spectrally overlapping contributions of the linker and the delocalized antenna states are clearly resolved in the chirality-induced signals. Strong correlations are observed between the delocalized antenna states, the linker states, and the RC states. The active space of the complex covering the RC, the linker, and the delocalized antenna states is common to PSI complexes in bacteria and plants.

Structural model and excitonic properties of the dimeric RC-LH1-PufX complex from Rhodobacter sphaeroides

The light-harvesting apparatus of the purple bacterial photosynthetic unit consists of a pool of peripheral light-harvesting complexes that transfer excitation energy to a reaction center (RC) via the surrounding pigment-protein complex LH1. Recent electron microscopy and atomic force microscopy studies have revealed that RC-LH1 units of Rhodobacter sphaeroides form membrane-bending dimeric complexes together with the polypeptide PufX. We present a structural model for these RC-LH1-PufX dimeric complexes constructed using the molecular dynamics flexible fitting method based on an EM density map. The arrangement of the LH1 BChls displays a distortion near the proposed location of the PufX polypeptide. The resulting atomic model for BChl arrays is used to compute the excitonic properties of the dimeric RC-LH1 complex. A comparison is presented between the structural and excitonic features of the S-shaped dimeric BChl array of Rhodobacter sphaeroides and the circular BChl arrangement found in other purple bacteria.

Structure of Photosystems I and II

Photosynthesis is the major process that converts solar energy into chemical energy on Earth. Two and a half billion years ago, the ancestors of cyanobacteria were able to use water as electron source for the photosynthetic process, thereby evolving oxygen and changing the atmosphere of our planet Earth. Two large membrane protein complexes, Photosystems I and II, catalyze the primary step in this energy conversion, the light-induced charge separation across the photosynthetic membrane. This chapter describes and compares the structure of two Photosystems and discusses their function in respect to the mechanism of light harvesting, electron transfer and water splitting.

Quantum yield of P700+ photodestruction in isolated photosystem I complexes of the cyanobacterium Arthrospira platensis

The photostability of P700 cation radical (P700+) was studied by evaluating the quantum yields of P700(+) photodestruction in photosystem I (PSI) complexes of the cyanobacterium Arthrospira platensis. The time courses of P700+ photodestruction in PSI trimers and monomers have been measured in aerobic conditions under selective excitation of far-red absorption band of P700+ by intense light of laser diodes. Long-term exposure of PSI complexes to 808 or 870 nm laser light caused destruction of P700+ and antenna chlorophylls. The true integral quantum yield of P700+ photodestruction calculated from these data was less than 0.7-1.4 x 10(-8). Illumination of PSI complexes by 650 nm light caused destruction of antenna chlorophylls with true quantum yield of about 6-7 x 10(-6) and damage of P700 with apparent quantum yield 2-3 x 10(-8). Preferential photodestruction of the long-wavelength antenna chlorophyll absorbing at 710 nm as compared with bulk chlorophylls was observed. About three orders of difference in magnitude between quantum yields of P700+ and bulk chlorophyll photodestruction indicates that P700+ is extremely photostable for functioning as an efficient quencher of singlet excitation energy in PSI.

Toward understanding molecular mechanisms of light harvesting and charge separation in photosystem II

Conversion of light energy in photosynthesis is extremely fast and efficient, and understanding the nature of this complex photophysical process is challenging. This review describes current progress in understanding molecular mechanisms of light harvesting and charge separation in photosystem II (PSII). Breakthroughs in X-ray crystallography have allowed the development and testing of more detailed kinetic models than have previously been possible. However, due to the complexity of the light conversion processes, satisfactory descriptions remain elusive. Recent advances point out the importance of variations in the photochemical properties of PSII in situ in different thylakoid membrane regions as well as the advantages of combining sophisticated time-resolved spectroscopic experiments with atomic level computational modeling which includes the effects of molecular dynamics.

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.

Natural photosystems from an engineer's perspective: length, time, and energy scales of charge and energy transfer

The vast structural and functional information database of photosynthetic enzymes includes, in addition to detailed kinetic records from decades of research on physical processes and chemical reaction-pathways, a variety of high and medium resolution crystal structures of key photosynthetic enzymes. Here, it is examined from an engineer's point of view with the long-term goal of reproducing the key features of natural photosystems in novel biological and non-biological solar-energy conversion systems. This survey reveals that the basic physics of the transfer processes, namely, the time constraints imposed by the rates of incoming photon flux and the various decay processes allow for a large degree of tolerance in the engineering parameters. Furthermore, the requirements to guarantee energy and electron transfer rates that yield high efficiency in natural photosystems are largely met by control of distance between chromophores and redox cofactors. This underlines a critical challenge for projected de novo designed constructions, that is, the control of spatial organization of cofactor molecules within dense array of different cofactors, some well within 1 nm from each other.

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.

Intermolecular coulomb couplings from ab initio electrostatic potentials: application to optical transitions of strongly coupled pigments in photosynthetic antennae and reaction centers

An accurate and numerically efficient method for the calculation of intermolecular Coulomb couplings between charge densities of electronic states and between transition densities of electronic excitations is presented. The coupling of transition densities yields the Förster type excitation energy transfer coupling, and from the charge density coupling, a shift in molecular excitation energies results. Starting from an ab initio calculation of the charge and transition densities, atomic partial charges are determined such as to fit the resulting electrostatic potentials of the different states and the transition. The different intermolecular couplings are then obtained from the Coulomb couplings between the respective atomic partial charges. The excitation energy transfer couplings obtained in the present TrEsp (transition charge from electrostatic potential) method are compared with couplings obtained from the simple point-dipole and extended dipole approximations and with those from the ab initio transition density cube method of Krüger, Scholes, and Fleming. The present method is of the same accuracy as the latter but computationally more efficient. The method is applied to study strongly coupled pigments in the light-harvesting complexes of green sulfur bacteria (FMO), purple bacteria (LH2), and higher plants (LHC-II) and the "special pairs" of bacterial reaction centers and reaction centers of photosystems I and II. For the pigment dimers in the antennae, it is found that the mutual orientation of the pigments is optimized for maximum excitonic coupling. A driving force for this orientation is the Coulomb coupling between ground-state charge densities. In the case of excitonic couplings in the "special pairs", a breakdown of the point-dipole approximation is found for all three reaction centers, but the extended dipole approximation works surprisingly well, if the extent of the transition dipole is chosen larger than assumed previously. For the "special pairs", a large shift in local transition energies is found due to charge density coupling.

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.

Steady-state and transient polarized absorption spectroscopy of photosytem I complexes from the cyanobacteria Arthrospira platensis and Thermosynechococcus elongatus

Core antenna and reaction centre of photosystem I (PS I) complexes from the cyanobacteria Arthrospira platensis and Thermosynechococcus elongatus have been characterized by steady-state polarized absorption spectroscopy, including linear dichroism (LD) and circular dichroism (CD). CD spectra and the second derivatives of measured 77 K CD spectra reveal the spectral components found in the polarized absorption spectra indicating the excitonic origin of the spectral forms of chlorophyll in the PS I complexes. The CD bands at 669-670(+), 673(+), 680(-), 683-685(-), 696-697(-), and 711(-) nm are a common feature of used PSI complexes. The 77 K CD spectra of the trimeric PS I complexes exhibit also low amplitude components around 736 nm for A. platensis and 720 nm for T. elongatus attributed to red-most chlorophylls. The LD measurements indicate that the transition dipole moments of the red-most states are oriented parallel to the membrane plane. The formation of P700(+)A(1)(-) or (3)P700 was monitored by time-resolved difference absorbance and LD spectroscopy to elucidate the spectral properties of the PS I reaction centre. The difference spectra give strong evidence for the delocalization of the excited singlet states in the reaction centre. Therefore, P700 cannot be considered as a dimer but should be regarded as a multimer of the six nearly equally coupled reaction centre chlorophylls in accordance with structure-based calculations. On the basis of the results presented in this work and earlier work in the literature it is concluded that the triplet state is localized most likely on P(A), whereas the cation is localized most likely on P(B).

Two equilibration pools of chlorophylls in the Photosystem I core antenna of Chlamydomonas reinhardtii

Femtosecond transient absorption spectroscopy was applied for a comparative study of excitation decay in several different Photosystem I (PSI) core preparations from the green alga Chlamydomonas reinhardtii. For PSI cores with a fully interconnected network of chlorophylls, the excitation energy was equilibrated over a pool of chlorophylls absorbing at approximately 683 nm, independent of excitation wavelength [Gibasiewicz et al. J Phys Chem B 105:11498-11506, 2001; J Phys Chem B 106:6322-6330, 2002]. In preparations with impaired connectivity between chlorophylls, we have found that the spectrum of chlorophylls connected to the reaction center (i.e., with approximately 20 ps decay time) over which the excitation is equilibrated becomes excitation-wavelength-dependent. Excitation at 670 nm is finally equilibrated over chlorophylls absorbing at approximately 675 nm, whereas excitation at 695 nm or 700 nm is equilibrated over chlorophylls absorbing at approximately 683 nm. This indicates that in the vicinity of the reaction center there are two spectrally different and spatially separated pools of chlorophylls that are equally capable of effective excitation energy transfer to the reaction center. We propose that they are related to the two groups of central PSI core chlorophylls lying on the opposite sides of reaction center.

Assignment of Red Antenna States in Photosystem I from Thermosynechoccocus elongatus by Single-Molecule Spectroscopy

Single-molecule spectroscopy at cryogenic temperatures was used to elucidate spectral properties, heterogeneities, and dynamics of the chlorophyll a (Chla) molecules responsible for the fluorescence in photosystem I (PSI) from the cyanobacteria Thermosynechococcus elongatus. Absorption and hole burning data suggest the presence of three pools absorbing at wavelengths greater than 700 nm with their absorption maxima at 708, 715, and 719 nm. The responsible Chla molecules are termed C708, C715, and C719. In the emission spectra of single PSI complexes, zero-phonon lines (ZPLs) were observed over the whole red emission range of PSI. The spectral region of the C708 pool is dominated by intense ZPLs; on the other hand, the broad emission of C715/C719 is unstructured and ZPLs are seen in this region much less frequently. Spectral jumps of ZPLs were observed. The dynamics as well as the spectral range covered by such jumps differ for C708 and C715/C719. This heterogeneity is likely caused by differences in the close environment of the chromophores. A tentative assignment of C708 and C715/C719 to Chla dimers and a Chla trimer is discussed, which is based on the remarkable structural differences in the environment of the most probable candidates for the red-most fluorescence.

Red Antenna States of Photosystem I from Cyanobacteria Synechocystis PCC 6803 and Thermosynechococcus elongatus: Single-Complex Spectroscopy and Spectral Hole-Burning Study

Hole-burning and single photosynthetic complex spectroscopy were used to study the excitonic structure and excitation energy-transfer processes of cyanobacterial trimeric Photosystem I (PS I) complexes from Synechocystis PCC 6803 and Thermosynechococcus elongatus at low temperatures. It was shown that individual PS I complexes of Synechocystis PCC 6803 (which have two red antenna states, i.e., C706 and C714) reveal only a broad structureless fluorescence band with a maximum near 720 nm, indicating strong electron-phonon coupling for the lowest energy C714 red state. The absence of zero-phonon lines (ZPLs) belonging to the C706 red state in the emission spectra of individual PS I complexes from Synechocystis PCC 6803 suggests that the C706 and C714 red antenna states of Synechocystis PCC 6803 are connected by efficient energy transfer with a characteristic transfer time of approximately 5 ps. This finding is in agreement with spectral hole-burning data obtained for bulk samples of Synechocystis PCC 6803. The importance of comparing the results of ensemble (spectral hole burning) and single-complex measurements was demonstrated. The presence of narrow ZPLs near 710 nm in addition to the broad fluorescence band at approximately 730 nm in Thermosynechococcus elongatus (Jelezko et al. J. Phys. Chem. B 2000, 104, 8093-8096) has been confirmed. We also demonstrate that high-quality samples obtained by dissolving crystals of PS I of Thermosynechococcus elongatus exhibit stronger absorption in the red antenna region than any samples studied so far by us and other groups.

One- and Two-Color Photon Echo Peak Shift Studies of Photosystem I

Wavelength-dependent one- and two-color photon echo peak shift spectroscopy was performed on the chlorophyll Qy band of trimeric photosystem I from Thermosynechococcus elongatus. Sub-100 fs energy transfer steps were observed in addition to longer time scales previously measured by others. In the main PSI absorption peak (675-700 nm), the peak shift decays more slowly with increasing wavelength, implying that energy transfer between pigments of similar excitation energy is slower for pigments with lower site energies. In the far-red region (715 nm), the decay of the peak shift is more rapid and is complete by 1 ps, a consequence of the strong electron-phonon coupling present in this spectral region. Two-color photon echo peak shift data show strong excitonic coupling between pigments absorbing at 675 nm and those absorbing at 700 nm. The one- and two-color peak shifts were simulated using the previously developed energy transfer model (J. Phys. Chem. B 2002, 106, 10251; Biophysical Journal 2003, 85, 140). The simulations agree well with the experimental data. Two-color photon echo peak shift is shown to be far more sensitive to variations in the molecular Hamiltonian than one-color photon echo peak shift spectroscopy.

Frequency-Domain Spectroscopic Study of the PS I−CP43‘ Supercomplex from the Cyanobacterium Synechocystis PCC 6803 Grown under Iron Stress Conditions

Absorption, fluorescence excitation, emission, and hole-burning (HB) spectra were measured at liquid helium temperatures for the PS I-CP43' supercomplexes of Synechocystis PCC 6803 grown under iron stress conditions and for respective trimeric PS I cores. Results are compared with those of room temperature, time-domain experiments (Biochemistry 2003, 42, 3893) as well as with the low-temperature steady-state experiments on PS I-CP43' supercomplexes of Synechococcus PCC 7942 (Biochim. Biophys. Acta 2002, 1556, 265). In contrast to the CP43' of Synechococcus PCC 7942, CP43' of Synechocystis PCC 6803 possesses two low-energy states analogous to the quasidegenerate states A and B of CP43 of photosystem II (J. Phys. Chem. B 2000, 104, 11805). Energy transfer between the CP43' and the PS I core occurs, to a significant degree, through the state A, characterized with a broader site distribution function (SDF). It is demonstrated that the low temperature (T = 5 K) excitation energy transfer (EET) time between the state A of CP43' (IsiA) and the PS I core in PS I-CP43' supercomplexes from Synechocystis PCC 6803 is about 60 ps, which is significantly slower than the EET observed at room temperature. Our results are consistent with fast (< or =10 ps) energy transfer from state B to state A in CP43'. Energy absorbed by the CP43' manifold has, on average, a greater chance of being transferred to the reaction center (RC) and utilized for charge separation than energy absorbed by the PS I core antenna. This indicates that energy is likely transferred from the CP43' to the RC along a well-defined path and that the "red antenna states" of the PS I core are localized far away from that path, most likely on the B7-A32 and B37-B38 dimers in the vicinity of the PS I trimerization domain (near PsaL subunit). We argue that the A38-A39 dimer does not contribute to the red antenna region.

Excitation migration in trimeric cyanobacterial photosystem I

A structure-based description of excitation migration in multireaction center light harvesting systems is introduced. The description is an extension of the sojourn expansion, which decomposes excitation migration in terms of repeated detrapping and recapture events. The approach is applied to light harvesting in the trimeric form of cyanobacterial photosystem I (PSI). Excitation is found to be shared between PSI monomers and the chlorophylls providing the strongest respective links are identified. Excitation sharing is investigated by computing cross-monomer excitation trapping probabilities. It is seen that on the average there is a nearly 40% chance of excitation cross transfer and trapping, indicating efficient coupling between monomers. The robustness and optimality of the chlorophyll network of trimeric PSI is examined.

A protein dynamics study of photosystem II: the effects of protein conformation on reaction center function

Molecular dynamics simulations have been performed to study photosystem II structure and function. Structural information obtained from simulations was combined with ab initio computations of chromophore excited states. In contrast to calculations based on the x-ray structure, the molecular-dynamics-based calculations accurately predicted the experimental absorbance spectrum. In addition, our calculations correctly assigned the energy levels of reaction-center (RC) chromophores, as well as the lowest-energy antenna chlorophyll. The primary and secondary quinone electron acceptors, Q(A) and Q(B), exhibited independent changes in position over the duration of the simulation. Q(B) fluctuated between two binding sites similar to the proximal and distal sites previously observed in light- and dark-adapted RC from purple bacteria. Kinetic models were used to characterize the relative influence of chromophore geometry, site energies, and electron transport rates on RC efficiency. The fluctuating energy levels of antenna chromophores had a larger impact on quantum yield than did their relative positions. Variations in electron transport rates had the most significant effect and were sufficient to explain the experimentally observed multi-component decay of excitation in photosystem II. The implications of our results are discussed in the context of competing evolutionary selection pressures for RC structure and function.

Density-functional geometry optimization of the 150 000-atom photosystem-I trimer

We present a linear-scaling method based on the use of density-functional theory (DFT) for the system-wide optimization of x-ray structural coordinates and apply it to optimize the 150,000 atoms of the photosystem-I (PS-I) trimer. The method is based on repetitive applications of a multilevel ONIOM procedure using the PW916-31G(d) DFT calculations for the high level and PM3 for the lower level; this method treats all atoms in the structure equivalently, a structure in which the majority of the atoms can be considered as part of some internal "active site." To obtain a realistic single structure, some changes to the original protein model were necessary but these are kept to a minimum in order that the optimized structure most closely resembles the original x-ray one. Optimization has profound effects on the perceived electronic properties of the cofactors, with, e.g., optimization lowering the internal energy of the chlorophylls by on average 53 kcal mol(-1) and eliminates the enormous 115 kcal mol(-1) energy spread depicted by the original x-ray heavy-atom coordinates. A highly precise structure for PS-I results that is suitable for analysis of device function. Significant qualitative features of the structure are also improved such as correction of an error in the stereochemistry of one of the chlorophylls in the "special pair" of the reaction center, as well as the replacement of a water molecule with a metal cation in a critical region on the C3 axis. The method also reveals other unusual features of the structure, leading both to suggestions concerning device functionality and possible mutations between gene sequencing and x-ray structure determination. The optimization scheme is thus shown to augment the molecular modeling schemes that are currently used to add medium-resolution structural information to the raw scattering data in order to obtain atomically resolved structures. System-wide optimization is now a feasible process and its use within protein x-ray data refinement should be considered.

Red Pool Chlorophylls of Photosystem I of the Cyanobacterium Thermosynechococcus elongatus: A Single-Molecule Study

Photosystem I reaction centers of the cyanobacterium Thermosynechococcus elongatus have been investigated using single-molecule spectroscopy. Single-molecule fluorescence emission spectra reveal a new fluorescence band located at 745 nm. Fluorescence polarization spectroscopy and fluorescence autocorrelation analysis show that only a few chlorophylls are responsible for the photoemission from the Photosystem I trimer at low temperature. Intersystem crossing parameters of the red pool chlorophylls have been determined via fluorescence autocorrelation measurements. The triplet yield of the red chlorophylls is strongly reduced in comparison to chlorophyll a in solution. Strong quenching of the triplet state indicates that the red chlorophylls are located in close contact to carotenoids.

Design and engineering of photosynthetic light-harvesting and electron transfer using length, time, and energy scales

Decades of research on the physical processes and chemical reaction-pathways in photosynthetic enzymes have resulted in an extensive database of kinetic information. Recently, this database has been augmented by a variety of high and medium resolution crystal structures of key photosynthetic enzymes that now include the two photosystems (PSI and PSII) of oxygenic photosynthetic organisms. Here, we examine the currently available structural and functional information from an engineer's point of view with the long-term goal of reproducing the key features of natural photosystems in de novo designed and custom-built molecular solar energy conversion devices. We find that the basic physics of the transfer processes, namely, the time constraints imposed by the rates of incoming photon flux and the various decay processes allow for a large degree of tolerance in the engineering parameters. Moreover, we find that the requirements to guarantee energy and electron transfer rates that yield high efficiency in natural photosystems are largely met by control of distance between chromophores and redox cofactors. Thus, for projected de novo designed constructions, the control of spatial organization of cofactor molecules within a dense array is initially given priority. Nevertheless, constructions accommodating dense arrays of different cofactors, some well within 1 nm from each other, still presents a significant challenge for protein design.

Structure and function of photosystems I and II

Oxygenic photosynthesis, the principal converter of sunlight into chemical energy on earth, is catalyzed by four multi-subunit membrane-protein complexes: photosystem I (PSI), photosystem II (PSII), the cytochrome b(6)f complex, and F-ATPase. PSI generates the most negative redox potential in nature and largely determines the global amount of enthalpy in living systems. PSII generates an oxidant whose redox potential is high enough to enable it to oxidize H(2)O, a substrate so abundant that it assures a practically unlimited electron source for life on earth. During the last century, the sophisticated techniques of spectroscopy, molecular genetics, and biochemistry were used to reveal the structure and function of the two photosystems. The new structures of PSI and PSII from cyanobacteria, algae, and plants has shed light not only on the architecture and mechanism of action of these intricate membrane complexes, but also on the evolutionary forces that shaped oxygenic photosynthesis.

Light Harvesting in Photosystem I Supercomplexes,

In photosynthetic membranes of cyanobacteria, algae, and higher plants, photosystem I (PSI) mediates light-driven transmembrane electron transfer from plastocyanin or cytochrome c6 to the ferredoxin-NADP complex. The oxidoreductase function of PSI is sensitized by a reversible photooxidation of primary electron donor P700, which launches a multistep electron transfer via a series of redox cofactors of the reaction center (RC). The excitation energy for the functioning of the primary electron donor in the RC is delivered via the chlorophyll core antenna in the complex with peripheral light-harvesting antennas. Supermolecular complexes of the PSI acquire remarkably different structural forms of the peripheral light-harvesting antenna complexes, including distinct pigment types and organizational principles. The PSI core antenna, being the main functional unit of the supercomplexes, provides an increased functional connectivity in the chlorophyll antenna network due to dense pigment packing resulting in a fast spread of the excitation among the neighbors. Functional connectivity within the network as well as the spectral overlap of antenna pigments allows equilibration of the excitation energy in the depth of the whole membrane within picoseconds and loss-free delivery of the excitation to primary donor P700 within 20-40 ps. Low-light-adapted cyanobacteria under iron-deficiency conditions extend this capacity via assembly of efficiently energy coupled rings of CP43-like complexes around the PSI trimers. In green algae and higher plants, less efficient energy coupling in the eukaryotic PSI-LHCI supercomplexes is probably a result of the structural adaptation of the Chl a/b binding LHCI peripheral antenna that not only extends the absorption cross section of the PSI core but participates in regulation of excitation flows between the two photosystems as well as in photoprotection.

Spectral and kinetic analysis of the energy coupling in the PS I-LHC I supercomplex from the green alga Chlamydomonas reinhardtii at 77 K

Energy transfer processes in the chlorophyll antenna of the PS I-LHCI supercomplexes from the green alga Chlamydomonas reinhardtii have been studied at 77 K using transient absorption spectroscopy with multicolor excitation in the 640-670 nm region. Comparison of the kinetic data obtained at low and room temperatures indicates that the slow approximately approximately 100 ps excitation equilibration phase that is characteristic of energy coupling of the LHCI peripheral antenna to the PS I core at physiological temperatures (Melkozernov AN, Kargul J, Lin S, Barber J and Blankenship RE (2004) J Phys Chem B 108: 10547-10555) is not observed in the excitation dynamics of the PS I-LHCI supercomplex at 77 K. This suggests that at low temperatures the peripheral antenna is energetically uncoupled from the PS I core antenna. Under these conditions the observed kinetic phases on the time scales from subpicoseconds to tens of picoseconds represent the superposition of the processes occurring independently in the PS I core antenna and the Chl a/b containing LHCI antenna. In the PS I-LHCI supercomplex with two uncoupled antennas the excitation is channeled to the excitation sinks formed at low temperature by clusters of red pigments. A better spectral resolution of the transient absorption spectra at 77 K results in detection of two DeltaA bands originating from the rise of photobleaching on the picosecond time scale of two clearly distinguished pools of low energy absorbing Chls in the PS I-LHCI supercomplex. The first pool of low energy pigments absorbing at 687 nm is likely to originate from the red pigments in the LHCI where the Lhca1 protein is most abundant. The second pool at 697 nm is suggested to result either from the structural interaction of the LHCI and the PS I core or from other Lhca proteins in the antenna. The kinetic data are discussed based on recent structural models of the PS I-LHCI. It is proposed that the uncoupling of pigment pools may be a control mechanism that regulates energy flow in Photosystem I.

Red chlorophylls in the exciton model of photosystem I

Structural arrangement of pigment molecules of Photosystem I of photosynthetic cyanobacterium Synechococcus elongatus is used for theoretical modeling of the excitation energy spectrum. It is demonstrated that a straightforward application of the exciton theory with the assumption of the same molecular transition energy does not describe the red side of the absorption spectrum. Since the inhomogeneity in the molecular transition energies caused by a dispersive interaction with the molecular surrounding cannot be identified directly from the structural model, the evolutionary search procedure is used for fitting the low temperature absorption and circular dichroism spectra. As a result, one dimer, three trimers and one tetramer of chlorophyll molecules responsible for the red side of the absorption spectrum with their assignment to the spectroscopically established three bands at 708, 714 and 719 nm are determined. All of them are found to be situated not in the very close vicinity of the reaction center but are encircling it almost at the same distance. In order to explain the unusual broadening on the red side of the spectrum the exciton state mixing with the charge transfer (CT) states is considered. It is shown that two effects can be distinguished as caused by mixing of those states: (i) the oscillator strength borrowing by the CT state from the exciton transition and (ii) the borrowing of the high density of the CT state by the exciton state. The intermolecular vibrations between two counter-charged molecules determine the high density in the CT state. From the broad red absorption wing it is concluded that the CT state should be the lowest state in the complexes under consideration. Such mixing effect enables resolving the diversity in the molecular transition energies as determined by different theoretical approaches.

Comparison of the light-harvesting networks of plant and cyanobacterial photosystem I

With the availability of structural models for photosystem I (PSI) in cyanobacteria and plants it is possible to compare the excitation transfer networks in this ubiquitous photosystem from two domains of life separated by over one billion years of divergent evolution, thus providing an insight into the physical constraints that shape the networks' evolution. Structure-based modeling methods are used to examine the excitation transfer kinetics of the plant PSI-LHCI supercomplex. For this purpose an effective Hamiltonian is constructed that combines an existing cyanobacterial model for structurally conserved chlorophylls with spectral information for chlorophylls in the Lhca subunits. The plant PSI excitation migration network thus characterized is compared to its cyanobacterial counterpart investigated earlier. In agreement with observations, an average excitation transfer lifetime of approximately 49 ps is computed for the plant PSI-LHCI supercomplex with a corresponding quantum yield of 95%. The sensitivity of the results to chlorophyll site energy assignments is discussed. Lhca subunits are efficiently coupled to the PSI core via gap chlorophylls. In contrast to the chlorophylls in the vicinity of the reaction center, previously shown to optimize the quantum yield of the excitation transfer process, the orientational ordering of peripheral chlorophylls does not show such optimality. The finding suggests that after close packing of chlorophylls was achieved, constraints other than efficiency of the overall excitation transfer process precluded further evolution of pigment ordering.

Structural and functional organization of the peripheral light-harvesting system in photosystem I

This review centers on the structural and functional organization of the light-harvesting system in the peripheral antenna of Photosystem I (LHC I) and its energy coupling to the Photosystem I (PS I) core antenna network in view of recently available structural models of the eukaryotic Photosystem I-LHC I complex, eukaryotic LHC II complexes and the cyanobacterial Photosystem I core. A structural model based on the 3D homology of Lhca4 with LHC II is used for analysis of the principles of pigment arrangement in the LHC I peripheral antenna, for prediction of the protein ligands for the pigments that are unique for LHC I and for estimates of the excitonic coupling in strongly interacting pigment dimers. The presence of chlorophyll clusters with strong pigment-pigment interactions is a structural feature of PS I, resulting in the characteristic red-shifted fluorescence. Analysis of the interactions between the PS I core antenna and the peripheral antenna leads to the suggestion that the specific function of the red pigments is likely to be determined by their localization with respect to the reaction center. In the PS I core antenna, the Chl clusters with a different magnitude of low energy shift contribute to better spectral overlap of Chls in the reaction center and the Chls of the antenna network, concentrate the excitation around the reaction center and participate in downhill enhancement of energy transfer from LHC II to the PS I core. Chlorophyll clusters forming terminal emitters in LHC I are likely to be involved in photoprotection against excess energy.

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.

Bridging the gap between structural and lattice models: a parameterization of energy transfer and trapping in Photosystem I

In the absence of an accurate structural model, the excited state dynamics of energy-transferring systems are often modeled using lattice models. To demonstrate the validity and other potential merits of such an approach we present the results of the modeling of the energy transfer and trapping in Photosystem I based upon the 2.5 A structural model, and show that these results can be reproduced in terms of a lattice model with only a few parameters. It has recently been shown that at room temperature the dynamics of a hypothetical Photosystem I particle, not containing any red chlorophylls (chls), are characterized by a longest (trapping) lifetime of 18 ps. The structure-based modeling of the dynamics of this particle yields an almost linear relationship between the possible values of the intrinsic charge-separation time at P700, 1/gamma, and the average single-site lifetime in the antenna, tauss. Lattice-based modeling, using the approach of a perturbed two-level model, reproduces this linear relation between tauss and 1/gamma. Moreover, this approach results in a value of the (modified) structure-function corresponding to a structure exhibiting a mixture of the characteristics of both a square and a cubic lattice, consistent with the structural model. These findings demonstrate that the lattice model describes the dynamics of the system appropriately. In the lattice model, the total trapping time is the sum of the delivery time to the reaction center and the time needed to quench the excitation after delivery. For the literature value of tauss=150 fs, both these times contribute almost equally to the total trapping time of 18 ps, indicating that the system is neither transfer- nor trap-limited. The value of approximately 9 ps for the delivery time is basically equal to the excitation-transfer time from the bulk chls to the red chls in Synechococcus elongatus, indicating that energy transfer from the bulk to the reaction center and to the red chls are competing processes. These results are consistent with low-temperature time-resolved and steady-state fluorescence measurements. We conclude that lattice models can be used to describe the global energy-transfer properties in complex chromophore networks, with the advantage that such models deal with only a few global, intuitive parameters rather than the many microscopic parameters obtained in structure-based modeling.

Ultrafast transient absorption studies on Photosystem I reaction centers from Chlamydomonas reinhardtii. 1. A new interpretation of the energy trapping and early electron transfer steps in Photosystem I

The energy transfer and charge separation kinetics in core Photosystem I (PSI) particles of Chlamydomonas reinhardtii has been studied using ultrafast transient absorption in the femtosecond-to-nanosecond time range. Although the energy transfer processes in the antenna are found to be generally in good agreement with previous interpretations, we present evidence that the interpretation of the energy trapping and electron transfer processes in terms of both kinetics and mechanisms has to be revised substantially as compared to current interpretations in the literature. We resolved for the first time i), the transient difference spectrum for the excited reaction center state, and ii), the formation and decay of the primary radical pair and its intermediate spectrum directly from measurements on open PSI reaction centers. It is shown that the dominant energy trapping lifetime due to charge separation is only 6-9 ps, i.e., by a factor of 3 shorter than assumed so far. The spectrum of the first radical pair shows the expected strong bleaching band at 680 nm which decays again in the next electron transfer step. We show furthermore that the early electron transfer processes up to approximately 100 ps are more complex than assumed so far. Several possibilities are discussed for the intermediate redox states and their sequence which involve oxidation of P700 in the first electron transfer step, as assumed so far, or only in the second electron transfer step, which would represent a fundamental change from the presently assumed mechanism. To explain the data we favor the inclusion of an additional redox state in the electron transfer scheme. Thus we distinguish three different redox intermediates on the timescale up to 100 ps. At this level no final conclusion as to the exact mechanism and the nature of the intermediates can be drawn, however. From comparison of our data with fluorescence kinetics in the literature we also propose a reversible first charge separation step which has been excluded so far for open PSI reaction centers. For the first time an ultrafast 150-fs equilibration process, occurring among exciton states in the reaction center proper, upon direct excitation of the reaction center at 700 nm, has been resolved. Taken together the data call for a fundamental revision of the present understanding of the energy trapping and early electron transfer kinetics in the PSI reaction center. Due to the fact that it shows the fastest trapping time observed so far of any intact PSI particle, the PSI core of C. reinhardtii seems to be best suited to further characterize the electron transfer steps and mechanisms in the reaction center of PSI.

Excitation wavelength dependence of the fluorescence kinetics in Photosystem I particles from Synechocystis PCC 6803 and Synechococcus elongatus

The excitation-wavelength dependence of the excited-state dynamics of monomeric and trimeric Photosystem I (PSI) particles from Synechocystis PCC 6803 as well as trimeric PSI particles from Synechococcus elongatus has been studied at room temperature using time-resolved fluorescence spectroscopy. For aselective (400 nm), carotenoid (505 nm), and bulk chlorophyll (approximately 650 nm) excitation in all species, a downhill energy-transfer component is observed, corresponding to a lifetime of 3.4-5.5 ps. For selective red excitation (702-719 nm) in all species, a significantly faster, an approximately 1-ps, uphill transfer component was recorded. In Synechococcus PSI, an additional approximately 10-ps downhill energy-transfer component is found for all wavelengths of excitation, except 719 nm. Each of the species exhibits its own characteristic trap spectrum, the shape of which is independent of the wavelength of excitation. This trap spectrum decays in approximately 23 ps in both monomeric and trimeric Synechocystis PSI and in approximately 35 ps in trimeric Synechococcus PSI. The data were simulated based on the 2.5 A structural model of PSI of Synechococcus elongatus using the Förster equation for energy transfer, and using the 0.6-1-ps charge-separation time and the value of 1.2-1.3 for the index of refraction that were obtained from the dynamics of a hypothetical PSI particle without red chls. The experimentally obtained lifetimes and spectra were reproduced well by assigning three of the chlorophyll-a (chla) dimers observed in the structure to the C708/C702RT pool of red chls present in PSI from both species. Essential for the simulation of the dynamics of Synechococcus PSI is the assignment of the single chla trimer in the structure to the C719/C708RT pool present in this species.

Glycerol conductance and physical asymmetry of the Escherichia coli glycerol facilitator GlpF

The aquaglyceroporin GlpF is a transmembrane channel of Escherichia coli that facilitates the uptake of glycerol by the cell. Its high glycerol uptake rate is crucial for the cell to survive in very low glycerol concentrations. Although GlpF allows both influx and outflux of glycerol, its structure, similar to the structure of maltoporin, exhibits a significant degree of asymmetry. The potential of mean force characterizing glycerol in the channel shows a corresponding asymmetry with an attractive vestibule only at the periplasmic side. In this study, we analyze the potential of mean force, showing that a simplified six-step model captures the kinetics and yields a glycerol conduction rate that agrees well with observation. The vestibule improves the conduction rate by 40% and 75% at 10- micro M and 10-mM periplasmic glycerol concentrations, respectively. In addition, neither the conduction rate nor the conduction probability for a single glycerol (efficiency) depends on the orientation of GlpF. GlpF appears to conduct equally well in both directions under physiological conditions.