Crystal structure of photosystem II from Synechococcus elongatus at 3.8 A resolution

Oxygenic photosynthesis is the principal energy converter on earth. It is driven by photosystems I and II, two large protein-cofactor complexes located in the thylakoid membrane and acting in series. In photosystem II, water is oxidized; this event provides the overall process with the necessary electrons and protons, and the atmosphere with oxygen. To date, structural information on the architecture of the complex has been provided by electron microscopy of intact, active photosystem II at 15-30 A resolution, and by electron crystallography on two-dimensional crystals of D1-D2-CP47 photosystem II fragments without water oxidizing activity at 8 A resolution. Here we describe the X-ray structure of photosystem II on the basis of crystals fully active in water oxidation. The structure shows how protein subunits and cofactors are spatially organized. The larger subunits are assigned and the locations and orientations of the cofactors are defined. We also provide new information on the position, size and shape of the manganese cluster, which catalyzes water oxidation.     

Three-dimensional structure of cyanobacterial photosystem I at 2.5 A resolution.

Life on Earth depends on photosynthesis, the conversion of light energy from the Sun to chemical energy. In plants, green algae and cyanobacteria, this process is driven by the cooperation of two large protein-cofactor complexes, photosystems I and II, which are located in the thylakoid photosynthetic membranes. The crystal structure of photosystem I from the thermophilic cyanobacterium Synechococcus elongatus described here provides a picture at atomic detail of 12 protein subunits and 127 cofactors comprising 96 chlorophylls, 2 phylloquinones, 3 Fe4S4 clusters, 22 carotenoids, 4 lipids, a putative Ca2+ ion and 201 water molecules. The structural information on the proteins and cofactors and their interactions provides a basis for understanding how the high efficiency of photosystem I in light capturing and electron transfer is achieved.     

The structure of a plant photosystem I supercomplex at 3.4 A resolution

All higher organisms on Earth receive energy directly or indirectly from oxygenic photosynthesis performed by plants, green algae and cyanobacteria. Photosystem I (PSI) is a supercomplex of a reaction centre and light-harvesting complexes. It generates the most negative redox potential in nature, and thus largely determines the global amount of enthalpy in living systems. We report the structure of plant PSI at 3.4 A resolution, revealing 17 protein subunits. PsaN was identified in the luminal side of the supercomplex, and most of the amino acids in the reaction centre were traced. The crystal structure of PSI provides a picture at near atomic detail of 11 out of 12 protein subunits of the reaction centre. At this level, 168 chlorophylls (65 assigned with orientations for Q(x) and Q(y) transition dipole moments), 2 phylloquinones, 3 Fe(4)S(4) clusters and 5 carotenoids are described. This structural information extends the understanding of the most efficient nano-photochemical machine in nature.     

Towards a resolution of the lek paradox

Genetic benefits in the shape of 'good genes' have been invoked to explain costly female choice in the absence of direct fitness benefits. Little genetic variance in fitness traits is expected, however, because directional selection tends to drive beneficial alleles to fixation. There seems to be little potential, therefore, for female choice to result in genetic benefits, giving rise to the 'lek paradox'. Nevertheless, evidence shows that genetic variance persists despite directional selection and genetic benefits of female choice are frequently reported. A theoretical solution to the lek paradox has been proposed on the basis of two assumptions: that traits are condition-dependent, and that condition shows high genetic variance. The observed genetic variability in sexual traits will be accounted for, because a proportion of the genetic variance in condition will be captured and expressed in the trait. Here we report results from experiments showing that male courtship rate in the dung beetle Onthophagus taurus is a condition-dependent trait that is preferred by females. More importantly, male condition has high genetic variance and is genetically correlated with courtship rate. Our results thereby represent a significant step towards a resolution of the lek paradox.     

Crystal structure of plant photosystem I

Oxygenic photosynthesis is the principal producer of both oxygen and organic matter on Earth. The conversion of sunlight into chemical energy is driven by two multisubunit membrane protein complexes named photosystem I and II. We determined the crystal structure of the complete photosystem I (PSI) from a higher plant (Pisum sativum var. alaska) to 4.4 A resolution. Its intricate structure shows 12 core subunits, 4 different light-harvesting membrane proteins (LHCI) assembled in a half-moon shape on one side of the core, 45 transmembrane helices, 167 chlorophylls, 3 Fe-S clusters and 2 phylloquinones. About 20 chlorophylls are positioned in strategic locations in the cleft between LHCI and the core. This structure provides a framework for exploration not only of energy and electron transfer but also of the evolutionary forces that shaped the photosynthetic apparatus of terrestrial plants after the divergence of chloroplasts from marine cyanobacteria one billion years ago.     

The crystal structure of the photoprotein aequorin at 2.3 A resolution

Aequorin is a calcium-sensitive photoprotein originally obtained from the jellyfish Aequorea aequorea. Because it has a high sensitivity to calcium ions and is biologically harmless, aequorin is widely used as a probe to monitor intracellular levels of free calcium. The aequorin molecule contains four helix-loop-helix 'EF-hand' domains, of which three can bind calcium. The molecule also contains coelenterazine as its chromophoric ligand. When calcium is added, the protein complex decomposes into apoaequorin, coelenteramide and CO2, accompanied by the emission of light. Apoaequorin can be regenerated into active aequorin in the absence of calcium by incubation with coelenterazine, oxygen and a thiol agent. Cloning and expression of the complementary DNA for aequorin were first reported in 1985 (refs 2, 6), and growth of crystals of the recombinant protein has been described; however, techniques have only recently been developed to prepare recombinant aequorin of the highest purity, permitting a full crystallographic study. Here we report the structure of recombinant aequorin determined by X-ray crystallography. Aequorin is found to be a globular molecule containing a hydrophobic core cavity that accommodates the ligand coelenterazine-2-hydroperoxide. The structure shows protein components stabilizing the peroxide and suggests a mechanism by which calcium activation may occur.     

Polyoma virus capsid structure at 22.5 A resolution

X-ray diffraction data from polyoma capsid crystals were phased by refinement of low-resolution starting models to obtain a self-consistent structural solution. The unexpected result that the hexavalent morphological unit is a pentamer shows that specificity of bonding is not conserved among the protein subunits in the icosahedrally symmetric capsid.     

Plants lacking the main light-harvesting complex retain photosystem II macro-organization

Photosystem II (PSII) is a key component of photosynthesis, the process of converting sunlight into the chemical energy of life. In plant cells, it forms a unique oligomeric macrostructure in membranes of the chloroplasts. Several light-harvesting antenna complexes are organized precisely in the PSII macrostructure-the major trimeric complexes (LHCII) that bind 70% of PSII chlorophyll and three minor monomeric complexes-which together form PSII supercomplexes. The antenna complexes are essential for collecting sunlight and regulating photosynthesis, but the relationship between these functions and their molecular architecture is unresolved. Here we report that antisense Arabidopsis plants lacking the proteins that form LHCII trimers have PSII supercomplexes with almost identical abundance and structure to those found in wild-type plants. The place of LHCII is taken by a normally minor and monomeric complex, CP26, which is synthesized in large amounts and organized into trimers. Trimerization is clearly not a specific attribute of LHCII. Our results highlight the importance of the PSII macrostructure: in the absence of one of its main components, another protein is recruited to allow it to assemble and function.     

Molecular structure of the acyl-enzyme intermediate in beta-lactam hydrolysis at 1.7 A resolution.

The X-ray crystal structure of the molecular complex of penicillin G with a deacylation-defective mutant of the RTEM-1 beta-lactamase from Escherichia coli shows how these antibiotics are recognized and destroyed. Penicillin G is covalently bound to Ser 70 0 gamma as an acyl-enzyme intermediate. The deduced catalytic mechanism uses Ser 70 0 gamma as the attacking nucleophile during acylation. Lys 73 N zeta acts as a general base in abstracting a proton from Ser 70 and transferring it to the thiazolidine ring nitrogen atom via Ser 130 0 gamma. Deacylation is accomplished by nucleophilic attack on the penicilloyl carbonyl carbon by a water molecule assisted by the general base, Glu 166.     

Bio-rational design of photosystem II inhibitors (I)

Molecular modeling of cyanoacrylates and ureas with D1 protein ofPisum sativum have been presented. Studies show that these two kinds of inhibitors occupy the similar region in the D1 protein. Cyanoacrylates have more bii aites than ureas, thus they have higher activities.     

Three-dimensional structure of an antigen-antibody complex at 6 A resolution

Present understanding of the three-dimensional structure of antibody combining sites is based on X-ray diffraction studies of myeloma immunoglobulins. The structures of the antigen-binding fragment (Fab) complexes of two of these immunoglobulins with small ligands have also been determined. However, there is no crystallographic information concerning the interactions of an antibody with an antigen, nor do we know the precise structure of antigenic determinants on protein molecules. We now report the first structure determination of an antigen-antibody complex at 6 A resolution. The structure of the complex between hen egg-white lysozyme and the Fab of a monoclonal anti-lysozyme antibody (D1.3) shows that the combining site of antibodies is not merely a cleft delineated by the complementarity-determining regions of the variable regions of the light and heavy chains, but is a larger area extending beyond it. A correspondingly large area of the antigen makes close contacts with the antibody, in agreement with the notion of a 'topographical' rather than 'sequential' antigenic determinant. The structural basis of cross-reactivities of an antibody with heterologous antigens and the effect of a single amino acid substitution on antigenic specificity can thus be visualized in the structural model presented here.     

Low pH-induced conformational changes in 33 kD protein of photosystem Ⅱ

33 kD protein, located on the lumen side ofthylakoid membranes, is one of three extrinsic proteins ofphotosystem Ⅱ (PS Ⅱ ). Previous study showed that NBSmodification of W241, the only tryptophan in 33 kD protein,is helpful for understanding the function of W241 in main-taining functional conformation of 33 kD protein. In thispaper, studies of both circular dichroism and fluorescencespectra showed that upon decreasing pH from 6.2 to 2.5, theconformation of soluble 33 kD protein changed significantly,with an increase or a decrease in percentage of random coilor (z-helix and turns. The changes in secondary structures ofthis protein are pH reversible. After NBS modification at pH2.5, the conformational change of 33 kD protein was keptfixed. The CD ellipticity at 200 nm for NBS-modified 33 kDprotein is much lower than that for control, indicating that the unfolding degree of 33 kD protein was enhanced after the NBS modification. Moreover, the conformational flexibility islost in NBS-modified 33 kD protein, and the conformationalchange becomes pH irreversible, indicating that NBS modi-fication blocked the reversibility of conformational change of33 kD protein. The specific binding capability of NBS-modi-fled 33 kD protein is much lower than that of low pH-treatedcontrol. Furthermore, the rebinding of modified protein on PS Ⅱ membranes cannot restore the activity of oxygen evo-lution. We suggest that it is low pH but not NBS modificationof W241 that leads to the conformational change of 33 kDprotein from one functional to another non-functional state.The significant capability of proton transport of 33 kD pro-tein is discussed.     

Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 A resolution

Calcium ATPase is a member of the P-type ATPases that transport ions across the membrane against a concentration gradient. Here we have solved the crystal structure of the calcium ATPase of skeletal muscle sarcoplasmic reticulum (SERCA1a) at 2.6 A resolution with two calcium ions bound in the transmembrane domain, which comprises ten alpha-helices. The two calcium ions are located side by side and are surrounded by four transmembrane helices, two of which are unwound for efficient coordination geometry. The cytoplasmic region consists of three well separated domains, with the phosphorylation site in the central catalytic domain and the adenosine-binding site on another domain. The phosphorylation domain has the same fold as haloacid dehalogenase. Comparison with a low-resolution electron density map of the enzyme in the absence of calcium and with biochemical data suggests that large domain movements take place during active transport.     

Protection of phosphatidylcholine to photosystem Ⅱ membrane during heat treatment

Photosystem Ⅱ membrane was reconstituted with phosphatidylcholine (PC) with different kinds of fatty acyl chains and the protection of PC to photosystem Ⅱ (PS Ⅱ)membrane during heat treatment was investigated using oxygen electrode, variable fluorescence and circular dichroism (CD) spectroscopy. Heat treatment decreased the oxygen evolution rate and the F′v/Fm′ ratio of PS Ⅱ membrane and influenced CD spectra of PS Ⅱ membrane, but PC inhibited the effect of heat treatment on the oxygen evolution rate, the F′v/F′m ratio and CD spectra of PS Ⅱ membrane. The results indicate that PC can protect PS Ⅱ membrane against heat treatment and the alterations in the unsaturated fatty acid extent in PC can cause the changes of the protection ability.     

Protection of phosphatidyl-choline to photosystem II membrane during heat treatment

Photosystem II membrane was reconstituted with phosphatidylcholine (PC) with different kinds of fatty acyl chains and the protection of PC to photosystem II (PS II) membrane during heat treatment was investigated using oxygen electrode, variable fluorescence and circular dichro-ism (CD) spectroscopy. Heat treatment decreased the oxygen evolution rate and the F'v/Fm' ratio of PS II membrane and influenced CD spectra of PS II membrane, but PC inhibited the effect of heat treatment on the oxygen evolution rate, the F'v/F'm ratio and CD spectra of PS II membrane. The results indicate that PC can protect PS II membrane against heat treatment and the alterations in the unsaturated fatty acid extent in PC can cause the changes of the protection ability.     

Kinetics of charge separation and energy transfer in photosystem II reaction center

Conclusion In the present study we investigated the kinetics of the initial charge separation and energy transfer in the PS II reaction center using pico-second and femto-second time-resolved techniques. We conclude that there are energy transfer processes between ?-Car or Pheo and P680 in the PSII reaction center. The time constant of energy transfer from Pheo to P680 is less than 100 ps, while that from (?-Car to P680 is about 350 ps. For the initial charge separation in the PS II reaction center, the preliminary finding supported the about 3-ps time constant of charge separation. The possible kinetic scheme in PS II reaction center was proposed. Further experiments are in progress.     

The three-dimensional structure of foot-and-mouth disease virus at 2.9 A resolution

The structure of foot-and-mouth disease virus has been determined at close to atomic resolution by X-ray diffraction without experimental phase information. The virus shows similarities with other picornaviruses but also several unique features. The canyon or pit found in other picornaviruses is absent; this has important implications for cell attachment. The most immunogenic portion of the capsid, which acts as a potent peptide vaccine, forms a disordered protrusion on the virus surface.     

Crystal structure of spinach major light-harvesting complex at 2.72 A resolution

The major light-harvesting complex of photosystem II (LHC-II) serves as the principal solar energy collector in the photosynthesis of green plants and presumably also functions in photoprotection under high-light conditions. Here we report the first X-ray structure of LHC-II in icosahedral proteoliposome assembly at atomic detail. One asymmetric unit of a large R32 unit cell contains ten LHC-II monomers. The 14 chlorophylls (Chl) in each monomer can be unambiguously distinguished as eight Chla and six Chlb molecules. Assignment of the orientation of the transition dipole moment of each chlorophyll has been achieved. All Chlb are located around the interface between adjacent monomers, and together with Chla they are the basis for efficient light harvesting. Four carotenoid-binding sites per monomer have been observed. The xanthophyll-cycle carotenoid at the monomer-monomer interface may be involved in the non-radiative dissipation of excessive energy, one of the photoprotective strategies that have evolved in plants.