Observation of the energy-level structure of the low-light adapted B800 LH4 complex by single-molecule spectroscopy.

Low-light adapted B800 light-harvesting complex 4 (LH4) from Rhodopseudomonas palustris is a complex in which the arrangement of the bacteriochloropyll a pigments is very different from the well-known B800-850 LH2 complex. For bulk samples, the main spectroscopic feature in the near-infrared is the occurrence of a single absorption band at 802 nm. Single-molecule spectroscopy can resolve the narrow bands that are associated with the exciton states of the individual complexes. The low temperature (1.2 K) fluorescence excitation spectra of individual LH4 complexes are very heterogeneous and display unique features. It is shown that an exciton model can adequately reproduce the polarization behavior of the complex, the experimental distributions of the number of observed peaks per complex, and the widths of the absorption bands. The results indicate that the excited states are mainly localized on one or a few subunits of the complex and provide further evidence supporting the recently proposed structure model.

Detergent structure in crystals of the integral membrane light-harvesting complex LH2 from Rhodopseudomonas acidophila strain 10050.

Integral membrane proteins are solubilized by their incorporation into a detergent micelle. The detergent micelle has a critical influence on the formation of a three-dimensional crystal lattice. The bulk detergent phase is not seen in X-ray crystal structures of integral membrane proteins, due to its disordered character. Here, we describe the detergent structure present in crystals of the peripheral light-harvesting complex of the purple bacteria Rhodopseudomonas acidophila strain 10050 at a maximal resolution of 12A as determined by neutron crystallography. The LH2 molecule has a toroidal shape and spans the membrane completely in vivo. A volume of 16% of the unit cell could be ascribed to detergent tails, localized on both the inner and outer hydrophobic surfaces of the molecule. The detergent tail volumes were found to be associated with individual LH2 molecules and had no direct role in the formation of the crystalline lattice.

Identification of copper-based green pigments in Jaume Huguet's Gothic altarpieces by Fourier transform infrared microspectroscopy and synchrotron radiation X-ray diffraction.

The scientific investigation of ancient paintings gives a unique insight into ancient painting techniques and their evolution through time and geographic location. This study deals with the identification of the green pigments used by one of the most important Catalan masters in Gothic times, Jaume Huguet. Other pigments and materials have also been characterized by means of conventional techniques such as optical microscopy, scanning electron microscopy and Fourier transform infrared spectroscopy. Synchrotron radiation X-ray diffraction has been used to produce maps of phases at a spatial resolution of 100 microm across chromatic layers.

An X-ray crystallographic study of the binding sites of the azide inhibitor and organic substrates to ceruloplasmin, a multi-copper oxidase in the plasma.

Ceruloplasmin is a multi-copper oxidase, which contains most of the copper present in the plasma. It is an acute-phase reactant that exhibits a two- to three-fold increase over the normal concentration of 300 microg/ml in adult plasma. However, the precise physiological role(s) of ceruloplasmin has been the subject of intensive debate and it is likely that the enzyme has a multi-functional role, including iron oxidase activity and the oxidation of biogenic amines. The three-dimensional X-ray structure of the human enzyme was elucidated in 1996 and showed that the molecule was composed of six cupredoxin-type domains arranged in a triangular array. There are six integral copper atoms per molecule (mononuclear sites in domains 2, 4 and 6 and a trinuclear site between domains 1 and 6) and two labile sites with roughly 50% occupancy. Further structural studies on the binding of metal cations by the enzyme indicated a putative mechanism for ferroxidase activity. In this paper we report medium-resolution X-ray studies (3.0-3.5 A) which locate the binding sites for an inhibitor (azide) and various substrates [aromatic diamines, biogenic amines and (+)-lysergic acid diethylamide, LSD]. The binding site of the azide moiety is topologically equivalent to one of the sites reported for ascorbate oxidase. However, there are two distinct binding sites for amine substrates: aromatic diamines bind on the bottom of domain 4 remote from the mononuclear copper site, whereas the biogenic amine series typified by serotonin, epinephrine and dopa bind in close vicinity to that utilised by cations in domain 6 and close to the mononuclear copper. These binding sites are discussed in terms of possible oxidative mechanisms. The binding site for LSD is also reported.

Derivative manipulation in the structure solution of the integral membrane LH2 complex.

The structure of the peripheral light-harvesting complex from Rhodopseudomonas acidophila strain 10050 was determined by multiple isomorphous replacement methods. The derivatization of the crystals was augmented by the addition of a backsoaking stage. The soak/backsoaked data comparison had greater isomorphism and showed simpler Patterson maps than the standard native/soak comparison. Amplitudes from the derivatized then backsoaked crystals and from the derivatized crystals were compared in order to extract a subset of heavy-atom sites. Using this information, the full array of sites were found from a derivative/native comparison, eventually leading to excellent electron-density maps.

Apoprotein structure in the LH2 complex from Rhodopseudomonas acidophila strain 10050: modular assembly and protein pigment interactions.

The refined structure of the peripheral light-harvesting complex from Rhodopseudomonas acidophila strain 10050 reveals a membrane protein with protein-protein interactions in the trans-membrane region exclusively of a van der Waals nature. The dominant factors in the formation of the complex appear to be extramembranous hydrogen bonds (suggesting that each apoprotein must achieve a fold close to its final structure in order to oligomerize), protein-pigment and pigment-pigment interactions within the membrane-spanning region. The pigment molecules are known to play an important role in the formation of bacterial light-harvesters, and their extensive mediation of structural contacts within the membrane bears this out. Amino acid residues determining the secondary structure of the apoproteins influence the oligomeric state of the complex. The assembly of the pigment array is governed by the apoproteins of LH2. The particular environment of each of the pigment molecules is, however, influenced directly by few protein contacts. These contacts produce functional effects that are not attributable to a single cause, e.g. the arrangement of an overlapping cycle of chromophores not only provides energy delocalisation and storage properties, but also has consequences for oligomer size, pigment distortion modes and pigment chemical environment, all of which modify the precise function of the complex. The evaluation of site energies for the pigment array requires the consideration of a number of effects, including heterogeneous pigment distortions, charge distributions in the local environment and mechanical interactions.

Pigment-pigment interactions and energy transfer in the antenna complex of the photosynthetic bacterium Rhodopseudomonas acidophila.

BACKGROUND: Photosynthesis starts with the absorption of solar radiation by antenna pigment molecules. In purple bacteria these chromophores, (bacteriochlorophyll a and carotenoid) are embedded in the membrane; they are non-covalently bound to apoproteins which have the ability to modulate the chromophores' absorbing characteristics. The first structure of the bacterial antenna complex from Rhodopseudomonas acidophila, strain 10050, shows a ring of nonameric symmetry. Two concentric cylinders of apoproteins enclose the pigment molecules. The current resolution of the structure, to 2.5 A, allows us to begin to explore the mechanism of energy transfer among these pigments. RESULTS: The mechanism of energy transfer, from the short- to long-wavelength-absorbing pigments, is largely determined by the relative distances and orientations of the chromophores. In this paper we provide evidence that energy transfer between the B800 and B850 bacteriochlorophylls is largely via Förster induced dipole-dipole resonance. Strong Coulombic (exciton) coupling among the 18 short distanced chromophores in the B850 macrocycle is promoted by good alignment of the Qy dipoles. Singlet-singlet energy transfer from carotenoid to the B800 macrocycle appears to be minimal, with most of the energy transfer going to B850. The higher energy state of both chromophores dominates in more complex situations. CONCLUSIONS: The structure of the antenna complex not only shows Nature at its most aesthetic but also illustrates how clever and efficient the energy transfer mechanism has become, with singlet-singlet excitation being passed smoothly down the spectral gradient to the reaction centre.

Trypanosoma cruzi trypanothione reductase. Crystallization, unit cell dimensions and structure solution.

We have reproducibly crystallized recombinant trypanothione reductase from Trypanosoma cruzi. Yellow tetragonal crystals in the shape of elongated prisms have unit cell dimensions of a = 92.8 A, c = 156.6 A, Laue symmetry of 4/m and are suitable for a detailed structural analysis. Diffraction data to 2.7 A resolution have been recorded using synchrotron radiation at the Daresbury laboratory. The structure has been solved by molecular replacement calculations using this synchrotron data and our previously determined Crithidia fasciculata enzyme structure as a search model. The space group has been identified as P4(3) with a homodimer of approximate molecular mass of 108 kDa in the asymmetric unit. Diffraction beyond 2.5 A has been recorded when large freshly grown crystals are exposed to X-rays. Refinement of the structure is in progress.

A progress report on the crystallographic studies on the B800-850 antenna complex from Rhodopseudomonas acidophila strain 10050.

Large single crystals (up to 1 mm in each dimension) of the B800-850 antenna complex from Rhodopseudomonas acidophila strain 10050 have been grown in the presence of beta-octyl-glucoside. These crystals have the space group R32 and unit cell dimensions of a = b = 119.9 A and c = 297.0 A. Recently we have improved our crystallization procedures so that all crystals now diffract reliably to beyond 3.5 A, with some diffracting to below 3 A. A range of isomorphous heavy atom derivatives have been prepared and we are now engaged in locating the heavy atom sites within the unit cell.

Crystallization and characterization of two crystal forms of the B800-850 light-harvesting complex from Rhodopseudomonas acidophila strain 10050.

Two different crystal forms of the B800-850-antenna complex from Rhodopseudomonas acidophila strain 10050 have been grown. This complex is an integral membrane protein and is isolated as an oligomeric assembly with a molecular weight of approximately 84 kDa. This assembly contains six alpha/beta apoprotein pairs, 18 molecules of bacteriochlorophyll a and nine molecules of carotenoid. The first crystal form has dimensions unit cell a = b = 75.8 A, c = 97.5 A with the space group P4 and diffracts to a resolution of 12.0 A. The second crystal form is rhombohedral with dimensions unit cell a = 121.1 A, alpha = 60 degrees, space group R32 and diffracts to a resolution of 3.5 A. Native data have been processes in both cases, to an Rmerge value of 9.0 to 11.0%. The X-ray data suggest that the asymmetric unit, in both crystal forms, contains one 84 kDa antenna complex.

The structure of the saccharide-binding site of concanavalin A.

A complex of concanavalin A with methyl alpha-D-mannopyranoside has been crystallized in space group P212121 with a = 123.9 A, b = 129.1 A and c = 67.5 A. X-ray diffraction intensities to 2.9 A resolution have been collected on a Xentronics/Nicolet area detector. The structure has been solved by molecular replacement where the starting model was based on refined coordinates of an I222 crystal of saccharide-free concanavalin A. The structure of the saccharide complex was refined by restrained least-squares methods to an R-factor value of 0.19. In this crystal form, the asymmetric unit contains four protein subunits, to each of which a molecule of mannoside is bound in a shallow crevice near the surface of the protein. The methyl alpha-D-mannopyranoside molecule is bound in the C1 chair conformation 8.7 A from the calcium-binding site and 12.8 A from the transition metal-binding site. A network of seven hydrogen bonds connects oxygen atoms O-3, O-4, O-5 and O-6 of the mannoside to residues Asn14, Leu99, Tyr100, Asp208 and Arg228. O-2 and O-1 of the mannoside extend into the solvent. O-2 is hydrogen-bonded through a water molecule to an adjacent asymmetric unit. O-1 is not involved in any hydrogen bond and there is no fixed position for its methyl substituent.

Chemical and Mössbauer spectroscopic evidence that iron-containing concanavalin A is a ferritin.

We report here the preparation of iron-containing concanavalin A. It has a protein-to-iron ratio of 2.0, and the iron compound it contains is particulate with an average diameter of 85 A. Iron-containing concanavalin A interacts reversibly with dextran and with methyl alpha-D-glucoside. The molecular basis of these findings is discussed and a possible mechanism suggested where one of the molecular forms of concanavalin A has the structure of an apoferritin into which iron is deposited in the form of ferrihydrite.

Properties of a new crystal form of the complex of concanavalin A with methyl alpha-D-glucopyranoside.

The complex of concanavalin A with methyl alpha-D-glucopyranoside crystallizes as regular rhombic dodecahedra containing 35% protein by weight. The crystal is of space group I23 with a = 167.8 A (1 A = 0.1 nm) and contains one concanavalin A dimer per asymmetric unit. It diffracts to a resolution of 1.9 A and is suitable for crystallographic investigation of the structure of the saccharide-binding site.

The structure of beta-lactoglobulin and its similarity to plasma retinol-binding protein.

Since its first isolation, bovine beta-lactoglobulin (BLG) has been an enigma: although it is abundant in the whey fraction of milk, its function is still not clear. The results of the many physicochemical studies on the protein need a structural interpretation. We report here the structure of the orthorhombic crystal form of cow BLG at pH 7.6, at a resolution of 2.8 A. It has an unusual protein fold, composed of two slabs of antiparallel beta-sheet, which shows a remarkable similarity to plasma retinol-binding protein. A possible binding site for retinol in BLG has been identified by model-building. This suggests a role for BLG in vitamin A transport and we have discovered specific receptors for the BLG-retinol complex in the intestine of neonate calves.

Protein microcrystal diffraction and the effects of radiation damage with ultra-high-flux synchrotron radiation.

By using ultra-high-flux synchrotron x-radiation from a wiggler source, good Laue diffraction data have been obtained from protein microcrystals of size 30 X 35 X 10 microns3, mounted wet in glass capillaries. At the flux level of 10(13)-10(14) photons per sec/mm2, the radiation damage is still low enough to allow a large survey of reciprocal space for a microcrystal and a complete survey for a normal-sized protein crystal. The development of sources for ultra-high-intensity synchrotron radiation is thus an important improvement in the technique for determination of structure through protein crystallography as well as in other cases where crystal size is often a limiting factor.