Miroslav Z. Papiz

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

Since its first isolation1, bovine β-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 Å. It has an unusual protein fold, composed of two slabs of antiparallel β-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.

Macromolecular TLS refinement in REFMAC at moderate resolutions.

Publisher Summary This chapter discusses the translation, rotation, and screw-rotation (TLS) parameterization of anisotropic displacement parameters (ADPs). In general, each atom can deviate anisotropically from its mean position, and six parameters are necessary to describe the mean square displacements fully. These parameters are referred to as the “ADPs,” are usually denoted U, and can be visualized as “thermal ellipsoids.” The addition of an extra six parameters per atom in macromolecular refinement is usually not justified by the data, except when atomic resolution data are available (

The Structure and Thermal Motion of the B800–850 LH2 Complex from Rps. acidophila at 2.0 Å Resolution and 100 K: New Structural Features and Functionally Relevant Motions

The structure at 100K of integral membrane light-harvesting complex II (LH2) from Rhodopseudomonas acidophila strain 10050 has been refined to 2.0A resolution. The electron density has been significantly improved, compared to the 2.5A resolution map, by high resolution data, cryo-cooling and translation, libration, screw (TLS) refinement. The electron density reveals a second carotenoid molecule, the last five C-terminal residues of the alpha-chain and a carboxy modified alpha-Met1 which forms the ligand of the B800 bacteriochlorophyll. TLS refinement has enabled the characterisation of displacements between molecules in the complex. B850 bacteriochlorophyll molecules are arranged in a ring of 18 pigments composed of nine approximate dimers. These pigments are strongly coupled and at their equilibrium positions the excited state dipole interaction energies, within and between dimers, are approximately 370cm(-1) and 280cm(-1), respectively. This difference in coupling energy is similar in magnitude to changes in interaction energies arising from the pigment displacements described by TLS tensors. The displacements appear to be non-random in nature and appear to be designed to optimise the modulation of pigment energy interactions. This is the first time that LH2 pigment displacements have been quantified experimentally. The calculated energy changes indicate that there may be significant contributions to inter-pigment energy interactions from molecular displacements and these may be of importance to photosynthetic energy transfer.

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.

A model for the photosynthetic apparatus of purple bacteria

Abstract The photosynthetic apparatus of purple bacteria is composed of light-harvesting complexes and reaction centres. Recent work on the structures of light-harvesting complexes combined with existing knowledge of the structure of the reaction centre now makes it feasible, for the first time, to model the entire photosynthetic apparatus. Questions can be asked about the functional implications of such a model in the light of the most recent spectroscopic data.

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

Abstract 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 μg/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 Å) 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.

The 7.5-A electron density and spectroscopic properties of a novel low-light B800 LH2 from Rhodopseudomonas palustris.

A novel low-light (LL) adapted light-harvesting complex II has been isolated from Rhodopseudomonas palustris. Previous work has identified a LL B800-850 complex with a heterogeneous peptide composition and reduced absorption at 850 nm. The work presented here shows the 850 nm absorption to be contamination from a high-light B800-850 complex and that the true LL light-harvesting complex II is a novel B800 complex composed of eight alpha beta(d) peptide pairs that exhibits unique absorption and circular dichroism near infrared spectra. Biochemical analysis shows there to be four bacteriochlorophyll molecules per alpha beta peptide rather than the usual three. The electron density of the complex at 7.5 A resolution shows it to be an octamer with exact 8-fold rotational symmetry. A number of bacteriochlorophyll geometries have been investigated by simulation of the circular dichroism and absorption spectra and compared, for consistency, with the electron density. Modeling of the spectra suggests that the B850 bacteriochlorophylls may be arranged in a radial direction rather than the usual tangential arrangement found in B800-850 complexes.

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.

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.

Piperazine Silicate (EU 19): the Structure of a Very Small Crystal Determined with Synchrotron Radiation

Single-crystal diffraction data have been recorded for a very small crystal of dimensions 8 x 18 × 175 ~rn 3. From these data the structure of piperazine silicate (EU 19) has been determined and refined to R = 0.094 for 490 observed reflections. Data collection for such a crystal has been made practicable by the high intensity of the Daresbury Synchrotron Radiation Source and the Enraf-Nonius FAST area detector diffractometer. The potential of this synchrotron radiation method for other small crystals including proteins is discussed. Crystal data: 2+ • 2