Structural fingerprinting: subgrouping of comoviruses by structural studies of red clover mottle virus to 2.4-A resolution and comparisons with other comoviruses.

Red clover mottle virus (RCMV) is a member of the comoviruses, a group of picornavirus-like plant viruses. The X-ray structure of RCMV strain S has been determined and refined to 2.4 A. The overall structure of RCMV is similar to that of two other comoviruses, Cowpea mosaic virus (CPMV) and Bean pod mottle virus (BPMV). The sequence of the coat proteins of RCMV strain O were modeled into the capsid structure of strain S without causing any distortion, confirming the close resemblance between the two strains. By comparing the RCMV structure with that of other comoviruses, a structural fingerprint at the N terminus of the small subunit was identified which allowed subgrouping of comoviruses into CPMV-like and BPMV-like viruses.

The refined crystal structure of cowpea mosaic virus at 2.8 A resolution.

Comoviruses are a group of plant viruses in the picornavirus superfamily. The type member of comoviruses, cowpea mosaic virus (CPMV), was crystallized in the cubic space group I23, a = 317 A and the hexagonal space group P6(1)22, a = 451 A, c = 1038 A. Structures of three closely similar nucleoprotein particles were determined in the cubic form. The roughly 300-A capsid was similar to the picornavirus capsid displaying a pseudo T = 3 (P = 3) surface lattice. The three beta-sandwich domains adopt two orientations, one with the long axis radial and the other two with the long axes tangential in reference to the capsid sphere. T = 3 viruses display one or the other of these two orientations. The CPMV capsid was permeable to cesium ions, leading to a disturbance of the beta-annulus inside a channel-like structure, suggesting an ion channel. The hexagonal crystal form diffracted X rays to 3 A resolution, despite the large unit cell. The large ( approximately 200 A) solvent channels in the lattice allow exchange of CPMV cognate Fab fragments. As an initial step in the structure determination of the CPMV/Fab complex, the P6(1)22 crystal structure was solved by molecular replacement with the CPMV model determined in the cubic cell.

The crystal structure of muscle phosphoglucomutase refined at 2.7-angstrom resolution.

A model of rabbit muscle phosphoglucomutase was refined at 2.7-A resolution by using two heavy atom derivatives for initial phasing and standard refinement procedures, including molecular replacement averaging about a 2-fold axis and dynamic simulation: final R-factor, 0.223 (no solvent modeling); RMS deviation from standard bond lengths and angles, 0.020 A and 3.6 degrees, respectively (all 8658 nonhydrogen atoms plus 36,953 reflections (F/sigma greater than or equal to 3) between 8- and 2.7-A resolutions); average of individually refined atomic B-factors, 40 A2 (all atoms) and 30 A2 (all atoms in domains I-III). An H-bonding scheme with 538 main chain H-bonds for the two monomers in the asymmetric unit and probable ligands for six uranyl ions in one heavy atom derivative is given. The monomer contains 42 strands/helices arranged into four alpha/beta-domains. Each of the first three domains contains an alpha 3 beta 4 alpha 1 motif, where the topology of beta 4 is 2,1,3,4:[arrows: see text] which is a topology not encountered in an extensive search among known protein structures. A spatial similarity is observed between corresponding residues in the three repetitions of this motif per monomer, but the minimal mutational distance between spatially corresponding residues is not statistically significant. The loop between the antiparallel strands in each of these domains is an important feature of the active site. In domain IV, beta-sheet topology is 2,1,3,4,5,6:[arrows:see text]. Noncovalent domain/domain interactions within the monomer are greatest between adjacent domains along the polypeptide chain, which are not substantially interdigitated and can be cleanly disengaged by altering the phi/psi torsional angles of three uniquely positioned residues in the model. The observed hierarchy of noncovalent interactions between structural units within the crystal, based on a semi-empirical paradigm, suggests that monomer-monomer contacts within the asymmetric unit are formed during growth of the lattice and provides a rationale for some of the diffraction characteristics of phosphoglucomutase crystals. An unusually deep crevice involving 58 residues is formed by the head-to-tail, twisted semicircular arrangement of the four domains of the monomer that places no atom more than 12 A from the water-accessible surface. The active site of the enzyme is extensively buried at the bottom of this crevice, at the approximate confluence of the four domains. Other features of the active site, including the surrounding helical dipoles, and the metal-ion binding pocket are described, together with structure/function comparisons with a number of other enzymes.

Studies on the crystal structure of (D-Ala)-B0 porcine insulin at 1.9 A resolution.

The crystal structure of (D-Ala)-B0 porcine insulin has been determined, using data to 1.9 A and atomic parameters of 2 Zn porcine insulin as a starting model, and through the use of the difference method and the restrained least square method, to a final R-factor of 0.211 and r.m.s. deviation of 0.057 A for the bond lengths. The electron densities of B0 residues were very clear. Introduction of B0 residues into the molecules had reduced the thermal vibration of the N-terminus of B-chain for both molecules I and II and made the molecules pack closer in the crystal. The obvious differences between the crystal structures of 2 Zn and (D-Ala)-B0 porcine insulin were the conformations of partial polar groups around the possible receptor binding surface and the assembly mode of two helixes of A-chain in molecule I. In the local environment of the N-terminus of B-chain there were great differences between the crystal structures of (D-Ala)-B0 porcine insulin, (Trp)-B1 porcine insulin and Des B1(Phe) bovine insulin. In this paper the structure-immunoactivity relationships of insulin molecule have also been discussed briefly.

Molecular structure and absolute configuration of suberogorgin.

In the present paper it is reported that the molecular structure and absolute configuration of poisonous suberogorgin are determined by using X-ray diffraction method. The crystal of suberogorgin belongs to orthogonal system with space group D4(2)-P2(1)2(1)2(1). The crystallographic parameters are: a = 16.135A, b = 13.189A, c = 12.901A, Z = 8. The initial model of the crystal structure was solved by the direct method. The refinement of the structure parameters was carried out by using the least square method and led to a final R-factor of 0.056. In accordance with the molecular structure of suberogorgin mentioned above, the solvent effect of NMR has been further discussed and the relationship between the molecular structure of suberogorgin and its toxicity has also been preliminarily investigated.

Molecular structure and absolute configuration of the diterpene lactone, praelolide.

Praelolide is a new compound which was isolated out from the gorgonian, Menella praelonga (Ridley), collected from the South Sea of China at Zhanjiang, Guangdong. The molecular formula is C28H35O12Cl. The research result by X-ray diffraction method on the crystal structure is presented. The compound is orthorhombic with space group P2(1)2(1)2, cell dimensions a = 16.936, b = 16.709, c = 10.333 A, and Z = 4. The structure has been solved by direct method and refined to R = 0.055 for 2257 unique observable reflexions by least-squares. The molecule is composed of the major conformational isomer in which the three main rings (a six-membered ring, an eight-membered ring, a six-membered ring) take separately the form of chair-chairboat-chair, a five-membered actone ring, a C1 substitution, 4 acetate groups, and a three-membered epoxide ring. The absolute configuration of the molecule has also been determined by statistics (R factor ratio R = 1.012) and Bijvoet pairs observation. For 30 pairs of the greatest anomalous contributions the residuals are R'(+) = 0.057 for the first enantiomorph and R'(-) = 0.005 for the second one, so the latter should unambiguously correspond to the absolute configuration of the molecule.