A Study of Some Organic Crystal Structures

The crystal structure determination, using single crystal X-ray diffraction methods, of three polycyclic aromatic hydrocarbons is described. The thesis is divided into three parts, each part corresponding to one compound. An appendix is added in which the history and. uses of ''generalized projections" is reviewed. An adaption of this technique was used extensively in the analysis of 1:9-5:10 diperinaphthylene anthracene. Part I of this thesis deals with the structure of 2:3-8:9 dibenzperylene. The short b axis of the monoclinic unit cell, and the regular nature of the rings in this aromatic compound, made the structure analysis easy. The good resolution of the atoms in the projection on the (010) plane made it possible for refinement, by means of two dimensional fourier series, to proceed to a good degree of accuracy. It was, therefore, surprising that refinement by successive difference maps did not yield the same answer as a back shift correction calculated from a comparison of electron density maps for which Fobs and Fcalc values had been used as coefficients in the Fourier series. However, both methods of refinement show clearly an intermolecular approach distance of less than 3.2 A. Bond lengths appear to indicate that this is apparently due to a lack of complete planarity of the molecule, although another explanation is possible. The overcrowded aromatic hydrocarbon 1:9-5:10 diperi-naphthylene anthracene is described in Part II. The work concerns itself mainly In the solution of the phase problem, for which a number of unusual methods had to be employed. Two co-ordinates of the atoms in the molecule were found by projections on the (010) plane and the third by means of generalized projections of the (hll) planes. No great accuracy could be achieved, but it was possible to distinguish which of the two possible methods the molecule adopted to relieve the overcrowding. In the third part of the thesis a description is given of the analysis and refinement of anthrovalene, the third member of the coronene, ovalene series. This analysis is of very great interest because of the extraordinary nature of the chemical reaction in which anthrovalene was formed. It is possible that this process may give an understanding of graphitization. When the work was started not even the empirical formula was known. The cell dimensions showed clearly that the unknown compound was loosely ("isomorphous") with coronene and ovalene. The molecular weight determination left little doubt about this, and a study of the intensities gave a final confirmation. Certain impurities were, however, found in the available crystals

Bacteriophage Assembly

Bacteriophages have been a model system to study assembly processes for over half a century. Formation of infectious phage particles involves specific protein-protein and protein-nucleic acid interactions, as well as large conformational changes of assembly precursors. The sequence and molecular mechanisms of phage assembly have been elucidated by a variety of methods. Differences and similarities of assembly processes in several different groups of bacteriophages are discussed in this review. The general principles of phage assembly are applicable to many macromolecular complexes

The Structure of Bovine Viral Diarrhea Virus RNA-Dependent RNA Polymerase and Its Amino-Terminal Domain

SummaryViral RNA-dependent RNA polymerases (RdRp) differ from DNA-dependent RNA polymerases, DNA-dependent DNA polymerases, and reverse transcriptases in that RdRps contain “fingertips” consisting of several polypeptide strands in the fingers domain interacting with the thumb domain. The crystal structure of bovine viral diarrhea virus (BVDV) RdRp containing an Asn438 duplication shows that the “N-terminal domain,” which occurs only in pestiviruses such as BVDV, interacts with the polymerase component of the same polypeptide chain. This contrasts with the domain swapping observed in the previously determined structure of the BVDV NADL strain RdRp. By comparison with the NADL structure and through the use of biochemical data, it is possible that the N-terminal domain, in conjunction with the fingertips, is required to bind and assist the translocation of the RNA template. The partial disorder of the loop containing the additional Asn438 residue may explain the low replication rate of the recombinant compared with the wild-type virus

Structure and Function of a Chlorella Virus Encoded Glycosyltransferase

Paramecium bursaria chlorella virus-1 encodes at least 5 putative glycosyltransferases that are probably involved in the synthesis of the glycan components of the viral major capsid protein. The 1.6 Å crystal structure of one of these glycosyltransferases (A64R) has a mixed α/β fold containing a central, six-stranded β-sheet flanked by α-helices. Crystal structures of A64R, complexed with UDP, CMP, or GDP, established that only UDP bound to A64R in the presence of Mn2+, consistent with its high structural similarity to glycosyltransferases which utilize UDP as the sugar carrier. The structure of the complex of A64R, UDP-glucose, and Mn2+ showed that the largest conformational change occurred when hydrogen bonds were formed with the ligands. Unlike UDP-glucose, UDPgalactose and UDP-GlcNAc did not bind to A64R, suggesting a selective binding of UDP-glucose. Thus, UDP-glucose is most likely the sugar donor for A64R, consistent with glucose occurring in the virus major capsid protein glycans

Structural analyses of \u3ci\u3ePhycodnaviridae\u3c/i\u3e and \u3ci\u3eIridoviridae\u3c/i\u3e

The Phycodnaviridae, Iridoviridae and related viruses, with diameters of 1500±2000 A Ê , are formed from large trigonal arrays of hexagonally close-packed capsomers forming the faces of icosahedra [Yan et al. (2000), Nature Struct. Biol. 7, 101-103; Nandhagopal et al. (2002), Proc. Natl Acad. Sci. USA, 99, 14758-14763]. Caspar and Klug predicted that such structures could be assembled from hexameric capsomers [Caspar & Klug (1962), Cold Spring Harbor. Symp. Quant. Biol. 27, 1-24], as was subsequently found in numerous icosahedral viruses. During the course of evolution, some viruses, including the virus families mentioned above, replaced hexameric capsomers with pseudo-hexameric trimers by gene duplication. In large dsDNA icosahedral viruses, the capsomers are organized into `pentasymmetrons\u27 and `trisymmetrons\u27. The interactions between the trimeric capsomers can be divided into three groups, one between similarly oriented trimers and two between oppositely oriented trimers (trimers related by an approximately sixfold rotation). The interactions within a trisymmetron belong to the ®rst class, whereas those between trisymmetrons and within the pentasymmetron are of the other two types. Knowledge of these distances permits a more accurate ®tting of the atomic structure of the capsomer into the cryo-electron microscopy (cryoEM) reconstruction of the whole virus. The adoption of pseudo-hexagonal capsomers places these viruses into a subset of the Caspar and Klug surface lattices

A human antibody against Zika virus crosslinks the E protein to prevent infection

The recent Zika virus (ZIKV) epidemic has been linked to unusual and severe clinical manifestations including microcephaly in fetuses of infected pregnant women and Guillian-Barré syndrome in adults. Neutralizing antibodies present a possible therapeutic approach to prevent and control ZIKV infection. Here we present a 6.2 Å resolution three-dimensional cryo-electron microscopy (cryoEM) structure of an infectious ZIKV (strain H/PF/2013, French Polynesia) in complex with the Fab fragment of a highly therapeutic and neutralizing human monoclonal antibody, ZIKV-117. The antibody had been shown to prevent fetal infection and demise in mice. The structure shows that ZIKV-117 Fabs cross-link the monomers within the surface E glycoprotein dimers as well as between neighbouring dimers, thus preventing the reorganization of E protein monomers into fusogenic trimers in the acidic environment of endosomes

Structure of acidic pH dengue virus showing the fusogenic glycoprotein trimers

Flaviviruses undergo large conformational changes during their life cycle. Under acidic pH conditions, the mature virus forms transient fusogenic trimers of E glycoproteins that engage the lipid membrane in host cells to initiate viral fusion and nucleocapsid penetration into the cytoplasm. However, the dynamic nature of the fusogenic trimer has made the determination of its structure a challenge. Here we have used Fab fragments of the neutralizing antibody DV2-E104 to stop the conformational change of dengue virus at an intermediate stage of the fusion process. Using cryo-electron microscopy, we show that in this intermediate stage, the E glycoproteins form 60 trimers that are similar to the predicted "open" fusogenic trimer. IMPORTANCE The structure of a dengue virus has been captured during the formation of fusogenic trimers. This was accomplished by binding Fab fragments of the neutralizing antibody DV2-E104 to the virus at neutral pH and then decreasing the pH to 5.5. These trimers had an "open" conformation, which is distinct from the "closed" conformation of postfusion trimers. Only two of the three E proteins within each spike are bound by a Fab molecule at domain III. Steric hindrance around the icosahedral 3-fold axes prevents binding of a Fab to the third domain III of each E protein spike. Binding of the DV2-E104 Fab fragments prevents domain III from rotating by about 130 degrees to the postfusion orientation and thus precludes the stem region from "zipping" together the three E proteins along the domain II boundaries into the "closed" postfusion conformation, thus inhibiting fusion

Pushing the resolution limit by correcting the Ewald sphere effect in single-particle Cryo-EM reconstructions

The Ewald sphere effect is generally neglected when using the Central Projection Theorem for cryo electron microscopy single-particle reconstructions. This can reduce the resolution of a reconstruction. Here we estimate the attainable resolution and report a “block-based” reconstruction method for extending the resolution limit. We find the Ewald sphere effect limits the resolution of large objects, especially large viruses. After processing two real datasets of large viruses, we show that our procedure can extend the resolution for both datasets and can accommodate the flexibility associated with large protein complexes

Structure of the chlorovirus PBCV-1 major capsid glycoprotein determined by combining crystallographic and carbohydrate molecular modeling approaches

The glycans of the major capsid protein (Vp54) of Paramecium bursaria chlorella virus (PBCV-1) were recently described and found to be unusual. This prompted a reexamination of the previously reported Vp54 X-ray structure. A detailed description of the complete glycoprotein was achieved by combining crystallographic data with molecular modeling. The crystallographic data identified most of the monosaccharides located close to the protein backbone, but failed to detect those further from the glycosylation sites. Molecular modeling complemented this model by adding the missing monosaccharides and examined the conformational preference of the whole molecule, alone or within the crystallographic environment. Thus, combining X-ray crystallography with carbohydrate molecular modeling resulted in determining the complete glycosylated structure of a glycoprotein. In this case, it is the chlorovirus PBCV-1 major capsid protein. Includes supplemental appendi