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R W Ruigrok

Publications and source records attributed to R W Ruigrok.

At least 37 records · Page 2Linked to original sources
PubMed1997

Adenovirus dodecahedron, a new vector for human gene transfer.

Recombinant adenovirus is one of most efficient delivery vehicles for gene therapy. However, the initial enthusiasm for the use of recombinant adenovirus for gene therapy has been tempered by strong immune responses that develop to the virus and virus-infected cells. Even though recombinant adenoviruses are replication-defective, they introduce into the recipient cell, together with the gene of interest, viral genetes that might lead to fortuitous recombination if the recipient is infected by wild-type adenovirus. We propose the use of a dodecahedron made of adenovirus pentons or penton bases as an alternative vector for human gene therapy. The penton is a complex of two oligomeric proteins, a penton base and fiber, involved in the cell attachment, internalization, and liberation of virus into the cytoplasm. The dodecahedron retains many of the advantages of adenovirus for gene transfer such as efficiency of entry, efficient release of DNA from endosomes, and wide range of cell and tissue targets. Because it consists of only one or two adenovirus proteins instead of the 11 contained in an adenovirus virion and it does not contain the viral genome, it is potentially a safer alternative to recombinant adenovirus.

Adenoviridae↗
PubMed1997

Influenza virus M1 protein binds to RNA through its nuclear localization signal.

The RNA-binding activity of influenza A virus M1 protein was studied by cross-linking the protein to viral RNA followed by sequence analysis of the oligoribonucleotide bound to the protein as well as sequence analysis of the M1 peptide bound to the RNA. M1 was found to bind to RNA without any RNA sequence specificity, as verified in a series of filter-binding experiments using a large variety of nucleic acids including DNA. The peptide sequence that bound to the RNA was the RKLKR nuclear localization signal of M1. Site-specific mutagenesis of recombinant M1 showed that most of the basic residues in that region had to be mutated in order to inhibit RNA-binding. We also constructed an M1 mutant that no longer bound to RNA but which was still able to inhibit the in vitro transcription activity of isolated viral ribonucleoprotein, albeit to a lower extent. Mutation of the zinc-binding sequence had no effect on RNA-binding or transcription-inhibition activity.

Amino Acid Sequence↗
PubMed1996

Rod-like shape of vesicular stomatitis virus matrix protein.

The shape of purified matrix protein (M) of vesicular stomatitis virus was determined using biophysical techniques like analytical centrifugation, dynamic light scattering, and small-angle neutron scattering. The data obtained are consistent with a rod-like model for M protein with a length of about 100 +/- 10 A and a radius of 9 +/- 1 A. These dimensions are in agreement with the substructure of M protein aggregates and with the fine morphology of the axial channel material found inside the viral nucleocapsid coil. This morphological information was combined with CD measurements and secondary structure predictions on four vesiculovirus M proteins leading to a proposal for the structure of M protein.

Amino Acid Sequence↗
PubMed1996

Identification of amino acids controlling the low-pH-induced conformational change of rabies virus glycoprotein.

The glycoprotein (G) of rabies virus assumes at least three different conformations: the native state detected at the viral surface above pH 7, the activated state involved in the first step of the fusion process, and the fusion-inactive conformation (I). A new category of monoclonal antibodies (MAbs) which recognized specifically the I conformation at the viral surface has recently been described. These MAbs (17A4 and 29EC2) became neutralizing when the virus was preincubated at acidic pH to induce the conformational change toward the I state of G. Mutants escaping neutralization were then selected. In this study, we have investigated the fusion and the low-pH-induced fusion inactivation properties of these mutants. All of these mutants have fusion properties similar to those of the CVS parental strain, but five mutants (E282K, M44I, M44V, V392G, and M396T) were considerably slowed in their conformational change leading to the I state. These mutants allow us to define regions that control this conformational change. These results also reinforce the idea that structural transition toward the I state is irrelevant to the fusion process. Other mutations in amino acids 10, 13, and 15 are probably located in the epitopes of selecting MAbs. Furthermore, in electron microscopy, we observed a hexagonal lattice of glycoproteins at the viral surface of mutants M44I and V392G as well as strong cooperativity in the conformational change toward the I state. This finding demonstrates the existence of lateral interactions between the spikes of a rhabdovirus.

Amino Acid Sequence↗
PubMed1995

The avian adenovirus penton: two fibres and one base.

The penton capsomer of mammalian adenoviruses consists of a trimeric, long and thin fibre inserted into a pentameric base. The avian adenoviruses possess a penton which presents another symmetry mismatch: each pentameric base is associated with two fibres. Here we have studied the morphology of the penton of CELO virus, an avian adenovirus, and we have determined the sequence of both fibres, one long and one short. The short fibre is probably associated with the base in the same way as the mammalian viral fibres and we will discuss how the long fibre could be attached. The shafts of all known adenovirus fibres consist of a series of 15-residue repeats. The avian virus fibres show a more complicated and less regular shaft repeat structure with single, double and triple repeats. The sequences of the receptor binding (head) domains of both fibres are very different from all other known fibre head domains and very different from each other, suggesting that the two fibres might bind to different receptors. The genome organization of the sequenced region is rather different from that in human adenoviruses. In particular, a region homologous to the human virus E3 region was not found at the position where it normally occurs in the human virus genome.

Amino Acid Sequence↗
PubMed1995

Photolabeling identifies a putative fusion domain in the envelope glycoprotein of rabies and vesicular stomatitis viruses.

Vesicular stomatitis and rabies viruses enter cells through receptor-mediated endocytosis, followed by fusion of the viral with the endosomal membrane. The latter step is catalyzed by the viral envelope glycoprotein, which, in the low pH environment of the endosome, undergoes a conformational transition to a fusion-competent state. To investigate whether fusion competence involves the low pH exposure of a hydrophobic fusion region(s), we have applied hydrophobic photolabeling using the recently developed phospholipid analogue 1-O-hexadecanoyl-2-O-[9-[[[2-[125I]iodo-4-(trifluoromethyl-3H- diazirin-3-yl)benzyl]oxy]carbonyl] nonanoyl]-sn-glycero-3-phosphocholine ([125I]TID-PC/16) (Weber, T., and Brunner, J. (1995) J. Am. Chem. Soc. 117, 3084-3095). Rosettes of rabies virus glycoprotein, whole rabies virus, or vesicular stomatitis virus were incubated with large unilamellar vesicles containing [125I]TID-PC/16. Following reagent activation, the labeled glycoprotein was isolated and analyzed. In all cases, labeling of the glycoprotein strongly increased as the pH was lowered from 7.0 to 6.0, suggesting the exposure at acidic pH of a domain capable of interacting with membranes. To identify the labeled region(s), CNBr fragments were generated and analyzed by SDS-polyacrylamide followed by autoradiography. In rabies glycoprotein, the labeled segment was found to be contained within fragment RCr5 (residues 103-179). Glycoprotein from vesicular stomatitis virus was labeled within fragment VCr1 (residues 59-221). These results demonstrate that rhabdovirus glycoprotein contains a domain that at low pH is capable of interacting with a target membrane in a hydrophobic manner. This domain may play a role similar to that of the fusion peptide found in many other viral fusion proteins.

Amino Acid Sequence↗
PubMed1995

Electron microscopy of antibody complexes of influenza virus haemagglutinin in the fusion pH conformation.

Activation of the membrane fusion potential of influenza haemagglutinin (HA) at endosomal pH requires changes in its structure. X-ray analysis of TBHA2, a proteolytic fragment of HA in the fusion pH conformation, indicates that at the pH of fusion the 'fusion peptide' is displaced by > 10 nm from its location in the native structure to the tip of an 11 nm triple-stranded coiled coil, and that the formation of this structure involves extensive re-folding or reorganization of HA. Here we examine the structure of TBHA2 with the electron microscope and compare it with the fusion pH structure of HA2 in virosomes, HA2 in aggregates formed at fusion pH by the soluble, bromelain-released ectodomain BHA and HA2 in liposomes with which BHA associates at fusion pH. We have oriented each HA2 preparation for comparison, using site-specific monoclonal antibodies. We conclude that the structural changes in membrane-anchored and soluble HA preparations at the pH of fusion appear to be the same; that in the absence of a target membrane, the 'fusion peptide' of HA in virosomes associates with the virosome membrane so that HA2 is membrane bound at both N- and C-termini, which implies that inversion of the re-folded HA can occur; and that the structural changes observed by X-ray analysis do not result from the proteolytic digestions used in the preparation of TBHA2.

Animals↗
PubMed1995

Aggregation of VSV M protein is reversible and mediated by nucleation sites: implications for viral assembly.

Purified M protein of VSV has been reported to aggregate at low NaCl concentration. Using light scattering, analytical centrifugation, and electron microscopy (EM), we have studied this phenomenon. Our results demonstrate that self aggregation of M protein can be reversed by increasing the salt concentration. Below 250 mM NaCl, there is an equilibrium between aggregates and monomeric M protein. Most importantly, we demonstrate that aggregation only occurs in the presence of nucleation sites and that these sites are sensitive to trypsin. We have found conditions under which these nucleation sites can be eliminated, after which M remains soluble even at low salt concentration. Finally, using EM, we show that the aggregates of purified M protein share common structural aspects with the previously described internal "cigar" around which the nucleocapsid is wrapped. These new results help to explain why M is a soluble protein in the cytoplasm of the infected cell just up to the moment that it is integrated into the budding virion.

Animals↗
PubMed1995

Adenovirus fiber.

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Adenoviridae↗
PubMed1995

Structure of influenza virus ribonucleoprotein particles. II. Purified RNA-free influenza virus ribonucleoprotein forms structures that are indistinguishable from the intact influenza virus ribonucleoprotein particles.

Influenza virus nucleoprotein (NP) was purified from the virus and found to be virtually free from RNA. The morphology of the negatively stained NP was studied using electron microscopy. The monomer protein was found to be a small rod with dimensions of 62 by 35 A. However, most of the protein was found to exist in polymeric forms ranging from trimers to large structures that were morphologically indistinguishable from the intact viral RNP. Each monomer has two sites for NP-NP contacts at one extremity of the rod. The consequences of this finding for crystallization studies, for in vitro studies on NP-RNA interactions and the possible consequences for in vivo ribonucleoprotein particle assembly are discussed.

Animals↗
PubMed1995

Biological function of the low-pH, fusion-inactive conformation of rabies virus glycoprotein (G): G is transported in a fusion-inactive state-like conformation.

The glycoprotein (G) of rabies virus can assume at least three different conformations: the native (N) state detected at the viral surface above pH 7; the activated (A) hydrophobic state, which is probably involved in the first steps of the fusion process; and the fusion-inactive (I) conformation. There is a pH-dependent equilibrium between these states, the equilibrium being shifted towards the I state at low pH. It has been supposed that the transition from the N to the I state mediates membrane fusion. By using a lipid-mixing assay, we studied the kinetics of fusion and fusion inactivation for two rabies virus strains, PV and CVS. In addition, by using electron microscopy and a trypsin sensitivity assay, we analyzed the kinetics of the conformational change towards the I state for both strains. Although the PV strain fuses faster, inactivation and the conformational change of PV G occur more slowly than for the CVS strain. This suggests that the structural transition towards the I state is irrelevant to the fusion process. Immunofluorescence and immunoprecipitation experiments performed with infected cells and two different monoclonal antibodies, one specific for the N form of G and one which recognizes both the N and the I states, suggest that G is transported in an I state-like conformation through the Golgi apparatus and acquires its N structure only near or at the cell surface. We propose that the role of the I state is to avoid unspecific fusion during transport of G in the acidic Golgi vesicles.

Animals↗
PubMed1994

Structure of influenza virus RNP. I. Influenza virus nucleoprotein melts secondary structure in panhandle RNA and exposes the bases to the solvent.

The influenza virus genome consists of eight segments of negative-sense RNA, i.e. the viral (v) RNA forms the template for the mRNA. Each segment is encapsidated by the viral nucleoprotein to form a ribonucleoprotein (RNP) particle and each RNP carries its own polymerase complex. We studied the interaction of purified nucleoprotein with RNA in vitro, by using a variety of enzymatic and chemical probes for RNA conformation. Our results suggest that the nucleoprotein binds to the vRNA backbone without apparent sequence specificity, exposing the bases to the outside and melting all secondary structure. In this way, the viral polymerase may transcribe the RNA without the need for dissociating the nucleoprotein and without being stopped by RNA secondary structure, and the viral RNPs are ready to start transcription as soon as they enter the host cell.

Base Composition↗
PubMed1994

Crystals of a fragment of influenza haemagglutinin in the low pH induced conformation.

Fusion of the influenza viral membrane with the membrane of the host cell is preceded by a low pH induced conformation change in the viral haemagglutinin. A fragment, consisting of much of the stem domain of influenza haemagglutinin in the low pH induced conformation, has been crystallized by the vapour diffusion method. Several crystal forms have been obtained and the molecular packing in these crystals is discussed. Crystals suitable for the recording of high angle X-ray diffraction data grow in space group C222(1). Diffraction data have been recorded from crystals cooled to -170 degrees C in a cryoprotectant buffer.

Crystallization↗
PubMed1994

A small percentage of influenza virus M1 protein contains zinc but zinc does not influence in vitro M1-RNA interaction.

A peptide containing the CCHH motif, the putative zinc-binding sequence of influenza virus M1 protein, was found to bind zinc in a one-to-one complex with the characteristics of a typical zinc-binding peptide. Intact influenza virus also contained zinc and we show that this zinc is bound to the M1 protein in the virus. However, only a small proportion of M1 contained zinc: 4% in virus and 6 to 9% in isolated protein. One strain, B/Yamagata/16/88, consistently contained more zinc: 15 to 20% both in virus and in isolated protein. We also determined the RNA binding and transcription inhibition activities of various M1 proteins and found that the zinc content of M1 had no influence on either activity. We suggest that the zinc in M1 has a structural role in the virion other than nucleic acid binding.

Amino Acid Sequence↗
PubMed1994

Calcium is needed for the thermostability of influenza B virus neuraminidase.

The activity and stability of influenza virus neuraminidase is known to depend on the presence of calcium ions. The atomic structure of the tetrameric neuraminidase head shows two distinct Ca2+ binding sites, one with low affinity on the molecular fourfold symmetry axis and one with high affinity close to the active site in each of the monomers. Here we show that Ca is essential for the thermostability of the isolated neuraminidase tetramer. Inactivation of Ca-free neuraminidase at high temperatures is accompanied by changes in protein structure leading to protease sensitivity. More than one Ca ion per tetramer is involved in stabilization, suggesting a role for the high affinity Ca binding site and the cooperative stabilization of the subunits. Sites which are located close to the fourfold axis of the neuraminidase tetramer and which are able to bind a variety of different metal ions are also described.

Calcium↗
PubMed1994

The fibre of bovine adenovirus type 3 is very long but bent.

The sequence of the fibre of bovine adenovirus type 3 (BAd3) predicts an extremely long structure due to a large number of 15-residue repeats in the fibre shaft, the tail and head domains being similar in size to the human adenovirus fibres. The length of the fibre was confirmed using negative-strain electron microscopy of BAd3 pentons (fibre plus penton base). The fibre was found to be bent in several discrete places and the bending sites appear to correspond with irregular repeats in the shaft. We suggest that bending of the fibre is needed for the interaction of the penton base with the secondary receptors on the cell surface.

Amino Acid Sequence↗
PubMed1993

Influenza B virus neuraminidase can synthesize its own inhibitor.

BACKGROUND: Neuraminidase, one of the two surface glycoproteins of influenza virus, cleaves terminal sialic acid residues from glycolipids or glycoproteins. Its crystal structure is known at high resolution, but the mechanism of glycosyl hydrolysis remains unclear. RESULTS: We have determined the crystal structure at 1.8 A resolution of two complexes of influenza B/Beijing neuraminidase containing either the reaction product, sialic acid, or the transition state analogue inhibitor, 2,3-dehydro-2-deoxy-N-acetylneuraminic acid (DANA). The sialic acid is bound in a distorted 'boat' conformation closely resembling that of bound DANA, stabilized by a conserved tyrosine residue (Tyr408). This distortion also gives rise to a suicidal side reaction that converts sialic acid to DANA at a low rate. CONCLUSIONS: The mechanism of neuraminidase action is distinct from that of other known glycosyl hydrolases. Substrate distortion appears to be the driving force in glycosyl bond hydrolysis and the proton required for catalysis can probably be donated by water, rather than by residues in the active site, thus allowing the enzyme to operate at high pH. The side reaction converting sialic acid to DANA appears reasonably favourable, and it is unclear how this is minimized by the enzyme.

Crystallography, X-Ray↗