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R W Ruigrok

Publications and source records attributed to R W Ruigrok.

At least 55 records · Page 3Linked to original sources
PubMed1993

The inactive form of recA protein: the 'compact' structure.

When recA protein is enzymatically inactive in vitro, it adopts a more compact helical polymer form than that of the active protein polymerized onto DNA in the presence of ATP. Here we describe some aspects of this structure. By cryo-electron microscopy, a pitch of 76 A is found for both the self-polymer and the inactive complex with ssDNA. A smaller pitch of 64 A is observed in conventional electron micrographs. The contour length of complexes with ssDNA was used to estimate the binding stoichiometry in the compact complex, 6 +/- 1 nt/recA. In addition, the compact structure was observed in vivo in Escherichia coli: inclusion bodies produced upon induction of recA expression in an overproducing strain have a fibrous morphology with the structural parameters of the compact polymer.

Bacteriophage T4↗
PubMed1993

Adenovirus type 40 virions contain two distinct fibers.

Human subgroup F adenoviruses, types 40 and 41, have two genes that could specify different fiber proteins, a long fiber with 21 or 22 pseudorepeat motifs in the shaft, and a short fiber with 12 motifs. We show that for adenovirus type 40, both proteins are expressed from separate late regions of the genome. They are incorporated into the virion with only one fiber per penton base, unlike avian adenoviruses which have two fibers extending from each penton. Comparison of known adenovirus fiber sequences suggests that the two fibers in adenovirus 40 and 41 arose through an external recombination event rather than having evolved from each other directly. Two alternative fibers on the virion may imply the existence of two distinct receptors.

Adenoviruses, Human↗
PubMed1993

Comparison of structure and sequence of influenza B/Yamagata and B/Beijing neuraminidases shows a conserved "head" but much greater variability in the "stalk" and NB protein.

In 1988 the B/Yamagata/16/88 influenza virus appeared, which was antigenically quite different from the other B viruses circulating at that time. Neuraminidase heads of this strain were purified, crystallized, and analyzed by X-ray crystallography and compared with the structure of B/Beijing/1/87 neuraminidase. Only two point mutations could be detected in the "head" of the molecule leading to local rearrangement of amino acid side-chains. The nucleotide sequence, however, revealed significant differences in the stalk region and in the NB protein.

Amino Acid Sequence↗
PubMed1993

Mechanisms of rabies virus neutralization.

The number of immunoglobulins necessary to neutralize rabies virus (CVS strain) was estimated using IgG and IgM monoclonal antibodies (MAb) specific to the three antigenic sites of the glycoprotein. It was estimated that below 130 IgG or 30 IgM bound per virions, infectivity was totally preserved. Neutralization occurred for an average of 1 or 2 IgG for 3 spikes and 1 IgM for 9 to 10 spikes on the virus surface. Saturation was obtained for 1 to 3 IgG per spike, depending on the antibody, and 1 IgM for 4 to 5 spikes. This result was confirmed by electron microscopy. Neutralization-resisting mutants which continued to fix the selecting MAb in ELISA were also investigated. In two cases, the lack of neutralization was due to the fact that the maximum number of immunoglobulins bound per virion was below the neutralizing dose. In one case, however, the mutant was able to fix the same number of IgG as the parental strain and was not neutralized, even at saturation. The capacity of the antibodies to reduce the attachment of the virus onto BSR cells was also examined. Every intermediate between no inhibition of the attachment and inhibition by a factor of 20 was found; even in this last case, inhibition of attachment was insufficient to explain the extent of neutralization. No correlation was found between the antigenic site recognized by the antibody and the level of inhibition. IgM inhibited attachment more than IgG and one IgG2b antibody did not inhibit attachment at all. The fusion of virions saturated with this antibody with artificial liposomes was totally inhibited, either specifically or because virus-antibody complexes did not attached to the liposomes.

Antibodies, Monoclonal↗
PubMed1993

Vesicular stomatitis virus M protein may be inside the ribonucleocapsid coil.

Vesicular stomatitis virus is an enveloped virus with an external glycoprotein G and a nucleocapsid that form, together with the M protein, a tight helically coiled structure: the skeleton. Negative staining and immunoelectron microscopy studies on skeleton preparations were performed to determine the localization of the M protein. These studies have resulted in a new model for the structure of rhabdoviruses in which the nucleocapsid is wound around a core containing the M protein. This model predicts contact between M and lipid only at the extreme ends of the skeleton, which is confirmed by skeleton-liposome binding studies.

Capsid↗
PubMed1993

Low-pH conformational changes of rabies virus glycoprotein and their role in membrane fusion.

Fusion of rabies virus with membranes occurs at acidic pH and is mediated by the viral spike glycoprotein (G). In this paper, we provide the basis for a description of structural transitions associated with exposure to low pH and of their role in membrane fusion. First, we have extended previous studies of fusion kinetics and we have shown that low-pH inhibition of fusion is detectable at 0.5 pH units higher than fusion. Second, low-pH-induced conformational changes were analyzed by using electron microscopy and monoclonal antibody binding assays. The existence of a pH-dependent equilibrium between the native and a low-pH inactive conformation was demonstrated. Third, besides these two conformations, we, using the fluorescent probe ANS (8-anilino-1-naphthalenesulfonic acid), provide evidence for the existence of a transient third state which appears to be more hydrophobic than the native state. Our results suggest that this transient state is responsible for viral aggregation at low pH and could play a role in the first steps of the fusion mechanism.

Anilino Naphthalenesulfonates↗
PubMed1992

New triple-helical model for the shaft of the adenovirus fibre.

The adenovirus fibre is a trimeric protein with a globular head on a long thin shaft that projects from the twelve fivefold vertices of the virion. The shaft region of the fibre primary sequence has a unique pseudo-repeating motif of 15 residues. Using constraints derived from sequence analysis, the trimeric nature of the fibre, the experimental determination of the shaft length and general knowledge about protein structure, an atomic model of the fibre shaft has been constructed by computer modelling techniques. In the final model the three monomers form a left-handed triple-helical structure with threefold symmetry and with successive 15-residue repeats on the same chain related by an axial rise of 13.1 A and a left-handed azimuthal rotation of close to 300 degrees. Three threefold related beta-sheets with short strands are formed by inter-monomer main-chain hydrogen bonds giving rise to superhelical ribbons covering the surface of the shaft. The model satisfies criteria of extensive hydrogen bonding, reasonable backbone torsion angles, burial of most hydrophobic residues and good packing of the hydrophobic core. Furthermore, the model is consistent with the observed shaft length of about 290 A and its calculated X-ray fibre diffraction patterns shows the characteristic features found in the diffraction pattern of crystals of fibre, notably layer lines with a spacing of about 1/26 A-1 and strong meridional intensity at 1/4.4 A-1.

Adenoviruses, Human↗
PubMed1992

Activation of recA protein. The open helix model for LexA cleavage.

RecA protein is induced by the binding of DNA and ATP to become active in the hydrolysis of ATP and the cleavage of repressors. These reactions appear to depend on the structural state of the protein polymerized along the DNA, i.e. a helical coat of six RecA per turn of 95 to 100 A pitch. In support of this model of the active conformation, it was shown that high concentrations of salt also induce this helical polymerized state as well as the enzymatic activities. Here, we describe that, in vitro and with the non-hydrolyzable analogue ATP gamma S, RNA and heparin can also induce both the structural transition and the enzymatic activation of RecA to LexA cleavage in accordance with the model. RNA and heparin do not support the reaction in the presence of ATP, and they do not induce the hydrolysis of ATP either, suggesting that, in contrast to ATP gamma S, the nucleotide is not bound stably enough, and that the combined affinities of polynucleotide and ATP actually modulate the discrimination of RecA for the various possible inducers in vivo.

Adenosine Triphosphate↗
PubMed1992

The 2.2 A resolution crystal structure of influenza B neuraminidase and its complex with sialic acid.

Influenza virus neuraminidase catalyses the cleavage of terminal sialic acid, the viral receptor, from carbohydrate chains on glycoproteins and glycolipids. We present the crystal structure of the enzymatically active head of influenza B virus neuraminidase from the strain B/Beijing/1/87. The native structure has been refined to a crystallographic R-factor of 14.8% at 2.2 A resolution and its complex with sialic acid refined at 2.8 A resolution. The overall fold of the molecule is very similar to the already known structure of neuraminidase from influenza A virus, with which there is amino acid sequence homology of approximately 30%. Two calcium binding sites have been identified. One of them, previously undescribed, is located between the active site and a large surface antigenic loop. The calcium ion is octahedrally co-ordinated by five oxygen atoms from the protein and one water molecule. Sequence comparisons suggest that this calcium site should occur in all influenza A and B virus neuraminidases. Soaking of sialic acid into the crystals has enabled the mode of binding of the reaction product in the putative active site pocket to be revealed. All the large side groups of the sialic acid are equatorial and are specifically recognized by nine fully conserved active site residues. These in turn are stabilized by a second shell of 10 highly conserved residues principally by an extensive network of hydrogen bonds.

Amino Acid Sequence↗
PubMed1992

Rabies virus glycoprotein is a trimer.

The oligomerization state of the rabies virus envelope glycoprotein (G protein) was determined using electron microscopy and sedimentation analysis of detergent solubilized G. Most of the detergents used in this study solubilized G in a 4 S monomeric form. However, when CHAPS was used, G had a sedimentation coefficient of 9 S. This high sedimentation coefficient allowed its further separation from M1 and M2. Using electron microscopy of negatively stained samples, we studied the morphology of G on virus and after detergent extraction. End-on views of G on virus clearly showed triangles consisting of three dots indicating the trimeric nature of native G. End-on views of CHAPS-isolated G showed very similar triangles confirming that, using this detergent, G was solubilized in its native trimeric structure. Electron microscopy also showed that G had a "head" and a "stalk" and provided the basis for a low-resolution model of the glycoprotein structure.

Antigens, Viral↗
PubMed1992

Low pH deforms the influenza virus envelope.

Influenza virus membrane fusion is induced by low pH, which triggers an irreversible conformational change in the viral haemagglutinin (HA). The result of this change is the extrusion of the HA fusion peptide, after which it may act in the fusion of virus and endosomal membranes. Here we describe electron microscopic observations on low pH-treated virus after negative staining or cryo-electron microscopy of virus in the frozen hydrated state. The results indicate a destabilization of the virus membrane at low pH that can be reversed by returning the pH to neutral.

Hydrogen-Ion Concentration↗
PubMed1991

Human adenovirus serotype 3 fiber protein. Comparison of native and recombinant proteins.

We were able to isolate viral fiber and penton from Ad3-infected KB cells using for their detection antibodies obtained against recombinant Ad3 fiber. The native material was examined by electron microscopy and the characteristic fiber shape of a shaft terminated by a globular head was observed. The native fiber was compared with two recombinant fibers synthesized in Escherichia coli cells. One, the Ad3 fiber protein expressed in E. coli with a 14-amino acid NH2-terminal fusion peptide, under the control of the T7 promoter has been described previously. The second is a recombinant Ad3 fiber without the fusion peptide (recAd3fib), expressed in the same system. As with the fusion protein recAd3fib was found to be insoluble upon expression. It was solubilized in 6 M urea and the gradual removal of urea during the purification cycle led to a soluble preparation. Biochemical and biophysical studies show that, similarly to fusion fiber, recAd3fib self-assembles as trimers in prokaryotic cells. Electron microscopy shows that, whereas the fusion fiber consists of a population of heterogeneous particles, recAd3fib has the characteristic morphology and size of the Ad3 trimeric native fiber. Small angle neutron scattering gives a molecular weight consistent with a trimeric fiber and a radius of gyration consistent with the dimensions derived from electron microscopy. These results suggest that the fusion peptide at the NH2 terminus prevents correct protein folding. They also indicate that after solubilization with urea and subsequent renaturation a correctly folded eukaryotic oligomeric protein can be produced in E. coli.

Adenoviridae↗
PubMed1991

Activation of recA protein: the pitch of the helical complex with single-stranded DNA.

The complex of recA protein with single-stranded DNA in the presence of ATP is the active species in the three enzymatic activities of recA: the initiation of strand exchange, the hydrolysis of ATP and the cleavage of repressors. Here we find by cryo-electron microscopy of unstained and unfixed samples that the helical structure of the protein coat in this complex differs slightly but significantly from the structure in the complex with double-stranded DNA. We discuss how the larger pitch of the complex with single strands (100 +/- 2 A compared with 95 +/- 2 A with double strands) could contribute to its higher enzymatic activity.

Adenosine Triphosphate↗
PubMed1991

Sequence and crystallization of influenza virus B/Beijing/1/87 neuraminidase.

Influenza B/Beijing/1/87 neuraminidase heads were isolated from virus via trypsin digestion and characterized by PAGE, N-terminal sequencing, electron microscopy, and enzyme activity. The heads were crystallized into two crystal forms; tetragonal plates, like other neuraminidase crystals described before, that diffract to medium resolution (3 A) and a new form consisting of trigonal prisms or needles that diffract to high resolution (at least 2 A). The gene segment coding for neuraminidase was sequenced and compared with the neuraminidase sequence of B/Lee/40. The deduced amino acid sequences for neuraminidase showed only a 7% difference, whereas those for the NB proteins differed by 20%.

Amino Acid Sequence↗
PubMed1991

The specific inhibition of influenza A virus maturation by amantadine: an electron microscopic examination.

Amantadine specifically inhibits the release of virus particles from cells infected with the Rostock (H7N1) strain of influenza A virus, apparently as a consequence of a membrane protein M2-mediated conversion of haemagglutinin (HA) to its low pH conformation. Electron microscopic observations, together with immunogold labelling, showed that amantadine action does not alter the distribution of HA on the cell surface nor does it prevent the formation of budding virus particles. It was not possible, however, to discern whether low pH HA inhibited the final stage in virus maturation, i.e. pinching off, or simply prevented release of fully formed particles.

Amantadine↗
PubMed1990

Structure of adenovirus fibre. II. Morphology of single fibres.

Adenovirus type 2 fibres in crystals appear to be significantly longer than found previously (accompanying paper). We therefore examined isolated fibre by electron microscopy and measured a length of 370 A, consistent with the length found in the crystals. The specific N-terminal structure of the fibre caused a heterogeneity in the length that may at least partially explain the values of 280 to 310 A published previously. Green et al. described a 15 amino acid repeat in the primary structure of the shaft of the fibre thought to be associated with the specific three-dimensional folding of the shaft. We compared the adenovirus type 2 (with 22 repeats) and type 3 (with 6 repeats) fibre lengths and derived a contribution of 13.2 A to the length of the shaft per 15 amino acid repeat. Specific morphological features of the fibre are discussed in relation to its amino acid sequence.

Capsid↗
PubMed1990

Complexes of RecA protein in solution. A study by small angle neutron scattering.

RecA complexes on DNA and self-polymers were analysed by small-angle neutron scattering in solution. By Guinier analysis at small angles and by model analysis of a subsidiary peak at wider angles, we find that the filaments fall into two groups: the DNA complex in the presence of ATP gamma S, an open helix with pitch 95 A, a cross-sectional radius of gyration of 33 A and a mass per length of about six RecA units per turn, which corresponds to the state of active enzyme; and the compact form (bound to single-stranded DNA in the absence of ATP, or binding ATP gamma S in the absence of DNA, or just the protein on its own), a helical structure with pitch 70 A, cross-sectional radius of gyration 40 A and mass per length about five RecA units per turn, which corresponds to the conditions of inactive enzyme. The results are discussed in the perspective of unifying previous conflicting structural results obtained by electron microscopy.

Adenosine Triphosphate↗