Fine structure of influenza A virus observed by electron cryo-microscopy.

A rapidly frozen vitrified aqueous suspension of influenza A virus was observed by high resolution electron cryomicroscopy. The influenza particles were grouped into small (diameter < 150 nm) spherical particles with well organized interiors, large spherical ones with less internal organization, and filamentous ones. Envelopes of most of the large virus particles were phospholipid bilayers, and the chromatography fraction containing these large particles was largely devoid of viral activity.

Crystallization and preliminary crystallographic data of vitelline membrane outer layer protein I, VMO-I.

The vitelline membrane outer layer protein I (VMO-I), which is isolated from the vitelline membrane outer layer of hen's eggs, has been crystallized from an acetate buffer solution by the hanging-drop method. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit cell dimensions a = 62.42 A, b = 110.

Nuclear magnetic resonance study of the interaction of T4 endonuclease V with DNA.

T4 endonuclease V catalyzes the DNA strand cleavage in the vicinity of a thymine dimer. In order to obtain insight into the specific recognition mechanism of this enzyme with a thymine photodimer within DNA, the conformations of five different DNA duplexes, [sequence: see text] with which the enzyme can interact, were studied by 1H NMR. DNA I, DNA IV, and DNA V do not contain the TT sequence or a thymine dimer and hence, are expected to bind the enzyme only in a nonspecific manner.

Crystallization and preliminary crystallographic data of the alpha-amylase inhibitors, Haim I and Paim I.

Two proteins that act as alpha-amylase inhibitors, Haim I and Paim I, were crystallized and preliminary X-ray diffraction studies on them were carried out. We also sequenced Haim I prepared from Streptomyces griseosporeus YM-25 and confirmed that it is composed of 78 amino acid residues. Crystals of Haim I were grown from ammonium sulfate solution mixed with ethanol by the vapor diffusion technique.

Response of dynamic structure to removal of a disulfide bond: normal mode refinement of C77A/C95A mutant of human lysozyme.

In order to investigate the response of dynamic structure to removal of a disulfide bond, the dynamic structure of human lysozyme has been compared to its C77A/C95A mutant. The dynamic structures of the wild type and mutant are determined by normal mode refinement of 1.5-A-resolution X-ray data.

The enhancement of the extracellular carboxyl-terminal domain of human growth hormone receptor on growth hormone dependent responses of 3T3-F442A cells.

We have expressed the carboxyl-terminal domain (C domain) of the cytokine receptor homologous (CRH) region of human growth hormone receptor (hGHR) as a protein fused with maltose binding protein (MBP) in E. coli. Following proteolytic cleavage by restriction protease factor Xa, the C domain was purified to homogeneity as a monomeric form.

Classification of doubly wound nucleotide binding topologies using automated loop searches.

A classification is presented of doubly wound alpha/beta nucleotide binding topologies, whose binding sites are located in the cleft formed by a topological switch point. In particular, the switch point loop nearest the N-terminus is used to identify specific structural classes of binding protein. This yields seven structurally distinct loop conformations, which are subsequently used as motifs for scanning the Protein Data Bank.

Crystal structure of Escherichia coli RNase HI in complex with Mg2+ at 2.8 A resolution: proof for a single Mg(2+)-binding site.

To obtain more precise insight into the Mg(2+)-binding site essential for RNase HI catalytic activity, we have determined the crystal structure of E. coli RNase HI in complex with Mg2+. The analyzed cocrystal, which is not isomorphous with the Mg(2+)-free crystal previously refined at 1.

A synthetic model of collagen structure taken from bovine macrophage scavenger receptor.

A putative collagen structure from macrophage scavenger receptors binds to a wide range of ligands. In order to elucidate the ligand's binding mode, this collagen structure was constructed using short peptides. This was accomplished by the reaction of a tri-bromoacetylated branched peptide with a purified unprotected 25-residue peptide, which contained Cys, 4 repeats of triplet, Gly-Pro-Hyp, and 12 residues from the bovine of the N-terminus cross-linked tripeptide show that it forms a collagen structure below 10 degrees C and an extended structure at high temperature with a midpoint of 20 degrees C.

Development of pseudoenergy potentials for assessing protein 3-D-1-D compatibility and detecting weak homologies.

Recent approaches to the 3-D-1-D compatibility problem have tried to predict protein 3-D structure from sequence. One of the critical factors in this issue is the evaluation of fitness between a given 3-D structure and any sequence mounted on it. We have developed an evaluation function composed of four terms, side chain packing, hydration, hydrogen bonding and local conformation potentials, which were empirically derived from 101 proteins of known structure.

Crystal structures of ribonuclease HI active site mutants from Escherichia coli.

In order to investigate the relationships between the three-dimensional structure and the enzymic activity of E. coli RNase HI, three mutant proteins, which were completely inactivated by the replacements of three functional residues, Asp10 by Asn (D10N), Glu48 by Gln (E48Q), and Asp70 by Asn (D70N), were crystallized. Their three-dimensional structures were determined by x-ray crystallography.

Binding of nucleic acids to E. coli RNase HI observed by NMR and CD spectroscopy.

To clarify the mechanism by which the RNA portion of a DNA/RNA hybrid is specifically hydrolyzed by ribonuclease H (RNase H), the binding of a DNA/RNA hybrid, a DNA/DNA duplex, or an RNA/RNA duplex to RNase HI from Escherichia coli was investigated by 1H-15N heteronuclear NMR. Chemical shift changes of backbone amide resonances were monitored while the substrate, a hybrid 9-mer duplex, a DNA/DNA 12-mer duplex, or an RNA/RNA 12-mer duplex was titrated. The amino acid residues affected by the addition of each 12-mer duplex were almost identical to those affected by the substrate hybrid binding, and resided close to the active site of the enzyme.

A study of structural determinants in the interleukin-1 fold.

The structures of interleukin-1 beta, basic fibroblast growth factor and Erythrina trypsin inhibitor have been analysed in order to determine whether the hydrophobic core remains conserved, even when the structures have extremely low sequence similarities. We find that there are significant differences in the way each protein achieves a satisfactory arrangement of core residues and that positions which contribute to the core of one structure are not guaranteed to contribute to the integrity of another. Furthermore, the side-chain packing arrangements of these core residues vary significantly between the three structures.

PDI and glutathione-mediated reduction of the glutathionylated variant of human lysozyme.

A mutant human lysozyme, designated as C77A-a, in which glutathione is bound to Cys95, has been shown to mimic an intermediate in the formation of a disulfide bond during folding of human (h)-lysozyme. Protein disulfide isomerase (PDI), which is believed to catalyze disulfide bond formation and associated protein folding in the endoplasmic reticulum, attacked the glutathionylated h-lysozyme C77A-a to dissociate the glutathione molecule. Structural analyses showed that the protein is folded and that the structure around the disulfide bond, buried in a hydrophobic core, between the protein and the bound glutathione is fairly rigid.

Molecular evolution of biotin-dependent carboxylases.

Amino-acid sequences of three functional units from various biotin-dependent carboxylases, biotin carboxylase, biotin-carboxyl-carrier protein and carboxyl transferase, were investigated by computer-assisted sequence comparison to obtain information about the structure, function, and molecular evolution of the enzymes. Biotin-dependent carboxylases, except transcarboxylase and oxaloacetate decarboxylase which lack biotin carboxylase, exert their catalytic activities through the three functional units. The three functional units correspond with functional domains or subunits of the enzymes, and the genetic information for the units is encoded in different ways from enzyme to enzyme.

X-Neu5Ac: a novel substrate for chromogenic assay of neuraminidase activity in bacterial expression systems.

A chromogenic substrate 1, 5-bromo-4-chloroindol-3-yl 5-acetamido-3,5-dideoxy-alpha-D-glycero-D-galacto-2-nonulopyranosidon ic acid (X-Neu5Ac), has been synthesized to facilitate the screening of bacterial colonies or plaques for the detection of either natural or mutant neuraminidase activity. Substrate 1 was hydrolyzed by neuraminidase isolated from Clostridium perfringens to release a halogenated indol-3-ol 2 that undergoes rapid aerobic oxidation to form the dark blue pigment, 5,5'-dibromo-4,-4'-dichloroindigo 3. Preliminary kinetic studies indicate that this compound is a good substrate (Km 0.

Cooperative stabilization of Escherichia coli ribonuclease HI by insertion of Gly-80b and Gly-77-->Ala substitution.

The insertion of a Gly residue (designated as Gly-80b) between the C-cap of the alpha II-helix (Gln-80) and the N-cap of the alpha III-helix (Trp-81) in Escherichia coli ribonuclease HI enhances the protein stability by 0.4 kcal/mol in delta G (Kimura, S., Nakamura, H.

Stabilization of Escherichia coli ribonuclease HI by cavity-filling mutations within a hydrophobic core.

The crystal structure of Escherichia coli ribonuclease HI has a cavity near Val-74 within the protein core. In order to fill the cavity space, we constructed two mutant proteins, V74L and V74I, in which Val-74 was replaced with either Leu or Ile, respectively. The mutant proteins are stabilized, as revealed by a 2.

Prodrug activation via catalytic antibodies.

Prodrug activation via antibodies was examined by using the antibiotic chloramphenicol as a model drug. Based on the conformational change between substrate and product, this antibody-catalyzed reaction was designed to prevent product inhibition, thus enhancing turnover. Antibodies elicited against a phosphonate transition-state analogue were found to catalyze hydrolysis of a nonbioactive chloramphenicol monoester as a prodrug at a significantly higher rate above the uncatalyzed background reaction to regenerate chloramphenicol as a parent molecule.

Indication of possible post-translational formation of disulphide bonds in the beta-sheet domain of human lysozyme.

Lysozyme has two distinct folding domains, and in most molecules the alpha-helical domain folds more quickly than the beta-sheet domain in vitro [Radford, Dobson and Evans (1992) Nature (London) 358, 302-307]. In order to investigate the relationship between the formation of disulphide bonds and protein folding in vivo, we carried out cysteine scanning mutagenesis to shift positions of the disulphide bonds in both the alpha-helical and beta-sheet domains of human lysozyme. Of the constructed mutants (nine in the beta-sheet domain and 13 in the alpha-helical domain), the mutant L79CC81A, in which Leu-79 and Cys-81 in the beta-sheet domain were replaced by Cys and Ala respectively, was secreted by yeast.

Prediction of a novel topology in the N-terminal, 14 kDa fragment of Ada protein.

Previously determined protein structures have been analysed, in order to find folding motifs similar to that proposed by NMR spectroscopy, for the N-terminal, 14 kDa fragment of the Ada protein. The analyses reveal only limited similarities with the NMR-derived structural data and strongly suggest that this region of the Ada protein adopts a previously unobserved topology. Characteristic structural features, which arise from the inferred chain connectivity, are examined through comparisons with other structures.

Folding topology and DNA binding of the N-terminal fragment of Ada protein.

Three amino terminal fragments of Escherichia coli Ada protein (39 kDa) with different molecular masses (14 kDa, 16 kDa and 20 kDa) were prepared in large quantities from an E. coli strain harboring plasmids constructed for the overproduction of the truncated proteins. The three fragments can be methylated to an extent similar to that of the intact molecule.

Structural and functional analyses of the Arg-Gly-Asp sequence introduced into human lysozyme.

To determine the functional conformation of the Arg-Gly-Asp (RGD) sequence, we have constructed mutant proteins by inserting 4-12 amino acid residues from the RGD region of human fibronectin between Val74 and Asn75 of human lysozyme. RGDS-, GRGDSP-, TGRGDSPA-, VTGRGDSPAS-, and AVTGRGDS-PASS-introduced mutant lysozymes were expressed in yeast, purified, and designated as RGD4, -6, -8, -10, and -12, respectively. Using baby hamster kidney cells, RGD8, RGD10, and RGD12 were shown to possess high cell adhesion activity nearly equal to 10% of human vitronectin activity.