Direct visualisation of plasmid DNA in individual chromatography adsorbent particles by confocal scanning laser microscopy.

Confocal microscopy was used for the measurement of plasmid DNA adsorbed to individual adsorbent particles intended for anion-exchange and triple helix affinity chromatography. Plasmid DNA was visualized with the fluorescent dye YOYO-1, that forms a highly fluorescent complex with double stranded DNA. Confocal images were translated into fluorescence intensity profiles and the distribution of plasmid DNA in the particles was measured. The results that adsorption of plasmid DNA mainly takes place in an outer layer of the particles. The described procedure can also be advantageously used to demonstrate triple helix formation between plasmid DNA and immobilized oligonucleotides.

Studies on the active site of deacetoxycephalosporin C synthase.

The Fe(II) and 2-oxoglutarate-dependent dioxygenase deacetoxycephalosporin C synthase (DAOCS) from Streptomyces clavuligerus was expressed at ca 25 % of total soluble protein in Escherichia coli and purified by an efficient large-scale procedure. Purified protein catalysed the conversions of penicillins N and G to deacetoxycephems. Gel filtration and light scattering studies showed that in solution monomeric apo-DAOCS is in equilibrium with a trimeric form from which it crystallizes. DAOCS was crystallized +/-Fe(II) and/or 2-oxoglutarate using the hanging drop method. Crystals diffracted to beyond 1.3 A resolution and belonged to the R3 space group (unit cell dimensions: a=b=106.4 A, c=71.2 A; alpha=beta=90 degrees, gamma=120 degrees (in the hexagonal setting)). Despite the structure revealing that Met180 is located close to the reactive oxidizing centre of DAOCS, there was no functional difference between the wild-type and selenomethionine derivatives. X-ray absorption spectroscopic studies in solution generally supported the iron co-ordination chemistry defined by the crystal structures. The Fe K-edge positions of 7121.2 and 7121.4 eV for DAOCS alone and with 2-oxoglutarate were both consistent with the presence of Fe(II). For Fe(II) in DAOCS the best fit to the Extended X-ray Absorption Fine Structure (EXAFS) associated with the Fe K-edge was found with two His imidazolate groups at 1.96 A, three nitrogen or oxygen atoms at 2.11 A and one other light atom at 2.04 A. For the Fe(II) in the DAOCS-2-oxoglutarate complex the EXAFS spectrum was successfully interpreted by backscattering from two His residues (Fe-N at 1.99 A), a bidentate O,O-co-ordinated 2-oxoglutarate with Fe-O distances of 2.08 A, another O atom at 2.08 A and one at 2.03 A. Analysis of the X-ray crystal structural data suggests a binding mode for the penicillin N substrate and possible roles for the C terminus in stabilising the enzyme and ordering the reaction mechanism.

Detection and characterization of oligosaccharides in column effluents using surface plasmon resonance.

Surface plasmon resonance was used to detect oligosaccharides derived from glycoproteins. No sample derivatization or labeling is required for this technique. Sensor surfaces were prepared by immobilizing lectins. In the case of Sambucus nigra agglutinin reactive to terminal sialic acid or Ricinus communis agglutinin preferring terminal beta-linked galactose, femtomole levels of oligosaccharides could be detected. Using this affinity detector system, oligosaccharides and glycopeptides from a chromatographic separation on a gel filtration column were detected either by on-line monitoring or by analyzing the fractions individually.

Determination of the interactions between lectins and glycoproteins by surface plasmon resonance.

A simple and rapid analytical method for detecting interactions between oligosaccharides of glycoproteins and different lectins was studied by surface plasmon resonance using a biosensor (BIAcore). The interactions of three lectins, Sambucus sieboldiana agglutinin (SSA), Ricinus communis agglutinin I (RCA I) and Concanavalin A (Con A) for fetuin and digested fetuins with glycosidases, asialo-, agalacto-, and aglucosamino-fetuin, were investigated as a model system. These fetuins were immobilized to the matrix of of the sensor chip and the lectins were injected into the sensor chip cartridge. The association and dissociation reactions could be monitored as resonance signals in real time. The interactions with lectins significantly changed as the oligosaccharides of fetuin were trimmed. The interactions between fetuin and SSA, asialofetuin and RCA I, and aglucosaminofetuin and Con A show the highest affinity properties, respectively. The association constants of these lectins were estimated to be 1.4 x 10(7), 1.9 x 10(8) and 5.3 x 10(7) (M-1), respectively. These results suggested that the interactions between lectins and glycoproteins could be well defined in real time and kinetically, and that the partial structure of oligosaccharides of glycoproteins can be estimated by determination of the interactions with various lectins after glycosidase digestions using the biosensor.

2.2 A resolution structure of the amino-terminal half of HIV-1 reverse transcriptase (fingers and palm subdomains).

BACKGROUND: HIV-1 reverse transcriptase (RT) catalyzes the transformation of single-stranded viral RNA into double-stranded DNA, which is integrated into host cell chromosomes. The molecule is a heterodimer of two subunits, p51 and p66. The amino acid sequence of p51 is identical to the sequence of the amino-terminal subdomains of p66. Earlier crystallographic studies indicate that the RT molecule is flexible, which may explain the difficulty in obtaining high-resolution data for the intact protein. We have therefore determined the structure of a fragment of RT (RT216), which contains only the amino-terminal half of the RT molecule ('finger' and 'palm' subdomains). RESULTS: The crystal structure of RT216 has been refined at 2.2 A resolution to a crystallographic R-value of 20.8%. The structure is very similar to that of the corresponding part of the p66 subunit in the p66/p51 heterodimer, although there is a small difference in the relative orientation of the two subdomains compared with the structure of an RT-DNA-antibody fragment complex. There are a large number of stabilizing contacts (mainly hydrogen bonds and hydrophobic interactions) between the subdomains. The locations of conserved amino acids and the position of some important drug-resistant mutations are described. CONCLUSIONS: The RT216 structure provides detailed three-dimensional information of one important part of HIV-1 RT (including the critical active site residues). We propose a model to explain the inhibitory effect of non-nucleoside inhibitors, which partially accounts for their effect in terms of conformational changes of active site residues.

Disruption of a salt bridge between Asp 488 and Lys 465 in HIV-1 reverse transcriptase alters its proteolytic processing and polymerase activity.

The conserved aspartic acid residue 488 in the RNase H domain of HIV-1 reverse transcriptase (RT) was mutated to alanine. RT was expressed in Escherichia coli alone or with the entire pol-gene polyprotein consisting of proteinase, RT, and integrase and processed by the HIV-1 proteinase in the bacterial cell. Expression of mutant RT together with the proteinase resulted in an overproduction of RT p51 vs p66. The mutation also altered the conformation of the RT p66/p51 heterodimer as shown by the loss of binding of monoclonal antibodies to mutant RT in ELISA. Crystallographic data shows that a salt bridge exists between Asp 488 and Lys 465 of RNase H which stabilizes the uncleavable form of RT p66, and that substitution of Asp for Ala would prevent the formation of this salt bridge. Our results indicate that disruption of this salt bridge through mutation of Asp 488 interferes with the conformational changes that regulate the limited processing of p66 to 51 by the virus proteinase. Homology data suggest that such a bridge may be present in other lentiviruses. The mutation introduced caused a moderate decrease in both the RNase H activity and the polymerase activity of RT, indicating that the proper folding of the RNase H domain of RT is necessary to achieve full polymerase activity.

Increased yield of homogeneous HIV-1 reverse transcriptase (p66/p51) using a slow purification approach.

A chromatographic procedure to purify recombinant reverse transcriptase (RT) from human immunodeficiency virus-1 is reported. A bacterial system which expressed large amounts of p66 RT polypeptide was used. The purification scheme was optimized for high-yield production of homogeneous p66/p51 RT using a combination of chromatographic matrices in the following order: Q-Sepharose, heparin-Sepharose, phenyl-Sepharose, S-Sepharose, Poly(A)-Sepharose and Q-Sepharose. The p66 polypeptide remained intact after the first chromatographic step on Q-Sepharose, where it was recovered in the non-adsorbed fraction. A high yield of p66/p51 RT was obtained when the time from application to elution of heparin-Sepharose in the second chromatographic step was prolonged. Phenyl-Sepharose was used in the next chromatographic step to separate the heterodimeric forms of RT from p66 RT on the basis of hydrophobicity. The chromatography on S-Sepharose resolved the major heterodimeric form, p66/p51, from other heterodimeric variants. Further purification was done by affinity chromatography on Poly(A)-Sepharose followed by anion-exchange chromatography on Q-Sepharose. Amounts of 25-35 mg of the pure heterodimer p66/p51 RT were recovered from 50 g of bacterial cells.

Kinetics of different human immunodeficiency virus type 1 reverse transcriptases resistant to human immunodeficiency virus type 1-specific reverse transcriptase inhibitors.

The human immunodeficiency virus type 1 (HIV-1)-specific reverse transcriptase (RT) inhibitors [tetrahydroimidazo[4,5,1-jk] [1,4]benzodiazepin-2(1H)-one and -thione (TIBO), 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine, nevirapine, pyridinone, bis(heteroaryl)piperazine, etc.] are potent inhibitors of HIV-1 replication in cell culture. The rapid emergence of drug-resistant escape mutants in vitro (cell culture) and in vivo (patients) is predominantly linked to the Y181C mutation. Because amino acids Y181 and Y188 appear to be located within the drug binding site of the enzyme, we studied the impact of mutations of both amino acids on the enzyme kinetics and on the susceptibility of the enzyme to different HIV-1-specific RT inhibitors. Mutations Y181C, Y181I, and Y188L led to reduced sensitivity, albeit of varying extents, to all HIV-1-specific RT inhibitors. No resistance was observed to 2',3'-dideoxyguanosine 5'-triphosphate or phosphonoformic acid. The kcat of the Y181C mutant was similar to that of the wild-type RT (18 sec-1 x 10(-3)). The catalytic constant of the Y181I mutant was 6-fold higher and that of the Y188L mutant was 6-fold lower. Whereas TIBO displayed a linear mixed-type (noncompetitive) inhibition with respect to the deoxynucleotide substrate when wild-type p66/p51 was used, the pattern of inhibition became competitive or uncompetitive with Y181C or Y181I, respectively. Thus, the TIBO binding site of HIV-1 RT seems to be functionally and/or spatially related to the natural deoxynucleoside triphosphate binding site.

Purification, characterization and crystallization of recombinant HIV-1 reverse transcriptase.

The pol I gene from HIV-1 encoding the protease, reverse transcriptase (RT) and endonuclease has been expressed in Escherichia coli. By modifying the fermentation conditions and developing a new purification scheme, the yield of purified RT has been increased substantially compared with that obtained in an earlier procedure. The expressed RT was purified to homogeneity by ammonium sulphate fractionation followed by chromatography on DEAE Sepharose, Heparin Sepharose, S Sepharose and Poly(A)-Sepharose. The purified HIV-RT is a heterodimer (p66/p51) with an isoelectric point close to 8 and with a tendency to aggregate. The proteolytic product (p51), corresponding to the N-terminal end of the RT molecule, was isolated and identified, as were also some bacterial polypeptides that co-elute with HIV-RT during the early stages of the purification. The heterodimer was crystallized in several morphological forms using the vapour-diffusion hanging drop technique. To concentrate the protein and to change the buffer for crystallization, reverse-salt-gradient chromatography and micropreparative columns were used. The best crystals diffracted to 9 A resolution. The best crystals of native RT diffracted to 9 A resolution and in complex with nucleic acids to 4.5 A resolution (using a rotating anode X-ray source).

Immunological characterization of the human immunodeficiency virus type 1 reverse transcriptase protein by the use of monoclonal antibodies.

Eighteen monoclonal antibodies (MAbs) directed against the purified human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) protein were produced. The antibodies were characterized by competitive ELISAs and Western blot experiments, and with nested, nine amino acid long peptides representing the whole 560 amino acid RT protein. By ELISA, the MAbs react with a minimum of seven epitopes of the protein. Four of the epitopes were located on the N-terminal 51K subunit and the remaining three epitopes were located at the C-terminal end of the protein. Using synthetic peptides, two epitopes at the N-terminal part were located at amino acids 294 to 302 and 350 to 354, respectively, from the N-terminal start of the protein. One epitope was located at amino acids 442 to 450, just after the cleavage site between the N-terminal and C-terminal subunit at position 440. Antibodies located at amino acids 294 to 302 could inhibit the RT enzymic activity of the protein. Two other MAbs, directed at the N-terminal and C-terminal parts of the protein, could also inhibit RT activity.

Carrier bound templates for single tube reverse transcriptase assays and for combined purification and activity analyses, with special reference to HIV.

Polyriboadenosine (prA) was coupled to polycarbonate macrobeads or magnetic beads. The efficiency of the beads and of prA-Sepharose, after priming with odT, as templates in activity assays of purified AMV- and HIV-reverse transcriptase (RT), using [125I]iododeoxyuridine-triphosphate as substrate, was studied. Although the use of immobilized templates, compared with soluble template, resulted in a decreased total molar turnover, it did not affect the sensitivity of the assay for detecting RT. The utility of the new assay was analyzed by mixing purified AMV- or HIV-Rt with different dilutions of the untreated clinical specimen. This showed that RT activity was unaffected by 100 microliters of an extract of whole blood cells resuspended to their original blood volume and diluted 1/64, and also by 100 microliters of serum diluted 1/64. To improve the utility of the assay at the inhibitory concentrations of clinical specimens, the following procedure was adopted: the sample to be analyzed was incubated with the carrier bound template in order to allow the RT to bind, the carrier was washed to remove inhibitory factors, and the reaction components were then added to determine the amount of bound RT. This procedure greatly enhanced the recovery of RT activity from crude specimens and made the direct detection of HIV-RT possible. The assay is easily automated and useful for RT determination in multiple samples and for determining RT-inhibiting substances such as substrate analogs and antibodies.

Expression, purification, and crystallization of the HIV-1 reverse transcriptase (RT).

The HIV-1 pol gene proteins (protease, reverse transcriptase, and endonuclease) were expressed in Escherichia coli N4830-1 by the use of the inducible expression vector pWS60 into which the pol gene was inserted. The p66/p51 heterodimer of reverse transcriptase (RT) was isolated in a highly pure and active form. Crystals of the p66/p51 heterodimer were obtained by the vapor diffusion hanging drop technique. The present crystal quality is still not adequate for high resolution X-ray investigation.

Homology between cellulase genes of Trichoderma reesei: complete nucleotide sequence of the endoglucanase I gene.

The filamentous fungus Trichoderma reesei produces several endoglucanases (EG) and cellobiohydrolases (CBH) which are involved in cellulose hydrolysis in a complex synergistic manner. We have cloned and sequenced the gene and the full-length cDNA coding for the major endoglucanase EG-I, and compared this to the cbh1 gene sequence to clarify the relationship between the EG and CBH classes of cellulases. The deduced 437-amino acids (aa) long EG-I protein with a 22-aa long signal peptide is 45% identical in aa sequence with CBH-I. The best conserved region is found at the C terminus and shows about 70% homology. The data suggest that the two enzymes have arisen from a common ancestor by gene duplication. Despite this, the intron positions have not been conserved in these genes which both contain two short introns. The deduced EG-I sequence contains six putative N-glycosylation sites, and a putative O-glycosylated region is found near the C terminus, closely resembling a similar region at the C terminus of CBH-I. Comparison of the aa sequences suggests that the evolutionary divergence of EG-I from CBH-I has involved four separate 10-20 aa "deletions" from the ancestral protein.

Isolation of cellulolytic enzymes from Trichoderma reesei QM 9414.

Two cellobiohydrolases and two endoglucanases were purified from a culture filtrate of the fungus Trichoderma reesei QM 9414 by simple and straightforward purification techniques. Molecular weights, isoelectric points, amino acid compositions, and carbohydrate contents are reported.

The disulphide bridges in a cellobiohydrolase and an endoglucanase from Trichoderma reesei.

The positions of the disulphide bridges of the 1,4-beta-glucan cellobiohydrolase (CBH I) of the fungus Trichoderma reesei have been investigated. The results can be summarized as follows. (1) The enzyme contains 12 disulphide bridges and no free cysteine residues. (2) The location of six disulphide bridges have been determined experimentally. (3) The bonding patterns of the two disulphide bridges in the C-terminal region is suggested on the basis of internal homology. (4) The remaining four disulphide bridges are put into two groups, each containing four half-cystine residues where two are adjacent. (5) A repeating bonding pattern is observed along the peptide chain and a non-local disulphide bond with an unusually long separation distance links the N-terminal and the C-terminal region. (6) The disulphide-bonded CNBr peptides of a 1,4-beta-glucan glucanohydrolase (endoglucanase II) from T. reesei have been isolated and a disulphide bonding pattern is suggested on the basis of the sequence homology between the two enzymes.