[A vaccine against HIV--status after ten years of research].
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AIDS Vaccines↗
Biomedical subjects
J E Hansen
Publications and source records attributed to J E Hansen.
O-GLYCBASE: a revised database of O-glycosylated proteins.
O-GLYCBASE is a comprehensive database of information on glycoproteins and their O-linked glycosylation sites. Entries are compiled and revised from the SWISS-PROT and PIR databases as well as directly from recently published reports. Nineteen percent of the entries extracted from the databases needed revision with respect to O-linked glycosylation. Entries include information about species, sequence, glycosylation site and glycan type, and are fully referenced. Sequence logos displaying the acceptor specificity for the GaINAc transferase are shown. A neural network method for prediction of mucin type O-glycosylation sites in mammalian glycoproteins exclusively from the primary sequence is made available by E-mail or WWW. The O-GLYCBASE database is also available electronically through our WWW server or by anonymous FTP.
Amino Acid Sequence↗
Prediction of the secondary structure of HIV-1 gp120.
The secondary structure of HIV-1 gp120 was predicted using multiple alignment and a combination of two independent methods based on neural network and nearest-neighbor algorithms. The methods agreed on the secondary structure for 80% of the residues in BH10 gp120. Six helices were predicted in HIV strain BH10 gp120, as well as in 27 other HIV-1 strains examined. Two helical segments were predicted in regions displaying profound sequence variation, one in a region suggested to be critical for CD4 binding. The predicted content of helix, beta-strand, and coil was consistent with estimates from Fourier transform infrared spectroscopy. The predicted secondary structure of gp120 compared well with data from NMR analysis of synthetic peptides from the V3 loop and the C4 region. As a first step towards modeling the tertiary structure of gp120, the predicted secondary structure may guide the design of future HIV subunit vaccine candidates.
Algorithms↗
Conserved N-linked oligosaccharides of the C-terminal portion of human immunodeficiency virus type 1 gp120 and viral susceptibility to neutralizing antibodies.
We have constructed a mutated infectious HIV variant lacking the signals for addition of three N-linked glycans situated in the V4, C4 and V5 regions of HIV gp120. When comparing mutated virus with wildtype virus we found essentially no differences in the phenotypic characteristics of the two viruses except for the expected electrophoretic mobility shift of radioimmuno-precipitated mutated gp120, resulting from the missing N-glycans. Thus, the infectivity titer and the capacity to induce syncytia were similar for the two viruses. The sensitivity of mutant and wildtype virus to a number of neutralizing agents was determined. As expected, the mutant virus was significantly less sensitive to neutralization by Con A, with affinity for the N-glycans eliminated. We found, however, that antibodies to the V3 loop and sCD4 neutralized wild-type virus as efficiently as mutant virus, whereas 2G12, a monoclonal antibody, binding to a discontinuous neutralization epitope, and GP13, binding to the CD4-binding domain, neutralized wildtype virus better than mutant virus. Altogether the data suggest that the three conserved N-linked glycans, despite their location in immediate association with the CD4-binding domain, which is an important neutralization epitope, are not essential for virus replication in cell culture and they are not engaged in shielding neutralization epitopes of gp120 from neutralizing antibodies. However, the glycans evidently influence the three-dimensional conformation of gp120, since their presence increases the availability of the neutralization epitope of 2G12.
Amino Acid Sequence↗
Sensitivity of HIV-1 to neutralization by antibodies against O-linked carbohydrate epitopes despite deletion of O-glycosylation signals in the V3 loop.
It has been suggested that threonine or serine residues in the V3 loop of HIV-1 gp120 are glycosylated with the short-chain O-linked oligosaccharides Tn or sialosyl-Tn that function as epitopes for broadly neutralizing carbohydrate specific antibodies. In this study we examined whether mutation of such threonine or serine residues could decrease the sensitivity to infectivity inhibition by Tn or sialosyl-Tn specific antibodies. All potentially O-glycosylated threonine and serine residues in the V3 loop of cloned HIV-1 BRU were mutagenized to alanine thus abrogating any O-glycosylation at these sites. Additionally, one of these T-A mutants (T308A) also abrogated the signal for N-glycosylation at N306 inside the V3-loop. The mutant clones were compared with the wild type virus as to sensitivity to neutralization with monoclonal and polyclonal antibodies specific for the tip of the V3 loop of BRU or for the O-linked oligosaccharides Tn or sialosyl-Tn. Deletion of the N-linked oligosaccharide at N306 increased the neutralization sensitivity to antibodies specific for the tip of the loop, which indicates that N-linked glycosylation modulates the accessibility to this immunodominant epitope. However, none of the mutants with deletions of O-glycosylation signals in the V3 loop displayed any decrease in sensitivity to anti-Tn or anti-sialosyl-Tn antibody. This indicates that these broadly specific neutralization epitopes are located outside the V3 loop of gp 120.
Amino Acid Sequence↗
Induction of homologous virus neutralizing antibodies in guinea-pigs immunized with two human immunodeficiency virus type 1 glycoprotein gp120-iscom preparations. A comparison with other adjuvant systems.
The immunogenicity in guinea-pigs of the human immunodeficiency virus type 1 envelope glycoprotein gp120 in immune stimulating complex (iscom) was compared to that of gp120 adjuvanted with QuilA-matrix (iscom without attached antigen), aluminium hydroxide (alum) and the Ribi adjuvant system. Gp120 was either incorporated into iscoms by covalent conjugation (iscom(c)) or by acid treatment of gp120 (iscom(a) and both these preparations induced high ELISA antibody titres to gp120. Virus neutralizing (VN) antibodies were most frequently induced by gp120 in iscom(c), iscom(a) or in alum and correlated to high titres to the V3-region of gp120. Further, antibodies induced by gp120-iscom(c) most efficiently inhibited binding of a VN monoclonal antibody GP13 to the CD4 binding region of gp120 whereas gp120-iscom(a) induced the highest mean titre of antibodies blocking the binding of [125I]gp120 to CD4. These results suggest that the gp120-iscom preparations efficiently induced high levels of gp120 specific antibodies and that the adjuvant formulation of gp120 affect the specificity and functional properties of elicited antibodies.
Adjuvants, Immunologic↗
Detection of a pH-dependent conformational change in azurin by time-resolved phosphorescence.
Azurin, a blue copper protein from the bacterial species Pseudomonas aeruginosa, contains a single tryptophan residue. Previous fluorescence measurements indicate that this residue is highly constrained and unusually inaccessible to water. In the apoprotein this residue also possesses a long-lived room-temperature phosphorescence (RTP), the nonexponential decay of which can be resolved into two major components associated with lifetimes of 417 and 592 ms, which likely originate from at least two conformations of the protein. The relative weights of these two decay components change with pH in good correlation with a change in protonation of His-35, which has been studied in Cu(II) azurin. Interestingly, the structural changes characterized in earlier work have little effect on the fluorescence decay and appear to occur away from the tryptophan residue. However, in the present work, the two RTP lifetimes suggest conformations with different structural rigidities in the vicinity of the tryptophan residue. The active conformation that predominates below a pH of 5.6 has the shorter lifetime and is less rigid. Phosphorescence decays of several metal derivatives of azurin were also measured and revealed strong similarities to that of apoazurin, indicating that the structural constraints upon the metal-binding site are imposed predominately by the protein.
Apoproteins↗
Distance distributions in proteins: a six-parameter representation.
We present a statistical analysis of protein structures based on interatomic C alpha distances. The overall distance distributions reflect in detail the contents of sequence-specific substructures maintained by local interactions (such as alpha-helixes) and longer range interactions (such as disulfide bridges and beta-sheets). We also show that a volume scaling of the distances makes distance distributions for protein chains of different length superimposable. Distance distributions were also calculated specifically for amino acids separated by a given number of residues. Specific features in these distributions are visible for sequence separations of up to 20 amino acid residues. A simple representation, which preserves most of the information in the distance distributions, was obtained using six parameters only. The parameters give rise to canonical distance intervals and when predicting coarse-grained distance constraints by methods such as data-driven artificial neural networks, these should preferably be selected from these intervals. We discuss the use of the six parameters for determining or reconstructing 3-D protein structures.
Amino Acid Sequence↗
Influence of N-linked glycans in V4-V5 region of human immunodeficiency virus type 1 glycoprotein gp160 on induction of a virus-neutralizing humoral response.
One of the functions of N-linked glycans of viral glycoproteins is protecting otherwise accessible neutralization epitopes of the viral envelope from neutralizing antibodies. The aim of the present study was to explore the possibility to obtain a more broadly neutralizing immune response by immunizing guinea pigs with gp160 depleted of three N-linked glycans in the CD4-binding domain by site-directed mutagenesis. Mutant and wild type gp160 were formulated into immunostimulating complexes and injected s.c. into guinea pigs. Both preparations induced high serum antibody response to native gp120 and V3 peptides. Both preparations also induced antibodies that bound equally well to the V3 loop or the CD4-binding region, as determined by a competitive enzyme-linked immunosorbent assay (ELISA). The sera from animals, immunized with mutated glycoprotein, did not neutralize nonrelated HIV strains better than did sera from animals, immunized with wild type glycoprotein. Instead, a pattern of preferred homologous neutralization was observed, i.e., sera from animals, immunized with mutant gp160, neutralized mutant virus better than wild type virus, and vice versa. These data indicated that elimination of the three N-linked glycans from gp160 resulted in an altered local antigenic conformation but did not uncover hidden neutralization epitopes, broadening the immune response.
AIDS Vaccines↗
Rapid selection for an N-linked oligosaccharide by monoclonal antibodies directed against the V3 loop of human immunodeficiency virus type 1.
The V3 loop of the human immunodeficiency virus (HIV) surface protein, gp 120, constitutes a principal neutralizing determinant. HIV strains lacking a naturally conserved N-linked oligosaccharide (at position 306) within the V3 loop are highly sensitive to neutralization. We subjected molecular clones of HIV(LAI) lacking this 306N-glycan to in vitro immune selection with MAbs directed against the V3 loop. In all, ten clones were characterized, and all proved resistant to V3-directed neutralization. Sequencing of the V3 loop revealed that six of the clones had become resistant at least partly by reacquisition of the 306N-glycan. Only two of the clones possessed mutations within the binding site of the antibody itself, while the two remaining clones did not display changes within the V3 loop itself. Thus, HIV strains lacking the 306N-glycan primarily develop resistance to V3-directed neutralization through acquisition of the specific oligosaccharide. This demonstrates that protein glycosylation can be a primary modifier of virus antigenicity of possible importance for the interaction of HIV with the host immune response.
Amino Acid Sequence↗
Pathophysiology of activity limitation in patients with interstitial lung disease.
OBJECTIVE: To analyze the relative importance of gas exchange, ventilatory, and circulatory abnormalities in limiting exercise in patients with interstitial lung disease. DESIGN AND SETTING: Retrospective study at a referral cardiopulmonary exercise laboratory in a university/county medical center. PATIENTS AND METHODS: A database with more than 1,300 patients with incremental cycle exercise studies was screened to find 42 patients with interstitial lung disease, but without accompanying airflow limitation, chest wall, primary heart, or systemic vascular disease, or poor motivation. All had spirometry, lung volume, and gas transfer index measures at rest and repeated gas exchange, ventilatory, and circulatory measures during exercise; 37 of the 42 patients had multiple blood gas measures during exercise. We graded the gas exchange, ventilatory and circulatory dysfunction during maximally tolerated cycle ergometry and correlated the grades of dysfunction of these three components of respiration with percent predicted peak O2 uptake (peak Vo2). RESULTS: Peak Vo2 values were not well correlated with the grades of ventilatory impairment but were well correlated with the grades of gas exchange and circulatory dysfunction. Patients who had reduced peak Vo2 values often had a normal breathing reserve with physiologic evidence of pulmonary vascular disease. CONCLUSIONS: The pathophysiology of the pulmonary circulation is usually more important than ventilatory mechanics in limiting exercise in patients with interstitial lung disease.
Activities of Daily Living↗
Neutralizing antibodies in slowly progressing HIV-1 infection.
Ten asymptomatic individuals who had experienced only limited CD4+ cell loss after prolonged infection with HIV-1 were studied. These individuals had a mean CD4+ cell count of 674 x 10(6) cells/L and a mean duration of infection of 8.5 years. Also included were 10 asymptomatic HIV-1-infected individuals who, over a similar period of infection (7.5 years), had experienced a profound loss of CD4+ cells (mean CD4+ cell count, 54 x 10(6) cells/L). Proviral load was determined using a semiquantitative polymerase chain reaction and was significantly lower in the subjects with slowly progressing infection (SPI) than in subjects with rapidly progressing infection (RPI) (4,000 vs. 40,000 proviral copies/10(6) peripheral blood mononuclear cells; p = 0.0089). Isolation of virus was attempted in all individuals but succeeded only in 6 of 10 individuals with SPI versus all 10 individuals with RPI. Four of six virus isolates obtained from individuals with SPI and 6 of 10 obtained from individuals with RPI were of the syncytia-inducing phenotype. We determined the neutralizing activity of serum against HIVMN, HIVIIIB, and the contemporaneous autologous isolate when available. Serum from individuals with SPI generally neutralized the contemporaneous isolate, whereas serum from individuals with RPI did not [geometric mean antibody titer (GMT), 45 vs. 3; p = 0.0047]. There was no difference in neutralizing ability against HIVMN (GMT,2,593 vs. 2,263; p = 0.74) and only a small difference against HIVIIIB (GMT, 115 vs. 50; p = 0.075). Our results indicate that individuals with SPI are characterized by an ability to neutralize their own HIV strain.(ABSTRACT TRUNCATED AT 250 WORDS)
Adult↗
[False results on elevated triiodothyronine values in radioimmunoassay].
Five patients with falsely elevated serum triiodothyronine (T3) concentrations (> 9 nmol/l) in a radioimmunoassay are reported. The high T3-values disagreed with the other thyroid variables investigated as well as with the clinical observations. In sera from all patients a normal non-specific binding of T3 was found, thus excluding abnormal serum-protein-binding of the hormone. An ethanol extraction of T3 from serum before RIA reduced the T3 content in serum from all patients to normal levels (2.0-2.4 nmol/l). These findings indicate the presence in the sera of substances, probably of protein nature, that were interfering with the assay by binding the reagent-antibody and not the antigen. Addition of non-immune rabbit serum prevented this interference and normalized the T3-values (1.8-2.4 nmol/l). Thus the interfering substance in T3-RIA could be an anti-rabbit antibody, the interaction of which can be eliminated by a minor modification of the assay making it possible to differentiate true from false T3-values.
Adult↗
Prediction of O-glycosylation of mammalian proteins: specificity patterns of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase.
The specificity of the enzyme(s) catalysing the covalent link between the hydroxyl side chains of serine or threonine and the sugar moiety N-acetylgalactosamine (GalNAc) is unknown. Pattern recognition by artificial neural networks and weight matrix algorithms was performed to determine the exact position of in vivo O-linked GalNAc-glycosylated serine and threonine residues from the primary sequence exclusively. The acceptor sequence context for O-glycosylation of serine was found to differ from that of threonine and the two types were therefore treated separately. The context of the sites showed a high abundance of proline, serine and threonine extending far beyond the previously reported region covering positions -4 through +4 relative to the glycosylated residue. The O-glycosylation sites were found to cluster and to have a high abundance in the N-terminal part of the protein. The sites were also found to have an increased preference for three different classes of beta-turns. No simple consensus-like rule could be deduced for the complex glycosylation sequence acceptor patterns. The neural networks were trained on the hitherto largest data material consisting of 48 carefully examined mammalian glycoproteins comprising 264 O-glycosylation sites. For detection neural network algorithms were much more reliable than weight matrices. The networks correctly found 60-95% of the O-glycosylated serine/threonine residues and 88-97% of the non-glycosylated residues in two independent test sets of known glycoproteins. A computer server using E-mail for prediction of O-glycosylation sites has been implemented and made publicly available. The Internet address is NetOglyc@cbs.dtu.dk.
Algorithms↗
[Episodic hypoxemia and coinciding ECG changes after acute myocardial infarction].
This study was conducted to document the trend in arterial hypoxaemia and electrocardiographic (ECG) abnormalities on second to sixth night after acute myocardial infarction (AMI). Nineteen consecutive patients with AMI were monitored continuously during the night with a Holter tape recorder and a pulse oxymeter. Five patients had > 30 episodic oxygen desaturations of > or = 5%, and many patients had episodes with oxygen desaturations < 80% ranging from 46-61% (from 7/15-11/18) during the nights of monitoring. Constant hypoxaemia was found in 11-13% of the patients. Many patients had simultaneous occurrence of episodic hypoxaemia and episodic sinustachycardia, ST-deviation and arrhythmias, giving a summarized simultaneous occurrence of episodic hypoxaemia and ECG-abnormalities ranging from 13/18 (72%) patients on the third night to 7/15 (46%) patients on the sixth night. Episodic and constant hypoxaemia are thus common during the first week after AMI. Episodic hypoxaemia was associated with ECG-abnormalities in the majority of patients.
Adult↗
The HIV-1 V3 domain on field isolates: participation in generation of escape virus in vivo and accessibility to neutralizing antibodies.
The V3 domain is highly variable and induces HIV neutralizing antibodies (NA). Here we addressed the issues of 1) the participation of mutations in V3 in generation of neutralization resistant escape virus in vivo and 2) the applicability of synthetic V3 peptides corresponding to field isolates to induce neutralizing immune sera. Seven peptides corresponding to the V3 region of primary and escape virus from 3 HIV-1 infected patients were synthesized and used for antibody (Abs) studies and immunizations. The anti-V3 Abs titre in patient serum was generally low against peptides corresponding to autologous virus isolated later than the serum sample in contrast to the titre against peptides corresponding to virus isolated earlier than the serum sample. Furthermore, neutralizing anti-V3 monoclonal antibodies (MAbs) raised against V3 peptides from laboratory strains of HIV-1 showed distinct binding patterns against V3 peptides corresponding to sequential primary and escape field isolates, with the strongest reactivity against late isolated escape virus. These observations suggest that the neutralization epitope was influenced by the appearance of mutations. When used as immunogen in rabbits, V3 peptides corresponding to field isolates were highly immunogenic but failed to induce neutralizing or gp120-precipitating Abs. On the contrary, V3 peptide corresponding to the laboratory strain HXB2 induced HIV neutralizing, gp120-precipitating immune serum. In conclusion, these data suggest a participation of the V3 domain in the immunoselection of escape virus, and that V3 on early field virus is less accessible to NA than that on laboratory strains.
Amino Acid Sequence↗
Inhibition of HIV-1 in vitro by C-5 propyne phosphorothioate antisense to rev.
A 15-mer C-5 propyne modified phosphorothioate oligodeoxynucleotide antisense to rev was approximately 5-fold more effective in providing viral inhibition compared to a 28-mer unmodified phosphorothioate oligodeoxynucleotide targeted to the same sequence and previously shown to inhibit HIV-1 in a sequence-dependent manner. The antiviral effect was obtained by lipofection or simple addition of 0.2-1 microM modified oligodeoxynucleotide to the culture medium of H9 cells chronically infected with the HIV-1LAI isolate of human immunodeficiency virus type 1. We conclude that C-5 propyne oligodeoxynucleotides in accordance with previous findings by others are superior to unmodified phosphorothioates in providing inhibition of HIV-1 in a sequence-dependent manner and that this inhibition can be conferred by oligodeoxynucleotides in free solution.
Antiviral Agents↗
Increased adhesion as a mechanism of antibody-dependent and antibody-independent complement-mediated enhancement of human immunodeficiency virus infection.
Enhancement of human immunodeficiency virus (HIV) infection by complement alone or in conjunction with antibodies was studied experimentally and theoretically. Experimental studies showed that while HIV-positive sera neutralize HIV infection, the addition of fresh complement abrogated neutralization and could even cause enhancement. Enhancement was blocked by anti-complement receptor 2 antibodies, and infection under enhancing conditions could be blocked by soluble CD4. Antibody-dependent complement-mediated enhancement (C'ADE) was dependent on the alternative complement activation pathway, as factor B-deficient serum could enhance only after the addition of factor B. The observed enhancement was also antibody dependent, since the addition of antibodies increased the level of enhancement. Under C'ADE conditions, infection reached a plateau within 5 min and was not caused by activation of cells by factors in the human serum. On the contrary, preincubation of cells with complement decreased the level of enhancement. A theoretical model of HIV infection in vitro which exhibited similar enhancement in an antibody- and complement concentration-dependent way was developed. Model studies indicated that the enhanced infection process could be explained by the fact that virions, because of complement deposition on the surface, bind more efficiently to cells. The model also indicated that the saturation of the enhanced infection process seen after a few minutes could be caused by saturation of the complement receptors. The effect of neutralizing antibodies can thus be overcome by the enhancing effect of complement that facilitates the contact between gp120 and CD4. These studies demonstrate that the main features of the complement-dependent enhancement phenomenon can be understood in terms of a simple mathematical model.
CD4 Antigens↗