Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: UMLS:C0021051 (immunodeficiency)
71,517 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The human immunodeficiency virus (HIV) integrase (IN) protein mediates an essential step in the retroviral lifecycle, the integration of viral DNA into human DNA. A DNA-binding domain of HIV IN has previously been identified in the C-terminal part of the protein. We tested truncated proteins of the C-terminal region of HIV-1 IN for DNA binding activity in two different assays: UV-crosslinking and southwestern blot analysis. We found that a polypeptide fragment of 50 amino acids (IN220-270) is sufficient for DNA binding. In contrast to full-length IN protein, this domain is soluble under low salt conditions. DNA binding of IN220-270 to both viral DNA and non-specific DNA occurs in an ion-independent fashion. Point mutations were introduced in 10 different amino acid residues of the DNA-binding domain of HIV-2 IN. Mutation of basic amino acid K264 results in strong reduction of DNA binding and of integrase activity.
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PMID:Characterization of the minimal DNA-binding domain of the HIV integrase protein. 793 37

Pepstatin A, a pentapeptide with the molecular weight of 686, is a naturally occurring inhibitor of aspartyl proteases secreted by Streptomyces species. Above a critical concentration of 0.1 mM at low ionic strength and neutral pH, it can polymerize into filaments which may extend over several micrometers. After negative staining, these filaments show a helical substructure with characteristic diameters ranging from 6 to 12 nm. Selected images at higher magnification suggest the filaments are composed of two intertwined 6 nm strands. This is in agreement with the optical diffraction analysis which additionally established a periodic pitch of 25 nm for the helical intertwining. Rotary shadowing of the pepstatin A filaments clearly demonstrated the right-handedness of the helical twist. In physiological salt solution or at higher concentrations of pepstatin A, a variety of higher order structures were observed, including ribbons, sheets and cylinders with both regular and twisted or irregular geometries. Pepstatin A can interact with intermediate filament subunit proteins. These proteins possess a long, alpha-helical rod domain that forms coiled-coil dimers, which through both hydrophobic and ionic interactions form tetramers which, in turn, in the presence of physiological salt concentrations, polymerize into the 10 nm intermediate filaments. In the absence of salt, pepstatin A and intermediate filament proteins polymerize into long filaments with a rough surface and a diameter of 15-17 nm. This polymerization appears to be primarily driven by nonionic interactions between pepstatin A and polymerization-competent forms of intermediate filament proteins, resulting in a composite filament. Polymerization-incompetent proteolytic fragments of vimentin, lacking portions of the head and/or tail domain, failed to copolymerize with pepstatin A into long filaments under these conditions. These peptides, as well as bovine serum albumin, were found to stick to the surface of pepstatin A filaments, ribbons and sheets. Independent evidence for direct association of pepstatin A with intermediate filament subunit proteins was provided not only by electron microscopy but also by UV difference spectra. Pepstatin A loses its ability to inhibit the aspartyl protease of the human immunodeficiency virus type 1 following polymerization into the higher order structures described here. The amazing fact that pepstatin A can spontaneously self-associate to form very large polymers seems to be a more rare event for such small peptides. The other examples of synthetic or naturally occurring oligopeptides discussed in this review which are able to polymerize into higher order structures possess a common property, their hydrophobicity, often manifested by clusters of valine or isoleucine residues.(ABSTRACT TRUNCATED AT 400 WORDS)
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PMID:Pepstatin A: polymerization of an oligopeptide. 805 47

The presence and survival of pathogens inside the gut of leeches were studied by means of light and electron microscopy. In African leeches from Cameroon, blood was serologically positive for human immunodeficiency virus (HIV) and hepatitis B; blood of Hirudo medicinalis bought in German pharmacies contained up to 11 different species of bacteria. In experiments done at low (3 degrees C) and high (22 degrees, 32 degrees C) temperatures, it was shown that ingested red and white blood cells survive for long periods. The time was prolonged to at least 6 months in cases in which the leeches were stored at 3 degrees C. The same effect occurred with pathogens. Bacteriophages (viruses of bacteria) and bacteria persisted in large numbers for at least 6 months in the gut of experimentally infected leeches. Protozoan parasites such as Toxoplasma gondii, Trypanosoma brucei brucei, or Plasmodium berghei were even capable of reproducing inside the gut of the leech. In the case of Plasmodium parasites, this proceeded at low (3 degrees C) and high (22 degrees C) temperatures until all erythrocytes were used up. These parasites survived as long as the erythrocytes and lymphocytes were of good shape, i.e., around 5-6 weeks p.i. Single stages survived longer, especially at low temperatures. However, electron microscopy studies gave no hint of penetration of such pathogens into the unicellular salivary glands, which would initiate a direct transmission. Such transmission, however, is possible--many fish leeches directly transmit several blood parasites--when the leeches are squeezed during skin attachment or when they are manipulated by dropping salt solution on their backs while they are sucking. Consequently, the leech is a potential vector of many pathogens, especially in regions with an endemic spread of human and/or animal pathogens.
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PMID:Experiments on the possible role of leeches as vectors of animal and human pathogens: a light and electron microscopy study. 807 13

Assembly of human immunodeficiency virus type 1 (HIV-1) particles occurs at the plasma membrane of infected cells. Myristylation of HIV-1 Gag precursor polyprotein Pr55Gag is required for stable membrane binding and for assembly of viral particles. We expressed a series of proteins representing major regions of the HIV-1 Gag protein both with and without an intact myristyl acceptor glycine and performed subcellular fractionation studies to identify additional regions critical for membrane binding. Myristylation-dependent binding of Pr55Gag was demonstrated by using the vaccinia virus/T7 hybrid system for protein expression. Domains within the matrix protein (MA) region downstream of the initial 15 amino acids were required for membrane binding which was resistant to a high salt concentration (1 M NaCl). A myristylated construct lacking most of the matrix protein did not associate with the plasma membrane but formed intracellular retrovirus-like particles. A nonmyristylated construct lacking most of the MA region also was demonstrated by electron microscopy to form intracellular particles. Retrovirus-like extracellular particles were produced with a Gag protein construct lacking all of p6 and most of the nucleocapsid region. These studies suggest that a domain within the MA region downstream from the myristylation site is required for transport of Gag polyprotein to the plasma membrane and that stable plasma membrane binding requires both myristic acid and a downstream MA domain. The carboxyl-terminal p6 region and most of the nucleocapsid region are not required for retrovirus-like particle formation.
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PMID:Identification of human immunodeficiency virus type 1 Gag protein domains essential to membrane binding and particle assembly. 815 85

Retroviral genomes consist of two identical RNA molecules joined noncovalently near their 5' ends, at domains called dimerization linked sequences (DLS). This physical linkage of the genomic RNAs is considered important for the control of several steps in the viral life cycle, such as recombination, translation, and encapsidation. The putative DLS of human immunodeficiency virus-1 (HIV-1), a 111-nucleotide, purine-rich stretch of RNA, has been found necessary and sufficient for a salt-induced dimerization of the genome in vitro. Our investigation into the mechanism of this dimerization reveals sharply varying influences of the different alkali cations on both the formation and the stabilization of the dimer, a pattern closely related to that of telomeric G-DNA complexes. To probe this phenomenon, we have carried out experiments using short antisense DNA oligomers to define the segments of the DLS that are required for dimerization and methylation protection to implicate sets of guanines in forming Hoogsteen hydrogen bonds within the dimer. Cumulatively, these data provide further evidence for the existence of guanine quartets within the dimerized HIV-1 DLS. We propose models in which guanine quartets not only allow the homodimerization of HIV-1 and other retroviral genomic RNAs but also permit the two RNA strands in a dimer to exist in an overall parallel orientation, as has been observed by electron microscopy.
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PMID:Mode of dimerization of HIV-1 genomic RNA. 821 11

rev is an RNA-binding protein of human immunodeficiency virus-1 and is required for the expression of incompletely spliced viral transcripts. Oligomerization of rev is thought to be associated with RNA binding and rev function. Here, we have characterized the oligomerization of rev using equilibrium analytical centrifugation. rev is predominantly monomeric at low concentrations, but reversibly polymerizes to produce large aggregates at higher concentrations. The data fit well to an unlimited isodesmic self-association model in which the association constants for the addition of a monomer to each aggregate are equal [K = 1.08 x 10(6) M-1 at 4 degrees C]. The association constant is essentially independent of monovalent salt concentration from 0.15 to 2 M at pH 6-9. Thermodynamic parameters derived from the temperature dependence of the association constant over the limited range of 0-30 degrees C reveal that the primary contribution to the free energy of oligomerization is a large negative enthalpy. Binding of rev to the rev-responsive element of RNA was characterized under the same conditions as the centrifugation experiments using a nitrocellulose filter assay. rev binds to the RRE at a protein concentration where rev is predominantly monomeric, suggesting that solution multimerization of rev is not required for rev function.
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PMID:Solution oligomerization of the rev protein of HIV-1: implications for function. 821 47

The predicted protease cleavage site (p7/p1; [J. Virol. 66 (1992) 1856-1865]) within the nucleocapsid precursor protein (p15) of human immunodeficiency virus, type 1, was confirmed using an in vitro assay employing recombinant HIV-1 protease and a chemically synthesized 72 amino acid polypeptide containing the p7 and p1 protein domains of the native gag polyprotein. The cleavage occurred between amino acid 55 (N) and amino acid 56 (F) of the polypeptide, as determined by N-terminal sequencing. The hydrolysis was optimal at pH 6.0 and at high salt concentration. The kinetic parameters Km, kcat and kcat/Km were 99 microM (+/- 8), 0.152 s-1 (+/- 0.002) and 1.56 mM-1.s-1 (+/- 0.11), respectively. Reconstituted as well as denatured polypeptides were cleaved at approximately the same rate, demonstrating that the conformation of the p7 protein, as a result of the Zn(2+)-binding, had no significant effect on the rate of hydrolysis of the p7/p1 cleavage.
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PMID:The gag precursor contains a specific HIV-1 protease cleavage site between the NC (P7) and P1 proteins. 822 64

Retroviral particles contain a dimeric genome consisting of two full-length, noncovalently linked RNA molecules. Linkage of the two genomes is thought to be critical for a productive reverse transcription reaction and may increase genetic recombination rates. The molecular nature of the dimer linkage structure (DLS) is poorly understood. It was recently shown that in vitro synthesized retroviral transcripts can dimerize in the absence of protein factors. We studied in vitro dimerization of human immunodeficiency virus type 2 (HIV-2) RNA. Specific dimerization of HIV-2 RNAs was observed upon incubation at 37 degrees C in high-salt buffer. Previously, physical and biochemical studies have mapped dimer linkage structures in retroviral leader RNA close to the gag open reading frame. In this study, we found efficient dimerization of HIV-2 RNAs containing only the 5' terminal 255 nucleotides of the leader RNA. Therefore, it seems likely that multiple dimerization signals are present in retroviral leader RNA. The implications for genome dimerization and genome packaging are discussed.
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PMID:In vitro dimerization of HIV-2 leader RNA in the absence of PuGGAPuA motifs. 842 65

The nef genes, derived from two different human immunodeficiency-virus-type-1 (HIV-1) strains, were expressed in procaryotic cells (Escherichia coli) and in eucaryotic cells (insect cells infected with nef-containing baculovirus). The oligomerization of recombinant Nef protein was studied by NMR spectroscopy and immunoblotting under various experimental conditions. 1H-NMR spectroscopy shows that native folded protein has the tendency to polymerize under low-salt conditions. These oligomers become covalently linked by disulfide bonds after decreasing the reduction potential, a process which is fully reversible. Cross-linking studies with bis(sulfo-succinimidyl)suberate and alkylation with iodoacetic acid under non-reducing and reducing conditions document for the first time that Nef can also form homomeric structures including monomers, dimers, trimers and tetramers in cell lysates and intact cells. We found disulfide-linked as well as non-covalently associated oligomers. Since the Nef molecules are not exclusively found in the cytoplasm of HIV infected cells and since the reduced glutathione concentration in lymphocytes of virus infected persons is known to be unusually low, it might be possible that these Nef oligomers have a biological function in vivo as well.
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PMID:Oligomerization of the Nef protein from human immunodeficiency virus (HIV) type 1. 851 95

AG1343 is a novel human immunodeficiency virus (HIV) protease inhibitor designed using protein structure-based techniques and intended for chronic oral administration in the treatment of AIDS-related conditions. The compound is the mesylate salt of a basic amine with a molecular weight of 663.90, pKa of 6.0, and partition coefficient (log P) of 4.1. Examination of the physicochemical properties of a bench-scale lot of the bulk drug was undertaken in order to establish a preformulation database and to begin development of an oral formulation suitable for phase I clinical trials. A stability-indicating gradient HPLC method was developed, and initial stability studies indicated that the compound is relatively stable under accelerated conditions. Water solubility and intrinsic dissolution rate studies, however, revealed the potential for dissolution rate-limited absorption. Alternative salts were prepared and evaluated for water solubility relative to the mesylate. A pH-solubility profile for AG1343 was generated and its solubility in various pharmaceutical solvents was determined. Formulation into several prototypical oral dosage forms for in-vitro evaluation in animal models prior to phase I clinical trials resulted in a several-fold difference in bioavailability between these formulations.
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PMID:Preformulation studies of a novel HIV protease inhibitor, AG1343. 853 87


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