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Reynolds JL, Mahajan SD, Aalinkeel R, Nair B, Sykes DE, Agosto-Mujica A, Hsiao CB, Schwartz SA. Modulation of the proteome of peripheral blood mononuclear cells from HIV-1-infected patients by drugs of abuse. J Clin Immunol 2009; 29:646-56. [PMID: 19543960 DOI: 10.1007/s10875-009-9309-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Accepted: 05/28/2009] [Indexed: 01/13/2023]
Abstract
INTRODUCTION We used proteomic analyses to assess how drug abuse modulates immunologic responses to infections with the human immunodeficiency virus type 1 (HIV-1). METHODS Two-dimensional difference gel electrophoresis was utilized to determine changes in the proteome of peripheral blood mononuclear cells (PBMC) isolated from HIV-1-positive donors that occurred after treatment with cocaine or methamphetamine. Both drugs differentially regulated the expression of several functional classes of proteins. We further isolated specific subpopulations of PBMC to determine which subpopulations were selectively affected by treatment with drugs of abuse. Monocytes, B cells, and T cells were positively or negatively selected from PBMC isolated from HIV-1-positive donors. RESULTS Our results demonstrate that cocaine and methamphetamine modulate gene expression primarily in monocytes and T cells, the primary targets of HIV-1 infection. Proteomic data were validated with quantitative, real-time polymerase chain reaction. These studies elucidate the molecular mechanisms underlying the effects of drugs of abuse on HIV-1 infections. Several functionally relevant classes of proteins were identified as potential mediators of HIV-1 pathogenesis and disease progression associated with drug abuse.
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Affiliation(s)
- Jessica L Reynolds
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, Buffalo General Hospital, University at Buffalo, State University of New York at Buffalo, 311 MultiLab Research Building, Buffalo, NY,14203, USA.
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2
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Gevaert K, Van Damme P, Ghesquière B, Impens F, Martens L, Helsens K, Vandekerckhove J. A la carte proteomics with an emphasis on gel-free techniques. Proteomics 2007; 7:2698-718. [PMID: 17640001 DOI: 10.1002/pmic.200700114] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Since the introduction of the proteome term somewhat more than a decade ago the field of proteomics witnessed a rapid growth mainly fueled by instrumental analytical improvements. Of particular notice is the advent of a diverse set of gel-free proteomics techniques. In this review, we discuss several of these gel-free techniques both for monitoring protein concentration changes and protein modifications, in particular protein phosphorylation, glycosylation, and protein processing. Furthermore, different approaches for (multiplexed) gel-free proteome analysis are discussed.
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Affiliation(s)
- Kris Gevaert
- Department of Medical Protein Research, VIB, Ghent, Belgium.
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Gevaert K, Van Damme P, Ghesquière B, Vandekerckhove J. Protein processing and other modifications analyzed by diagonal peptide chromatography. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:1801-10. [PMID: 17035109 DOI: 10.1016/j.bbapap.2006.09.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Revised: 09/06/2006] [Accepted: 09/06/2006] [Indexed: 11/29/2022]
Abstract
Diagonal peptide chromatography consists of two consecutive, identical peptide separations with in between an enzymatic or chemical alteration of the side-chain structure of selected peptides. Such selected and altered peptides acquire different chromatographic properties thereby segregating from non-altered peptides in a series of secondary peptide separations. Originally described by Brown and Hartley in 1966, we have modified the technique such that it can be used for higher throughput gel-free proteomics. Our technique is termed COmbined FRActional DIagonal Chromatography (COFRADIC) and exploits evoked differences of the hydrophobicity of peptides in reverse-phase liquid chromatography. One important advantage of COFRADIC is its versatility: by changing the alteration reaction, different classes of peptides are sorted and finally analyzed. We previously published protocols and applications for separating methionyl, cysteinyl, amino terminal and phosphorylated peptides. In this review, we assess the potential of COFRADIC for the analysis of several posttranslational modifications emphasizing on in vivo protein processing events. Additional modifications that can be analyzed include phosphorylation and N-glycosylation. The potential of COFRADIC for isolating peptides holding such modified amino acids are discussed here.
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Affiliation(s)
- Kris Gevaert
- Department of Medical Protein Research and Biochemistry, Flanders Interuniversity Institute for Biotechnology and Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent, Belgium.
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Ikuta K, Suzuki S, Horikoshi H, Mukai T, Luftig RB. Positive and negative aspects of the human immunodeficiency virus protease: development of inhibitors versus its role in AIDS pathogenesis. Microbiol Mol Biol Rev 2000; 64:725-45. [PMID: 11104817 PMCID: PMC99012 DOI: 10.1128/mmbr.64.4.725-745.2000] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In this review we summarize multiple aspects of the human immunodeficiency virus (HIV) protease from both structural and functional viewpoints. After an introductory overview, we provide an up-to-date status report on protease inhibitors (PI). This proceeds from a discussion of PI structural design, to how PI are optimally utilized in highly active antiretroviral triple therapy (one PI along with two reverse transcriptase inhibitors), the emergence of PI resistance, and the natural role of secretory leukocyte PI. Then we switch to another focus: the interaction of HIV protease with other genes in acute and persistent infection, which in turn may have an effect on AIDS pathogenesis. We conclude with a discussion on future directions in HIV treatment, involving multiple-target anti-HIV therapy, vaccine development, and novel reactivation-inhibitory reagents.
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Affiliation(s)
- K Ikuta
- Department of Virology, Research Institute for Microbial Diseases (Biken), Osaka University, Suita, Osaka 565-0871, Japan.
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Utz PJ, Gensler TJ, Anderson P. Death, autoantigen modifications, and tolerance. ARTHRITIS RESEARCH 2000; 2:101-14. [PMID: 11094420 PMCID: PMC129993 DOI: 10.1186/ar75] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/04/2000] [Revised: 01/17/2000] [Accepted: 01/20/2000] [Indexed: 12/18/2022]
Abstract
Autoantibodies present in the serum of patients with a variety of inflammatory diseases have proven useful as diagnostic markers and as probes with which to elucidate biochemical and signaling pathways. The mechanisms governing the generation of autoantibodies remain elusive, constituting a critical missing link in our understanding of rheumatologic illnesses. Several lines of experimentation in recent years have strongly implicated events surrounding cell death in this process. This review will address the potential role played by death-specific modifications of autoantigens in bypassing tolerance to highly conserved autoantigens, including nucleic acids, lipids, and proteins.
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Affiliation(s)
- P J Utz
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA.
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Konvalinka J, Litterst MA, Welker R, Kottler H, Rippmann F, Heuser AM, Kräusslich HG. An active-site mutation in the human immunodeficiency virus type 1 proteinase (PR) causes reduced PR activity and loss of PR-mediated cytotoxicity without apparent effect on virus maturation and infectivity. J Virol 1995; 69:7180-6. [PMID: 7474139 PMCID: PMC189639 DOI: 10.1128/jvi.69.11.7180-7186.1995] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Infectious retrovirus particles are derived from structural polyproteins which are cleaved by the viral proteinase (PR) during virion morphogenesis. Besides cleaving viral polyproteins, which is essential for infectivity, PR of human immunodeficiency virus (HIV) also cleaves cellular proteins and PR expression causes a pronounced cytotoxic effect. Retroviral PRs are aspartic proteases and contain two copies of the triplet Asp-Thr-Gly in the active center with the threonine adjacent to the catalytic aspartic acid presumed to have an important structural role. We have changed this threonine in HIV type 1 PR to a serine. The purified mutant enzyme had an approximately 5- to 10-fold lower activity against HIV type 1 polyprotein and peptide substrates compared with the wild-type enzyme. It did not induce toxicity on bacterial expression and yielded significantly reduced cleavage of cytoskeletal proteins in vitro. Cleavage of vimentin in mutant-infected T-cell lines was also markedly reduced. Mutant virus did, however, elicit productive infection of several T-cell lines and of primary human lymphocytes with no significant difference in polyprotein cleavage and with similar infection kinetics and titer compared with wild-type virus. The discrepancy between reduced processing in vitro and normal virion maturation can be explained by the observation that reduced activity was due to an increase in Km which may not be relevant at the high substrate concentration in the virus particle. This mutation enables us therefore to dissociate the essential function of PR in viral maturation from its cytotoxic effect.
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Affiliation(s)
- J Konvalinka
- Angewandte Tumorvirologie, Deutsches Krebsforschungszentrum, Heidelberg, Germany
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Gaedigk-Nitschko K, Schön A, Wachinger G, Erfle V, Kohleisen B. Cleavage of recombinant and cell derived human immunodeficiency virus 1 (HIV-1) Nef protein by HIV-1 protease. FEBS Lett 1995; 357:275-8. [PMID: 7835426 DOI: 10.1016/0014-5793(94)01370-g] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Recombinant purified Nef protein of HIV-1, as well as Nef protein derived from extracts of permanently HIV-1 infected glioblastoma cells and monocytes, are specifically cleaved by the HIV-1 protease. Nef cleavage products in cellular extracts treated with protease showed identical molecular weights as those obtained by digestion of purified Nef with recombinant HIV-1 protease. Since cellular extracts were prepared by detergent and mechanical lysis it cannot be excluded that physiological cytoplasmic conditions were altered. The lack of Nef cleavage by endogenous HIV-1 protease in infected cells might be due to low concentrations of viral protease and the presence of Gag precursor molecules as natural substrate. Using a panel of monoclonal antibodies two cleavage fragments of 19 kDa and 8 kDa were defined. The cleavage site was located by microsequencing between amino acid 57 and 58 (AW*LEAQEEEEVGF). The conserved cleavage motif within HIV-1 Nef suggests a potential biological function of Nef processing.
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Affiliation(s)
- K Gaedigk-Nitschko
- GSF-Forschungszentrum für Umwelt und Gesundheit, Institut für Molekulare Virologie, Oberschleissheim, Germany
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Phylip LH, Griffiths JT, Mills JS, Graves MC, Dunn BM, Kay J. Activities of precursor and tethered dimer forms of HIV proteinase. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1995; 362:467-72. [PMID: 8540359 DOI: 10.1007/978-1-4615-1871-6_61] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- L H Phylip
- Department of Biochemistry, University of Wales, Cardiff, U.K
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Rappaport J, Kopp JB, Klotman PE. Host virus interactions and the molecular regulation of HIV-1: role in the pathogenesis of HIV-associated nephropathy. Kidney Int 1994; 46:16-27. [PMID: 7933833 DOI: 10.1038/ki.1994.240] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Luftig RB, Lupo LD. Viral interactions with the host-cell cytoskeleton: the role of retroviral proteases. Trends Microbiol 1994; 2:178-82. [PMID: 8055183 DOI: 10.1016/0966-842x(94)90669-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A surprisingly large number of animal viruses interact with cytoskeletal elements inside infected cells at different stages of replication. For example, a viral protease is activated during assembly of murine leukemia viruses at the cell surface, which causes both the morphological conversion of 'immature' to 'mature' particles and a drastic reduction of the actin stress fiber network.
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Affiliation(s)
- R B Luftig
- Dept of Microbiology, Immunology and Parasitology, Louisiana State University Medical Center, New Orleans 70112-1393
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Phylip LH, Mills JS, Parten BF, Dunn BM, Kay J. Intrinsic activity of precursor forms of HIV-1 proteinase. FEBS Lett 1992; 314:449-54. [PMID: 1468583 DOI: 10.1016/0014-5793(92)81524-p] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The wild-type -Phe*Pro- bond located at the N-terminus of the mature aspartic proteinase of HIV-1 was replaced by -Ile-Pro- or -Val-Pro-. By this means, processing at this cleavage junction was prevented and so, extended or precursor forms of HIV-proteinase were generated. These constructs were expressed in Escherichia coli, purified therefrom, and their specificity, activity at different pH values and susceptibility to the potent inhibitor, Ro31-8959, was assessed. A hitherto unobserved cleavage junction (at approximately Ala-Phe*Leu-Gln approximately) in the frame-shift region of the gag-pol viral genome was identified and confirmed by demonstrating cleavage of a synthetic peptide corresponding to this region. The implications for viral replication of self-processing at neural pH by proteinase whilst still present (in a precursor form) as a component of the polyprotein are considered; such reactions, however, are still blocked even at pH values as high as 8.0 by Ro31-8959.
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Affiliation(s)
- L H Phylip
- Department of Biochemistry, University of Wales College of Cardiff, UK
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