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Minadakis G, Tomazou M, Dietis N, Spyrou GM. Vir2Drug: a drug repurposing framework based on protein similarities between pathogens. Brief Bioinform 2022; 24:6895455. [PMID: 36513376 PMCID: PMC9851336 DOI: 10.1093/bib/bbac536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/25/2022] [Accepted: 11/08/2022] [Indexed: 12/15/2022] Open
Abstract
We draw from the assumption that similarities between pathogens at both pathogen protein and host protein level, may provide the appropriate framework to identify and rank candidate drugs to be used against a specific pathogen. Vir2Drug is a drug repurposing tool that uses network-based approaches to identify and rank candidate drugs for a specific pathogen, combining information obtained from: (a) ranked pathogen-to-pathogen networks based on protein similarities between pathogens, (b) taxonomy distance between pathogens and (c) drugs targeting specific pathogen's and host proteins. The underlying pathogen networks are used to screen drugs by means of specific methodologies that account for either the host or pathogen's protein targets. Vir2Drug is a useful and yet informative tool for drug repurposing against known or unknown pathogens especially in periods where the emergence for repurposed drugs plays significant role in handling viral outbreaks, until reaching a vaccine. The web tool is available at: https://bioinformatics.cing.ac.cy/vir2drug, https://vir2drug.cing-big.hpcf.cyi.ac.cy.
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Affiliation(s)
- George Minadakis
- Corresponding author: George Minadakis, Bioinformatics Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Ayios Dometios, PO Box 23462, 1683 Nicosia, Cyprus. Tel.: +357-22-392852; Fax: +357-22-358238; E-mail:
| | - Marios Tomazou
- Bioinformatics Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Ayios Dometios, Nicosia, Cyprus
- PO Box 23462, 1683 Nicosia, Cyprus,The Cyprus School of Molecular Medicine, 6 Iroon Avenue, 2371 Ayios Dometios, PO Box 23462, 1683 Nicosia, Cyprus
| | - Nikolas Dietis
- Medical School, University of Cyprus, Nicosia 1678, Cyprus
| | - George M Spyrou
- Bioinformatics Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Ayios Dometios, Nicosia, Cyprus
- PO Box 23462, 1683 Nicosia, Cyprus,The Cyprus School of Molecular Medicine, 6 Iroon Avenue, 2371 Ayios Dometios, PO Box 23462, 1683 Nicosia, Cyprus
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2
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Brune KD, Liekniņa I, Sutov G, Morris AR, Jovicevic D, Kalniņš G, Kazāks A, Kluga R, Kastaljana S, Zajakina A, Jansons J, Skrastiņa D, Spunde K, Cohen AA, Bjorkman PJ, Morris HR, Suna E, Tārs K. N-Terminal Modification of Gly-His-Tagged Proteins with Azidogluconolactone. Chembiochem 2021; 22:3199-3207. [PMID: 34520613 DOI: 10.1002/cbic.202100381] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/13/2021] [Indexed: 01/07/2023]
Abstract
Site-specific protein modifications are vital for biopharmaceutical drug development. Gluconoylation is a non-enzymatic, post-translational modification of N-terminal HisTags. We report high-yield, site-selective in vitro α-aminoacylation of peptides, glycoproteins, antibodies, and virus-like particles (VLPs) with azidogluconolactone at pH 7.5 in 1 h. Conjugates slowly hydrolyse, but diol-masking with borate esters inhibits reversibility. In an example, we multimerise azidogluconoylated SARS-CoV-2 receptor-binding domain (RBD) onto VLPs via click-chemistry, to give a COVID-19 vaccine. Compared to yeast antigen, HEK-derived RBD was immunologically superior, likely due to observed differences in glycosylation. We show the benefits of ordered over randomly oriented multimeric antigen display, by demonstrating single-shot seroconversion and best virus-neutralizing antibodies. Azidogluconoylation is simple, fast and robust chemistry, and should accelerate research and development.
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Affiliation(s)
- Karl D Brune
- Genie Biotech Ltd., Lido Medical Centre, St. Saviour, JE2 7LA, United Kingdom.,Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Ilva Liekniņa
- Latvian Biomedical Research and Study Centre, Ratsupites 1, 1067, Riga, Latvia
| | - Grigorij Sutov
- Genie Biotech Ltd., Lido Medical Centre, St. Saviour, JE2 7LA, United Kingdom.,Lab Group LT, UAB, Vilnius, Lithuania
| | - Alexander R Morris
- Genie Biotech Ltd., Lido Medical Centre, St. Saviour, JE2 7LA, United Kingdom.,Lab Group LT, UAB, Vilnius, Lithuania.,BioPharmaSpec Ltd., Suite 3.1, Lido Medical Centre, St. Saviour, JE2 7LA, UK
| | - Dejana Jovicevic
- Genie Biotech Ltd., Lido Medical Centre, St. Saviour, JE2 7LA, United Kingdom
| | - Gints Kalniņš
- Latvian Biomedical Research and Study Centre, Ratsupites 1, 1067, Riga, Latvia
| | - Andris Kazāks
- Latvian Biomedical Research and Study Centre, Ratsupites 1, 1067, Riga, Latvia
| | - Rihards Kluga
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006, Riga, Latvia.,University of Latvia, Jelgavas 1, 1004, Riga, Latvia
| | - Sabine Kastaljana
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006, Riga, Latvia.,University of Latvia, Jelgavas 1, 1004, Riga, Latvia
| | - Anna Zajakina
- Latvian Biomedical Research and Study Centre, Ratsupites 1, 1067, Riga, Latvia
| | - Juris Jansons
- Latvian Biomedical Research and Study Centre, Ratsupites 1, 1067, Riga, Latvia
| | - Dace Skrastiņa
- Latvian Biomedical Research and Study Centre, Ratsupites 1, 1067, Riga, Latvia
| | - Karīna Spunde
- Latvian Biomedical Research and Study Centre, Ratsupites 1, 1067, Riga, Latvia
| | - Alexander A Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Howard R Morris
- BioPharmaSpec Ltd., Suite 3.1, Lido Medical Centre, St. Saviour, JE2 7LA, UK.,Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Edgars Suna
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006, Riga, Latvia.,University of Latvia, Jelgavas 1, 1004, Riga, Latvia
| | - Kaspars Tārs
- Latvian Biomedical Research and Study Centre, Ratsupites 1, 1067, Riga, Latvia.,University of Latvia, Jelgavas 1, 1004, Riga, Latvia
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3
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Abstract
In HIV-infected patients on combination antiretroviral therapy (cART), greater than 95% of proviruses in the peripheral blood are “defective.” Historically, these defective proviruses have been thought to be dead-end products with no real pathophysiological significance, as they do not encode replication-competent viruses. Contrary to this view, we have identified cells in tissue culture and from cART-treated patients that harbor defective proviruses and produce viral proteins. Features found in these translationally competent yet defective proviruses suggest that HIV-1 infection results in modification of the CD4+ T cell genome analogous to human endogenous retroviruses. We propose that these defective HIV-1 proviruses are biologically significant, despite being “replication incompetent,” have the potential to elicit immune activation, and may serve as a barrier to HIV-1 cure. HIV-1 proviruses persist in the CD4+ T cells of HIV-infected individuals despite years of combination antiretroviral therapy (cART) with suppression of HIV-1 RNA levels <40 copies/mL. Greater than 95% of these proviruses detected in circulating peripheral blood mononuclear cells (PBMCs) are referred to as “defective” by virtue of having large internal deletions and lethal genetic mutations. As these defective proviruses are unable to encode intact and replication-competent viruses, they have long been thought of as biologically irrelevant “graveyard” of viruses with little significance to HIV-1 pathogenesis. Contrary to this notion, we have recently demonstrated that these defective proviruses are not silent, are capable of transcribing novel unspliced forms of HIV-RNA transcripts with competent open reading frames (ORFs), and can be found in the peripheral blood CD4+ T cells of patients at all stages of HIV-1 infection. In the present study, by an approach of combining serial dilutions of CD4+ T cells and T cell–cloning technologies, we are able to demonstrate that defective proviruses that persist in HIV-infected individuals during suppressive cART are translationally competent and produce the HIV-1 Gag and Nef proteins. The HIV-RNA transcripts expressed from these defective proviruses may trigger an element of innate immunity. Likewise, the viral proteins coded in the defective proviruses may form extracellular virus-like particles and may trigger immune responses. The persistent production of HIV-1 proteins in the absence of viral replication helps explain persistent immune activation despite HIV-1 levels below detection, and also presents new challenges to HIV-1 eradication.
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4
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Palmeira JDF, Argañaraz GA, de Oliveira GXLM, Argañaraz ER. Physiological relevance of ACOT8-Nef interaction in HIV infection. Rev Med Virol 2019; 29:e2057. [PMID: 31179598 DOI: 10.1002/rmv.2057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 04/29/2019] [Accepted: 05/01/2019] [Indexed: 11/06/2022]
Abstract
During human immunodeficiency virus (HIV) infection, Nef viral protein plays a crucial role in viral pathogenesis and progression of acquired immunodeficiency syndrome. Nef is expressed in the early stages of infection and alters the cellular environment increasing infectivity, viral replication, and the evasion of host immune response through several mechanisms. Nef has numerous functional domains that allow it to interact with a number of proteins, interfering with intracellular traffic. Among these proteins, human peroxisomal thioesterase 8, ACOT8, has been shown to be an important cellular partner of Nef. It has been suggested that this interaction may be involved in Nef-dependent endocytosis and also in the modulation of lipid composition in membrane rafts. However, the actual role of this interaction, as well as the mechanisms involved, has not yet been fully elucidated. In this review, we focused on the interplay between Nef and ACOT8 proteins, highlighting the possible physiological relevance in HIV infection.
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Affiliation(s)
| | - Gustavo A Argañaraz
- Laboratory of Molecular Neurovirology, Faculty of Health Science, University of Brasília, Brazil
| | | | - Enrique R Argañaraz
- Laboratory of Molecular Neurovirology, Faculty of Health Science, University of Brasília, Brazil
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5
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Moroco JA, Alvarado JJ, Staudt RP, Shi H, Wales TE, Smithgall TE, Engen JR. Remodeling of HIV-1 Nef Structure by Src-Family Kinase Binding. J Mol Biol 2018; 430:310-321. [PMID: 29258818 PMCID: PMC5801098 DOI: 10.1016/j.jmb.2017.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/07/2017] [Accepted: 12/10/2017] [Indexed: 11/25/2022]
Abstract
The HIV-1 accessory protein Nef controls multiple aspects of the viral life cycle and host immune response, making it an attractive therapeutic target. Previous X-ray crystal structures of Nef in complex with key host cell binding partners have shed light on protein-protein interactions critical to Nef function. Crystal structures of Nef in complex with either the SH3 or tandem SH3-SH2 domains of Src-family kinases reveal distinct dimer conformations of Nef. However, the existence of these Nef dimer complexes in solution has not been established. Here we used hydrogen exchange mass spectrometry (HX MS) to compare the solution conformation of Nef alone and in complexes with the SH3 or the SH3-SH2 domains of the Src-family kinase Hck. HX MS revealed that interaction with the Hck SH3 or tandem SH3-SH2 domains induces protection of the Nef αB-helix from deuterium uptake, consistent with a role for αB in dimer formation. HX MS analysis of a Nef mutant (position Asp123, a site buried in the Nef:SH3 dimer but surface exposed in the Nef:SH3-SH2 complex), showed a Hck-induced conformational change in Nef relative to wild-type Nef. These results support a model in which Src-family kinase binding induces conformational changes in Nef to expose residues critical for interaction with the μ1 subunit of adaptor protein 1 and the major histocompatibility complex-1 tail, and subsequent major histocompatibility complex-1 downregulation and immune escape of HIV-infected cells required for functional interactions with downstream binding partners.
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Affiliation(s)
- Jamie A Moroco
- Department of Chemistry and Chemical Biology, Maildrop 412TF, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA.
| | - John Jeff Alvarado
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 450 Technology Drive, Pittsburgh, PA 15219, USA.
| | - Ryan P Staudt
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 450 Technology Drive, Pittsburgh, PA 15219, USA.
| | - Haibin Shi
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 450 Technology Drive, Pittsburgh, PA 15219, USA.
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Maildrop 412TF, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA.
| | - Thomas E Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 450 Technology Drive, Pittsburgh, PA 15219, USA.
| | - John R Engen
- Department of Chemistry and Chemical Biology, Maildrop 412TF, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA.
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6
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Abstract
Supplemental Digital Content is Available in the Text. Background: Antiretroviral drug discovery and formulation design will facilitate viral clearance in infectious reservoirs. Although progress has been realized for selected hydrophobic integrase and nonnucleoside reverse transcriptase inhibitors, limited success has been seen to date with hydrophilic nucleosides. To overcome these limitations, hydrophobic long-acting drug nanoparticles were created for the commonly used nucleoside reverse transcriptase inhibitor, lamivudine (2′,3′-dideoxy-3′-thiacytidine, 3TC). Methods: A 2-step synthesis created a slow-release long-acting hydrophobic 3TC. Conjugation of 3TC to a fatty acid created a myristoylated prodrug which was encased into a folate-decorated poloxamer 407. Both in vitro antiretroviral efficacy in human monocyte-derived macrophages and pharmacokinetic profiles in mice were evaluated for the decorated nanoformulated drug. Results: A stable drug formulation was produced by poloxamer encasement that improved monocyte–macrophage uptake, antiretroviral activities, and drug pharmacokinetic profiles over native drug formulations. Conclusions: Sustained release of long-acting antiretroviral therapy is a new therapeutic frontier for HIV/AIDS. 3TC depot formation in monocyte-derived macrophages can be facilitated through stable subcellular internalization and slow drug release.
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8
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Flamm AG, Le Roux AL, Mateos B, Díaz-Lobo M, Storch B, Breuker K, Konrat R, Pons M, Coudevylle N. N-Lauroylation during the Expression of Recombinant N-Myristoylated Proteins: Implications and Solutions. Chembiochem 2016; 17:82-9. [PMID: 26522884 PMCID: PMC4736449 DOI: 10.1002/cbic.201500454] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Indexed: 12/12/2022]
Abstract
Incorporation of myristic acid onto the N terminus of a protein is a crucial modification that promotes membrane binding and correct localization of important components of signaling pathways. Recombinant expression of N-myristoylated proteins in Escherichia coli can be achieved by co-expressing yeast N-myristoyltransferase and supplementing the growth medium with myristic acid. However, undesired incorporation of the 12-carbon fatty acid lauric acid can also occur (leading to heterogeneous samples), especially when the available carbon sources are scarce, as it is the case in minimal medium for the expression of isotopically enriched samples. By applying this method to the brain acid soluble protein 1 and the 1-185 N-terminal region of c-Src, we show the significant, and protein-specific, differences in the membrane binding properties of lauroylated and myristoylated forms. We also present a robust strategy for obtaining lauryl-free samples of myristoylated proteins in both rich and minimal media.
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Affiliation(s)
- Andrea Gabriele Flamm
- Department of Computational and Structural Biology, F. Max Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Anabel-Lise Le Roux
- Biomolecular NMR Laboratory, Department of Organic Chemistry, University of Barcelona, Baldiri Reixac 10-12, 08028, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10-12, 08028, Barcelona, Spain
| | - Borja Mateos
- Biomolecular NMR Laboratory, Department of Organic Chemistry, University of Barcelona, Baldiri Reixac 10-12, 08028, Barcelona, Spain
| | - Mireia Díaz-Lobo
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10-12, 08028, Barcelona, Spain
| | - Barbara Storch
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, CCB, Innrain 80/82, 6020, Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, CCB, Innrain 80/82, 6020, Innsbruck, Austria
| | - Robert Konrat
- Department of Computational and Structural Biology, F. Max Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Miquel Pons
- Biomolecular NMR Laboratory, Department of Organic Chemistry, University of Barcelona, Baldiri Reixac 10-12, 08028, Barcelona, Spain
| | - Nicolas Coudevylle
- Department of Computational and Structural Biology, F. Max Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria.
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9
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Pirrone GF, Emert-Sedlak LA, Wales TE, Smithgall TE, Kent MS, Engen JR. Membrane-Associated Conformation of HIV-1 Nef Investigated with Hydrogen Exchange Mass Spectrometry at a Langmuir Monolayer. Anal Chem 2015; 87:7030-5. [PMID: 26133569 PMCID: PMC4509969 DOI: 10.1021/acs.analchem.5b01725] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the companion paper to this work, we described development of a new type of hydrogen exchange (HX) mass spectrometry (MS) measurement that integrates Langmuir monolayers. With Langmuir monolayers, the lipid packing density can be reproducibly controlled and changed as desired. Analysis of HX in proteins that may undergo conformational changes as a function of lipid packing (for example, conformational rearrangements after insertion into a lipid layer) are then possible. We previously used neutron reflection to characterize just such a conformational change in the myristoylated HIV-1 Nef protein (myrNef): at high lipid packing density, myrNef could not insert into the lipids and maintained a compact conformation adjacent to the monolayer, whereas at lower lipid packing density, myrNef was able to insert N-terminal arm residues, causing displacement of the core domain away from the monolayer. In order to locate where conformation may have been altered by lipid association, we applied the HX MS Langmuir monolayer method to myrNef associated with monolayers of packing densities identical to those used for the prior neutron reflection measurements. The results show that the N-terminal region and the C-terminal unstructured loop undergo conformational changes when associated with a low density lipid monolayer. The results are not consistent with the hypothesis of myrNef dimerization upon membrane association in the absence of other myrNef binding partners. The HX MS Langmuir monolayer method provides new and meaningful information for myrNef that helps explain necessary conformational changes required for function at the membrane.
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Affiliation(s)
- Gregory F. Pirrone
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115
| | - Lori A. Emert-Sedlak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219
| | - Thomas E. Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115
| | - Thomas E. Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219
| | - Michael S. Kent
- Bioenergy and Defense Technologies, Sandia National Laboratories, Albuquerque, NM 87185
| | - John R. Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115
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10
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Pirrone GF, Vernon BC, Kent MS, Engen JR. Hydrogen Exchange Mass Spectrometry of Proteins at Langmuir Monolayers. Anal Chem 2015; 87:7022-9. [PMID: 26134943 DOI: 10.1021/acs.analchem.5b01724] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Hydrogen exchange (HX) mass spectrometry (MS) is valuable for providing conformational information for proteins/peptides that are very difficult to analyze with other methods such as peripheral membrane proteins and peptides that interact with membranes. We developed a new type of HX MS measurement that integrates Langmuir monolayers. A lipid monolayer was generated, a peptide or protein associated with it, and then the monolayer-associated peptide or protein was exposed to deuterium. The deuterated species was recovered from the monolayer, digested, and deuterium incorporation monitored by MS. Test peptides showed that deuterium recovery in an optimized protocol was equivalent to deuterium recovery in conventional solution HX MS. The reproducibility of the measurements was high, despite the requirement of generating a new monolayer for each deuterium labeling time. We validated that known conformational changes in the presence of a monolayer/membrane could be observed with the peptide melittin and the myristoylated protein Arf-1. Results in an accompanying paper show that the method can reveal details of conformational changes in a protein (HIV-1 Nef), which adopts a different conformation, depending on whether or not it is able to insert into the lipid layer. Overall, the HX MS Langmuir monolayer method provided new and meaningful conformational information for proteins that associate with lipid layers. The combination of HX MS results with neutron or X-ray reflection of the same proteins in Langmuir monolayers can be more informative than the isolated use of either method.
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Affiliation(s)
- Gregory F Pirrone
- †Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115-5000, United States
| | - Briana C Vernon
- ‡Bioenergy and Defense Technologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Michael S Kent
- ‡Bioenergy and Defense Technologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - John R Engen
- †Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115-5000, United States
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11
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Colquhoun DR, Lyashkov AE, Ubaida Mohien C, Aquino VN, Bullock BT, Dinglasan RR, Agnew BJ, Graham DRM. Bioorthogonal mimetics of palmitoyl-CoA and myristoyl-CoA and their subsequent isolation by click chemistry and characterization by mass spectrometry reveal novel acylated host-proteins modified by HIV-1 infection. Proteomics 2015; 15:2066-77. [PMID: 25914232 DOI: 10.1002/pmic.201500063] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 03/15/2015] [Accepted: 04/23/2015] [Indexed: 01/28/2023]
Abstract
Protein acylation plays a critical role in protein localization and function. Acylation is essential for human immunodeficiency virus 1 (HIV-1) assembly and budding of HIV-1 from the plasma membrane in lipid raft microdomains and is mediated by myristoylation of the Gag polyprotein and the copackaging of the envelope protein is facilitated by colocalization mediated by palmitoylation. Since the viral accessory protein NEF has been shown to alter the substrate specificity of myristoyl transferases, and alter cargo trafficking lipid rafts, we hypothesized that HIV-1 infection may alter protein acylation globally. To test this hypothesis, we labeled HIV-1 infected cells with biomimetics of acyl azides, which are incorporated in a manner analogous to natural acyl-Co-A. A terminal azide group allowed us to use a copper catalyzed click chemistry to conjugate the incorporated modifications to a number of substrates to carry out SDS-PAGE, fluorescence microscopy, and enrichment for LC-MS/MS. Using LC-MS/MS, we identified 103 and 174 proteins from the myristic and palmitic azide enrichments, with 27 and 45 proteins respectively that differentiated HIV-1 infected from uninfected cells. This approach has provided us with important insights into HIV-1 biology and is widely applicable to many virological systems.
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Affiliation(s)
- David R Colquhoun
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alexey E Lyashkov
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ceereena Ubaida Mohien
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Veronica N Aquino
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Brandon T Bullock
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rhoel R Dinglasan
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Brian J Agnew
- Biosciences Group, Thermo Fisher Scientific, Eugene, OR, USA
| | - David R M Graham
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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12
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Geist MM, Pan X, Bender S, Bartenschlager R, Nickel W, Fackler OT. Heterologous Src homology 4 domains support membrane anchoring and biological activity of HIV-1 Nef. J Biol Chem 2014; 289:14030-44. [PMID: 24706755 DOI: 10.1074/jbc.m114.563528] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The HIV-1 pathogenicity factor Nef enhances viral replication by modulation of multiple host cell transport and signaling pathways. Nef associates with membranes via an N-terminal Src homology 4 (SH4) domain, and membrane association is believed to be essential for its biological functions. At which subcellular site(s) Nef exerts its different functions and how kinetics of membrane interactions contribute to its biological activity are unknown. To address how specific characteristics of Nef membrane association affect its biological properties, the SH4 domain of Nef was replaced by heterologous membrane targeting domains. The use of a panel of heterologous SH4 domains resulted in chimeric Nef proteins with distinct steady state subcellular localization, membrane association efficiency, and anterograde transport routes. Irrespective of these modifications, cardinal Nef functions affecting host cell vesicular transport and actin dynamics were fully preserved. In contrast, stable targeting of Nef to the surface of mitochondria, peroxisomes, or the Golgi apparatus, and thus prevention of plasma membrane delivery, caused potent and broad loss of Nef activity. These results support the concept that Nef adopts its active conformation in the membrane-associated state but exclude that membrane-associated Nef simply acts by recruiting soluble factors independently of its local microenvironment. Rather than its steady state subcellular localization or membrane affinity, the ability to undergo dynamic anterograde and internalization cycles appear to determine Nef function. These results reveal that functional membrane interactions of Nef underlie critical spatiotemporal regulation and suggest that delivery to distinct subcellular sites via such transport cycles provides the basis for the multifunctionality of Nef.
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Affiliation(s)
- Miriam M Geist
- From the Department of Infectious Diseases, Integrative Virology and
| | - Xiaoyu Pan
- From the Department of Infectious Diseases, Integrative Virology and
| | - Silke Bender
- Molecular Virology, University Hospital Heidelberg,69120 Heidelberg, Germany and
| | - Ralf Bartenschlager
- Molecular Virology, University Hospital Heidelberg,69120 Heidelberg, Germany and
| | - Walter Nickel
- the Biochemistry Center, Heidelberg University, 69120 Heidelberg, Germany
| | - Oliver T Fackler
- From the Department of Infectious Diseases, Integrative Virology and
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13
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Jacob D, Hunegnaw R, Sabyrzyanova TA, Pushkarsky T, Chekhov VO, Adzhubei AA, Kalebina TS, Bukrinsky M. The ABCA1 domain responsible for interaction with HIV-1 Nef is conformational and not linear. Biochem Biophys Res Commun 2014; 444:19-23. [PMID: 24406162 DOI: 10.1016/j.bbrc.2013.12.141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 12/30/2013] [Indexed: 12/11/2022]
Abstract
HIV-1 Nef is an accessory protein responsible for inactivation of a number of host cell proteins essential for anti-viral immune responses. In most cases, Nef binds to the target protein and directs it to a degradation pathway. Our previous studies demonstrated that Nef impairs activity of the cellular cholesterol transporter, ABCA1, and that Nef interacts with ABCA1. Mutation of the (2226)DDDHLK motif in the C-terminal cytoplasmic tail of ABCA1 disrupted interaction with Nef. Here, we tested Nef interaction with the ABCA1 C-terminal cytoplasmic fragment using yeast 2-hybrid system assay and co-immunoprecipitation analysis in human cells. Surprisingly, analysis in a yeast 2-hybrid system did not reveal any interaction between Nef and the C-terminal cytoplasmic fragment of ABCA1. Using co-immunoprecipitation from HEK 293T cells expressing these polypeptides, only a very weak interaction could be detected. The (2226)DDDHLK motif in the C-terminal cytoplasmic tail of ABCA1 found previously to be essential for interaction between ABCA1 and Nef is insufficient to bestow strong binding to Nef. Molecular modeling suggested that interaction with Nef may be mediated by a conformational epitope composed of the sequences within the cytoplasmic loop of ABCA1 and the C-terminal cytoplasmic domain. Studies are now underway to characterize this epitope.
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Affiliation(s)
- Daria Jacob
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119899, Russia
| | - Ruth Hunegnaw
- Department of Microbiology, Immunology and Tropical Medicine, GWU School of Medicine and Health Sciences, Washington, DC 20037, USA
| | - Tatyana A Sabyrzyanova
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119899, Russia
| | - Tatiana Pushkarsky
- Department of Microbiology, Immunology and Tropical Medicine, GWU School of Medicine and Health Sciences, Washington, DC 20037, USA
| | - Vladimir O Chekhov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov St. 32, 119991 Moscow, Russia
| | - Alexei A Adzhubei
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov St. 32, 119991 Moscow, Russia
| | - Tatyana S Kalebina
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119899, Russia
| | - Michael Bukrinsky
- Department of Microbiology, Immunology and Tropical Medicine, GWU School of Medicine and Health Sciences, Washington, DC 20037, USA.
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14
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Akgun B, Satija S, Nanda H, Pirrone GF, Shi X, Engen JR, Kent MS. Conformational transition of membrane-associated terminally acylated HIV-1 Nef. Structure 2013; 21:1822-33. [PMID: 24035710 DOI: 10.1016/j.str.2013.08.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 07/08/2013] [Accepted: 08/02/2013] [Indexed: 01/26/2023]
Abstract
Many proteins are posttranslationally modified by acylation targeting them to lipid membranes. While methods such as X-ray crystallography and nuclear magnetic resonance are available to determine the structure of folded proteins in solution, the precise position of folded domains relative to a membrane remains largely unknown. We used neutron and X-ray reflection methods to measure the displacement of the core domain of HIV Nef from lipid membranes upon insertion of the N-terminal myristate group. Nef is one of several HIV-1 accessory proteins and an essential factor in AIDS progression. Upon insertion of the myristate and residues from the N-terminal arm, Nef transitions from a closed-to-open conformation that positions the core domain 70 Å from the lipid headgroups. This work rules out previous speculation that the Nef core remains closely associated with the membrane to optimize interactions with the cytoplasmic domain of MHC-1.
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Affiliation(s)
- Bulent Akgun
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742, USA; Department of Chemistry, Boğaziçi University, Bebek 34342, Istanbul, Turkey
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15
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Majumdar R, Manikwar P, Hickey JM, Arora J, Middaugh CR, Volkin DB, Weis DD. Minimizing carry-over in an online pepsin digestion system used for the H/D exchange mass spectrometric analysis of an IgG1 monoclonal antibody. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:2140-2148. [PMID: 22993047 DOI: 10.1007/s13361-012-0485-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 08/21/2012] [Accepted: 08/22/2012] [Indexed: 06/01/2023]
Abstract
Chromatographic carry-over can severely distort measurements of amide H/D exchange in proteins analyzed by LC/MS. In this work, we explored the origin of carry-over in the online digestion of an IgG1 monoclonal antibody using an immobilized pepsin column under quenched H/D exchange conditions (pH 2.5, 0 °C). From a consensus list of 169 different peptides consistently detected during digestion of this large, ~150 kDa protein, approximately 30% of the peptic peptides exhibited carry-over. The majority of carry-over originates from the online digestion. Carry-over can be substantially decreased by washing the online digestion flow-path and pepsin column with two wash cocktails: [acetonitrile (5%)/isopropanol (5%)/acetic acid (20%) in water] and [2 M guanidine hydrochloride in 100 mM phosphate buffer pH 2.5]. Extended use of this two-step washing procedure does not adversely affect the specificity or activity of the immobilized pepsin column. The results suggest that although the mechanism of carry-over appears to be chemical in nature, and not hydrodynamic, carry-over cannot be attributed to a single factor such as mass, abundance, pI, or hydrophobicity of the peptides.
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Affiliation(s)
- Ranajoy Majumdar
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66047, USA
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16
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Lim JC, Gruschus JM, Ghesquière B, Kim G, Piszczek G, Tjandra N, Levine RL. Characterization and solution structure of mouse myristoylated methionine sulfoxide reductase A. J Biol Chem 2012; 287:25589-95. [PMID: 22661718 PMCID: PMC3408158 DOI: 10.1074/jbc.m112.368936] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 06/01/2012] [Indexed: 11/06/2022] Open
Abstract
Methionine sulfoxide reductase A is an essential enzyme in the antioxidant system which scavenges reactive oxygen species through cyclic oxidation and reduction of methionine and methionine sulfoxide. The cytosolic form of the enzyme is myristoylated, but it is not known to translocate to membranes, and the function of myristoylation is not established. We compared the biochemical and biophysical properties of myristoylated and nonmyristoylated mouse methionine sulfoxide reductase A. These were almost identical for both forms of the enzyme, except that the myristoylated form reduced methionine sulfoxide in protein much faster than the nonmyristoylated form. We determined the solution structure of the myristoylated protein and found that the myristoyl group lies in a relatively surface exposed "myristoyl nest." We propose that this structure functions to enhance protein-protein interaction.
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Affiliation(s)
| | | | - Bart Ghesquière
- From the Laboratory of Biochemistry
- the Department of Biochemistry, Ghent University and Department for Medical Protein Research, VIB, B-9000 Ghent, Belgium
| | | | - Grzegorz Piszczek
- Biophysics Core Facility, NHLBI, National Institutes of Health, Bethesda, Maryland 20892-8012 and
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17
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Intracellular overexpression of HIV-1 Nef impairs differentiation and maturation of monocytic precursors towards dendritic cells. PLoS One 2012; 7:e40179. [PMID: 22808111 PMCID: PMC3392284 DOI: 10.1371/journal.pone.0040179] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 06/02/2012] [Indexed: 12/31/2022] Open
Abstract
Nef functions as an immunosuppressive factor critical for HIV-1 replication, survival and development of AIDS following HIV-1 infection. What effects Nef exerts on differentiation and maturation of monocytes towards dendritic cells (DCs) remains greatly controversial. In this study, we used THP-1 (human monocytic leukemia cell line) as monocytic DC precursors to investigate how overexpression of HIV-1 Nef influences the processes of differentiation and maturation of dendritic cells. In striking contrast to negative controls, our results showed that morphological and phenotypical changes (CD11c, CD14, CD40, CD80, CD83, CD86, and HLA-DR) occurred on recombinant THP-1 expressing HIV-1 Nef (short for Nef) upon co-stimulation of GM-CSF/IL-4 or GM-CSF/IL-4/TNF-α/ionomycin. Moreover, CD4, CCR5, and CXCR4 were also down-regulated on Nef. It might be hypothesized that Nef prevents superinfection and signal transduction in HIV-1 infected monocytes. Collectively, our study demonstrates that long-lasting expression of Nef at high levels indeed retards differentiation and maturation of dendritic cells in terms of phenotype and morphology. We are hopeful that potentially, stable expression of intracellular Nef in vivo may function as a subtle mode to support long-lasting HIV-1 existence.
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18
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Wei H, Ahn J, Yu YQ, Tymiak A, Engen JR, Chen G. Using hydrogen/deuterium exchange mass spectrometry to study conformational changes in granulocyte colony stimulating factor upon PEGylation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:498-504. [PMID: 22227798 PMCID: PMC3438904 DOI: 10.1007/s13361-011-0310-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 11/22/2011] [Accepted: 11/28/2011] [Indexed: 05/12/2023]
Abstract
PEGylation is the covalent attachment of polyethylene glycol to proteins, and it can be used to alter immunogenicity, circulating half life and other properties of therapeutic proteins. To determine the impact of PEGylation on protein conformation, we applied hydrogen/deuterium exchange mass spectrometry (HDX MS) to analyze granulocyte colony stimulating factor (G-CSF) upon PEGylation as a model system. The combined use of HDX automation technology and data analysis software allowed reproducible and robust measurements of the deuterium incorporation levels for peptic peptides of both PEGylated and non-PEGylated G-CSF. The results indicated that significant differences in deuterium incorporation were induced by PEGylation of G-CSF, although the overall changes observed were quite small. PEGylation did not result in gross conformational rearrangement of G-CSF. The data complexity often encountered in HDX MS measurements was greatly reduced through a data processing and presentation format designed to facilitate the comparison process. This study demonstrates the practical utility of HDX MS for comparability studies, process monitoring, and protein therapeutic characterization in the biopharmaceutical industry.
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Affiliation(s)
- Hui Wei
- Department of Bioanalytical and Discovery Analytical Sciences, Bristol-Myers Squibb, Princeton, NJ, USA.
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