1
|
Kammula EC, Mötter J, Gorgels A, Jonas E, Hoffmann S, Willbold D. Brain transcriptome-wide screen for HIV-1 Nef protein interaction partners reveals various membrane-associated proteins. PLoS One 2012; 7:e51578. [PMID: 23284715 PMCID: PMC3524239 DOI: 10.1371/journal.pone.0051578] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 11/02/2012] [Indexed: 01/23/2023] Open
Abstract
HIV-1 Nef protein contributes essentially to the pathology of AIDS by a variety of protein-protein-interactions within the host cell. The versatile functionality of Nef is partially attributed to different conformational states and posttranslational modifications, such as myristoylation. Up to now, many interaction partners of Nef have been identified using classical yeast two-hybrid screens. Such screens rely on transcriptional activation of reporter genes in the nucleus to detect interactions. Thus, the identification of Nef interaction partners that are integral membrane proteins, membrane-associated proteins or other proteins that do not translocate into the nucleus is hampered. In the present study, a split-ubiquitin based yeast two-hybrid screen was used to identify novel membrane-localized interaction partners of Nef. More than 80% of the hereby identified interaction partners of Nef are transmembrane proteins. The identified hits are GPM6B, GPM6A, BAP31, TSPAN7, CYB5B, CD320/TCblR, VSIG4, PMEPA1, OCIAD1, ITGB1, CHN1, PH4, CLDN10, HSPA9, APR-3, PEBP1 and B3GNT, which are involved in diverse cellular processes like signaling, apoptosis, neurogenesis, cell adhesion and protein trafficking or quality control. For a subfraction of the hereby identified proteins we present data supporting their direct interaction with HIV-1 Nef. We discuss the results with respect to many phenotypes observed in HIV infected cells and patients. The identified Nef interaction partners may help to further elucidate the molecular basis of HIV-related diseases.
Collapse
Affiliation(s)
- Ellen C. Kammula
- Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
- Institute of Physical Biology, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Jessica Mötter
- Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
- Institute of Physical Biology, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Alexandra Gorgels
- Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
| | - Esther Jonas
- Institute of Physical Biology, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Silke Hoffmann
- Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
| | - Dieter Willbold
- Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
- Institute of Physical Biology, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- * E-mail:
| |
Collapse
|
2
|
Singh P, Yadav GP, Gupta S, Tripathi AK, Ramachandran R, Tripathi RK. A novel dimer-tetramer transition captured by the crystal structure of the HIV-1 Nef. PLoS One 2011; 6:e26629. [PMID: 22073177 PMCID: PMC3206816 DOI: 10.1371/journal.pone.0026629] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 09/29/2011] [Indexed: 11/19/2022] Open
Abstract
HIV-1 Nef modulates disease progression through interactions with over 30 host proteins. Individual chains fold into membrane-interacting N-terminal and C-terminal core (Nef(core)) domains respectively. Nef exists as small oligomers near membranes and associates into higher oligomers such as tetramers or hexadecamers in the cytoplasm. Earlier structures of the Nef(core) in apo and complexed forms with the Fyn-kinase SH3 domain revealed dimeric association details and the role of the conserved PXXP recognition motif (residues 72-78) of Nef in SH3-domain interactions. The crystal structure of the tetrameric Nef reported here corresponds to the elusive cytoplasmic stage. Comparative analyses show that subunits of Nef(core) dimers (open conformation) swing out with a relative displacement of ~22 Å and rotation of ~174° to form the 'closed' tetrameric structure. The changes to the association are around Asp125, a conserved residue important for viral replication and the important XR motif (residues 107-108). The tetramer associates through C4 symmetry instead of the 222 symmetry expected when two dimers associate together. This novel dimer-tetramer transition agrees with earlier solution studies including small angle X-ray scattering, analytical ultracentrifugation, dynamic laser light scattering and our glutaraldehyde cross-linking experiments. Comparisons with the Nef(core)--Fyn-SH3 domain complexes reveal that the PXXP motif that interacts with the SH3-domain in the dimeric form is sterically occluded in the tetramer. However the 151-180 loop that is distal to the PXXP motif and contains several protein interaction motifs remains accessible. The results suggest how changes to the oligomeric state of Nef can help it distinguish between protein partners.
Collapse
Affiliation(s)
- Pankaj Singh
- Toxicology Division, Central Drug Research Institute (Council of Scientific & Industrial Research), Chattar Manzil, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, India
| | - Gaya Prasad Yadav
- Molecular and Structural Biology Division, Central Drug Research Institute (Council of Scientific & Industrial Research), Chattar Manzil, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, India
| | - Sudeepti Gupta
- Toxicology Division, Central Drug Research Institute (Council of Scientific & Industrial Research), Chattar Manzil, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, India
| | - Anil Kumar Tripathi
- Chatrapati Shahuji Maharaj Medical University, Chowk, Lucknow, Uttar Pradesh, India
| | - Ravishankar Ramachandran
- Molecular and Structural Biology Division, Central Drug Research Institute (Council of Scientific & Industrial Research), Chattar Manzil, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, India
| | - Raj Kamal Tripathi
- Toxicology Division, Central Drug Research Institute (Council of Scientific & Industrial Research), Chattar Manzil, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, India
| |
Collapse
|
3
|
Abstract
The HIV-1 accessory protein Nef is N-terminally myristoylated, and this post-translational modification is essential for Nef function in AIDS progression. Transfer of a myristate group from myristoyl coenzyme A to Nef occurs cotranslationally and is catalyzed by human N-myristoyltransferase 1 (NMT). To investigate the conformational effects of myristoylation on Nef structure as well as to probe the nature of the Nef:NMT complex, we investigated various forms of Nef with hydrogen exchange mass spectrometry. Conformational changes in Nef were not detected as a result of myristoylation, and NMT had no effect on deuterium uptake by Nef in a myrNef:NMT complex. However, myrNef binding did have an effect on NMT deuterium uptake. Major HX differences in NMT were primarily located around the active site, with more subtle differences, at the longer time points, across the structure. At the shortest time point, significant differences between the two states were observed in two regions which interact strongly with the phosphate groups of coenzyme A. On the basis of our results, we propose a model of the Nef:NMT complex in which only the myristoyl moiety holds the two proteins together in complex and speculate that perhaps NMT chaperones Nef to the membrane and thereby protects the myristic acid group from the cytosol rather than Nef operating through a myristoyl switch mechanism.
Collapse
Affiliation(s)
- Christopher R. Morgan
- Department of Chemistry & Chemical Biology and The Barnett Institute of Chemical & Biological Analysis, Northeastern University, Boston, MA 02115, USA
| | - Brian V. Miglionico
- Department of Chemistry & Chemical Biology and The Barnett Institute of Chemical & Biological Analysis, Northeastern University, Boston, MA 02115, USA
| | - John R. Engen
- Department of Chemistry & Chemical Biology and The Barnett Institute of Chemical & Biological Analysis, Northeastern University, Boston, MA 02115, USA
| |
Collapse
|
4
|
Kent MS, Murton JK, Sasaki DY, Satija S, Akgun B, Nanda H, Curtis JE, Majewski J, Morgan CR, Engen JR. Neutron reflectometry study of the conformation of HIV Nef bound to lipid membranes. Biophys J 2011; 99:1940-8. [PMID: 20858440 DOI: 10.1016/j.bpj.2010.07.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 06/16/2010] [Accepted: 07/06/2010] [Indexed: 01/04/2023] Open
Abstract
Nef is an HIV-1 accessory protein that directly contributes to AIDS progression. Nef is myristoylated on the N-terminus, associates with membranes, and may undergo a transition from a solution conformation to a membrane-associated conformation. It has been hypothesized that conformational rearrangement enables membrane-associated Nef to interact with cellular proteins. Despite its medical relevance, to our knowledge there is no direct information about the conformation of membrane-bound Nef. In this work, we used neutron reflection to reveal what we believe are the first details of the conformation of membrane-bound Nef. The conformation of Nef was probed upon binding to Langmuir monolayers through the interaction of an N-terminal His tag with a synthetic metal-chelating lipid, which models one of the possible limiting cases for myr-Nef. The data indicate that residues are inserted into the lipid headgroups during interaction, and that the core domain lies directly against the lipid headgroups, with a thickness of ∼40 A. Binding of Nef through the N-terminal His tag apparently facilitates insertion of residues, as no insertion occurred upon binding of Nef through weak electrostatic interactions in the absence of the specific interaction through the His tag.
Collapse
Affiliation(s)
- Michael S Kent
- Sandia National Laboratories, Albuquerque, New Mexico, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Kwak YT, Raney A, Kuo LS, Denial SJ, Temple BRS, Garcia JV, Foster JL. Self-association of the Lentivirus protein, Nef. Retrovirology 2010; 7:77. [PMID: 20863404 PMCID: PMC2955668 DOI: 10.1186/1742-4690-7-77] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 09/23/2010] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The HIV-1 pathogenic factor, Nef, is a multifunctional protein present in the cytosol and on membranes of infected cells. It has been proposed that a spatial and temporal regulation of the conformation of Nef sequentially matches Nef's multiple functions to the process of virion production. Further, it has been suggested that dimerization is required for multiple Nef activities. A dimerization interface has been proposed based on intermolecular contacts between Nefs within hexagonal Nef/FynSH3 crystals. The proposed dimerization interface consists of the hydrophobic B-helix and flanking salt bridges between R105 and D123. Here, we test whether Nef self-association is mediated by this interface and address the overall significance of oligomerization. RESULTS By co-immunoprecipitation assays, we demonstrated that HIV-1Nef exists as monomers and oligomers with about half of the Nef protomers oligomerized. Nef oligomers were found to be present in the cytosol and on membranes. Removal of the myristate did not enhance the oligomerization of soluble Nef. Also, SIVNef oligomerizes despite lacking a dimerization interface functionally homologous to that proposed for HIV-1Nef. Moreover, HIV-1Nef and SIVNef form hetero-oligomers demonstrating the existence of homologous oligomerization interfaces that are distinct from that previously proposed (R105-D123). Intracellular cross-linking by formaldehyde confirmed that SF2Nef dimers are present in intact cells, but surprisingly self-association was dependent on R105, but not D123. SIV(MAC239)Nef can be cross-linked at its only cysteine, C55, and SF2Nef is also cross-linked, but at C206 instead of C55, suggesting that Nefs exhibit multiple dimeric structures. ClusPro dimerization analysis of HIV-1Nef homodimers and HIV-1Nef/SIVNef heterodimers identified a new potential dimerization interface, including a dibasic motif at R105-R106 and a six amino acid hydrophobic surface. CONCLUSIONS We have demonstrated significant levels of intracellular Nef oligomers by immunoprecipitation from cellular extracts. However, our results are contrary to the identification of salt bridges between R105 and D123 as necessary for self-association. Importantly, binding between HIV-1Nef and SIVNef demonstrates evolutionary conservation and therefore significant function(s) for oligomerization. Based on modeling studies of Nef self-association, we propose a new dimerization interface. Finally, our findings support a stochastic model of Nef function with a dispersed intracellular distribution of Nef oligomers.
Collapse
Affiliation(s)
- Youn Tae Kwak
- Baylor Institute for Immunology Research, 3434 Live Oak, Dallas, TX 75204, USA
| | - Alexa Raney
- Department of Internal Medicine, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Y9.206, Dallas, Texas 75390, USA
| | - Lillian S Kuo
- Department of Internal Medicine, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Y9.206, Dallas, Texas 75390, USA
| | - Sarah J Denial
- Division of Infectious Diseases, Center for AIDS Research, University of North Carolina, Chapel Hill, North Carolina 27599-7042, USA
| | - Brenda RS Temple
- Department of Biochemistry and Biophysics, R. L. Juliano Structural Bioinformatics Core, University of North Carolina, Chapel Hill, North Carolina 27599-7042, USA
| | - J Victor Garcia
- Division of Infectious Diseases, Center for AIDS Research, University of North Carolina, Chapel Hill, North Carolina 27599-7042, USA
| | - John L Foster
- Division of Infectious Diseases, Center for AIDS Research, University of North Carolina, Chapel Hill, North Carolina 27599-7042, USA
| |
Collapse
|
6
|
Glück JM, Hoffmann S, Koenig BW, Willbold D. Single vector system for efficient N-myristoylation of recombinant proteins in E. coli. PLoS One 2010; 5:e10081. [PMID: 20404920 PMCID: PMC2852408 DOI: 10.1371/journal.pone.0010081] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Accepted: 03/17/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND N-myristoylation is a crucial covalent modification of numerous eukaryotic and viral proteins that is catalyzed by N-myristoyltransferase (NMT). Prokaryotes are lacking endogenous NMT activity. Recombinant production of N-myristoylated proteins in E. coli cells can be achieved by coexpression of heterologous NMT with the target protein. In the past, dual plasmid systems were used for this purpose. METHODOLOGY/PRINCIPAL FINDINGS Here we describe a single vector system for efficient coexpression of substrate and enzyme suitable for production of co- or posttranslationally modified proteins. The approach was validated using the HIV-1 Nef protein as an example. A simple and efficient protocol for production of highly pure and completely N-myristoylated Nef is presented. The yield is about 20 mg myristoylated Nef per liter growth medium. CONCLUSIONS/SIGNIFICANCE The single vector strategy allows diverse modifications of target proteins recombinantly coexpressed in E. coli with heterologous enzymes. The method is generally applicable and provides large amounts of quantitatively processed target protein that are sufficient for comprehensive biophysical and structural studies.
Collapse
Affiliation(s)
- Julian M. Glück
- Institute of Structural Biology and Biophysics, Research Centre Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Silke Hoffmann
- Institute of Structural Biology and Biophysics, Research Centre Jülich, Jülich, Germany
| | - Bernd W. Koenig
- Institute of Structural Biology and Biophysics, Research Centre Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Dieter Willbold
- Institute of Structural Biology and Biophysics, Research Centre Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- * E-mail:
| |
Collapse
|