The DOI matches its Crossref record; 29 of the 29 references it cites were found in a registry or an index.
Global landscape of HIV–human protein complexes
Open accessAbstract
Human immunodeficiency virus (HIV) has a small genome and therefore relies heavily on the host cellular machinery to replicate. Identifying which host proteins and complexes come into physical contact with the viral proteins is crucial for a comprehensive understanding of how HIV rewires the host's cellular machinery during the course of infection. Here we report the use of affinity tagging and purification mass spectrometry to determine systematically the physical interactions of all 18 HIV-1 proteins and polyproteins with host proteins in two different human cell lines (HEK293 and Jurkat). Using a quantitative scoring system that we call MiST, we identified with high confidence 497 HIV-human protein-protein interactions involving 435 individual human proteins, with ∼40% of the interactions being identified in both cell types. We found that the host proteins hijacked by HIV, especially those found interacting in both cell types, are highly conserved across primates. We uncovered a number of host complexes targeted by viral proteins, including the finding that HIV protease cleaves eIF3d, a subunit of eukaryotic translation initiation factor 3. This host protein is one of eleven identified in this analysis that act to inhibit HIV replication. This data set facilitates a more comprehensive and detailed understanding of how the host machinery is manipulated during the course of HIV infection.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“In recent years, cellular factors interacting with HIV-1 proteins and RNAs have been identified using proteomic approaches (122-124).”
From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [122]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“The MA domain of Gag is a major interaction partner of the MSC, and MA has also been reported to interact with a few non-MSC ARSs (Table 1) (122).”
From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [122]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“| Interacts with HIV-1 5ЈUTR | ArgRS a , EPRS a | 122 |”
From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [122]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“| Interacts with RSV 5ЈUTR | LysRS a , SerRS2 | 122 |”
From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [122]
Experimental — accuracy not yet measuredIn the citing paper
“For example, in a large-scale interactome study, all the viral proteins encoded by the HIV genome were individually expressed in 293 and Jurkat cells and subjected to TAP AP-MS analysis (61).”
From The Impact of Mass Spectrometry–Based Proteomics on Fundamental Discoveries in Virology (2014) · cites this paper as [61]
In the citing paper
“Moreover, 97 of 127 selected interactions were confirmed by reciprocal isolations, highlighting the confidence of this data set.”
From The Impact of Mass Spectrometry–Based Proteomics on Fundamental Discoveries in Virology (2014) · cites this paper as [61]
In the citing paper
“Almost 200 interactions were identified in both cell types.”
From The Impact of Mass Spectrometry–Based Proteomics on Fundamental Discoveries in Virology (2014) · cites this paper as [61]
In the citing paper
“Another interaction specificity predictor, MiST, distinguished high-confidence virus-host protein interactions of epitope-tagged HIV proteins individually expressed in human cells (61).”
From The Impact of Mass Spectrometry–Based Proteomics on Fundamental Discoveries in Virology (2014) · cites this paper as [61]
In the citing paper
“Using AP-MS, nearly 500 specific HIV–host protein interactions were identified”
From Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection (2016) · cites this paper as [54]
In the citing paper
“When eIF3d was knocked down via RNA interference, an additional 10 host factors were found to hinder HIV replication by means of virus–host protein interactions.”
From Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection (2016) · cites this paper as [54]
In the citing paper
“approximately 40% of which were prevalent in both cell types.”
From Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection (2016) · cites this paper as [54]
In the citing paper
“the observed overlap in interactions between HEK293 and Jurkat cells was limited.”
From Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection (2016) · cites this paper as [54]
In the citing paper
“A host subunit of eukaryotic translation initiation factor 3, eIF3d, was found to be targeted for cleavage by an HIV protease.”
From Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection (2016) · cites this paper as [54]
In the citing paper
“the comparison of HEK293 cells with Jurkat cells, which are immortalized CD4+ T cells commonly used in HIV-1 studies, helped to substantiate the potential biological relevance of the subset of protein associations identified in both human cell types.”
From Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection (2016) · cites this paper as [54]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
BioGRID: a general repository for interaction datasets
Stark, C. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj109 · Cited by 3,960
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
Krogan, N. J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A., et al. (2006) · Nature · doi:10.1038/nature04670 · Cited by 2,964
Self-citationProteome survey reveals modularity of the yeast cell machinery
Gavin, A., Aloy, P., Grandi, P., Krause, R., Böesche, M., Marzioch, M., Rau, C., Jensen, L. J., Bastuck, S., Dümpelfeld, B., et al. (2006) · Nature · doi:10.1038/nature04532 · Cited by 2,570
A Human Protein-Protein Interaction Network: A Resource for Annotating the Proteome
Stelzl, U., Worm, U., Lalowski, M. M., Haenig, C., Brembeck, F. H., Goehler, H., Strödicke, M., Zenkner, M., Schoenherr, A., Koeppen, S., et al. (2005) · Cell · doi:10.1016/j.cell.2005.08.029 · Cited by 2,433
The Structural Basis for 14-3-3:Phosphopeptide Binding Specificity
Yaffe, M. B., Rittinger, K., Volinia, S., Caron, P. R., Aitken, A., Leffers, H. C. B., Gamblin, S. J., Smerdon, S. J., & Cantley, L. C. (1997) · Cell · doi:10.1016/s0092-8674(00)80487-0 · Cited by 1,604
Defining the Human Deubiquitinating Enzyme Interaction Landscape
Sowa, M. E., Bennett, E. J., Gygi, S. P., & Harper, J. W. (2009) · Cell · doi:10.1016/j.cell.2009.04.042 · Cited by 1,523
Identification of host proteins required for HIV infection through a functional genomic screen
Brass, A. L., Dykxhoorn, D. M., Benita, Y., Yan, N., Engelman, A., Xavier, R. J., Lieberman, J., & Elledge, S. J. (2008) · Science · doi:10.1126/science.1152725 · Cited by 1,449
High-Quality Binary Protein Interaction Map of the Yeast Interactome Network
Yu, H., Braun, P., Yıldırım, M. A., Lemmens, I., Venkatesan, K., Sahalie, J., Hirozane-Kishikawa, T., Gebreab, F., Li, N., Simonis, N., et al. (2008) · Science · doi:10.1126/science.1158684 · Cited by 1,392
CORUM: the comprehensive resource of mammalian protein complexes—2009
Ruepp, A., Wägele, B., Lechner, M., Brauner, B., Dunger-Kaltenbach, I., Fobo, G., Frishman, G., Montrone, C., & Mewes, H. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp914 · Cited by 1,299
Global Analysis of Host-Pathogen Interactions that Regulate Early-Stage HIV-1 Replication
König, R., Zhou, Y., Elleder, D., Diamond, T. L., Bonamy, G. M. C., Irelan, J. T., Chiang, C.-Y., Tu, B. P., De Jesus, P. D., Lilley, C. E., et al. (2008) · Cell · doi:10.1016/j.cell.2008.07.032 · Cited by 960
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Items 101–200 of 721
Mutations in the X-linked ATP6AP2 cause a glycosylation disorder with autophagic defects
Rujano, M. A., Serio, M. C., Panasyuk, G., Péanne, R., Reunert, J., Rymen, D., Hauser, V., Park, J. H., Freisinger, P., Souche, E. L., et al. (2017) · The Journal of Experimental Medicine · doi:10.1084/jem.20170453 · Cited by 91
Self-citationLi, M., Johnson, J. R., Truong, B., Kim, G. E., Weinbren, N. L., Dittmar, M., Shah, P. S., Dollen, J. V., Newton, B. W., Jang, G. Μ., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0375-z · Cited by 90
Self-citationHow host genetics dictates successful viral zoonosis
Warren, C. J., & Sawyer, S. L. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000217 · Cited by 90
Integration of Mass Spectrometry Data for Structural Biology
Britt, H. M., Cragnolini, T., & Thalassinos, K. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.1c00356 · Cited by 87
Valiente‐Echeverría, F., Melnychuk, L., Vyboh, K., Ajamian, L., Gallouzi, I., Bernard, N. F., & Mouland, A. J. (2014) · Nature Communications · doi:10.1038/ncomms5819 · Cited by 84
Inclán, Y. F., Persat, A., Greninger, A. L., Dollen, J. V., Johnson, J. R., Krogan, N. J., Gitai, Z., & Engel, J. N. (2016) · Molecular Microbiology · doi:10.1111/mmi.13410 · Cited by 84
Self-citationHuman Virus Transcriptional Regulators
Liu, X., Hong, T., Parameswaran, S., Ernst, K., Marazzi, I., Weirauch, M. T., & Bass, J. I. F. (2020) · Cell · doi:10.1016/j.cell.2020.06.023 · Cited by 83
Flavonoids as Promising Antiviral Agents against SARS-CoV-2 Infection: A Mechanistic Review
Tabari, M. A. K., Iranpanah, A., Bahramsoltani, R., & Rahimi, R. (2021) · Molecules · doi:10.3390/molecules26133900 · Cited by 85
Global mapping of Salmonella enterica-host protein-protein interactions during infection
Walch, P., Selkrig, J., Knodler, L. A., Rettel, M., Stein, F., Fernandez, K. C., Viéitez, C., Potel, C. M., Scholzen, K., Geyer, M., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.06.004 · Cited by 83
Dynamics of HIV Latency and Reactivation in a Primary CD4+ T Cell Model
Mohammadi, P., di Iulio, J., Muñoz, M., Martínez, R., Bartha, I., Cavassini, M. L., Thorball, C. W., Fellay, J., Beerenwinkel, N., Ciuffi, A., et al. (2014) · PLoS Pathogens · doi:10.1371/journal.ppat.1004156 · Cited by 89
Wagner, S., Herrmannová, A., Malı́k, R., Peclinovská, L., & Valášek, L. S. (2014) · Molecular and Cellular Biology · doi:10.1128/mcb.00663-14 · Cited by 81
Human Paraoxonase-2 (PON2): Protein Functions and Modulation
Manco, G., Porzio, E., & Carusone, T. M. (2021) · Antioxidants · doi:10.3390/antiox10020256 · Cited by 79
The AFF4 scaffold binds human P-TEFb adjacent to HIV Tat
Schulze‐Gahmen, U., Upton, H. E., Birnberg, A., Bao, K., Chou, S., Krogan, N. J., Zhou, Q., & Alber, T. (2013) · eLife · doi:10.7554/elife.00327 · Cited by 79
Self-citationVirus-producing cells determine the host protein profiles of HIV-1 virion cores
Santos, S., Obukhov, Y., Nekhai, S. A., Bukrinsky, M., & Iordanskiy, S. (2012) · Retrovirology · doi:10.1186/1742-4690-9-65 · Cited by 82
Multifaceted HIV integrase functionalities and therapeutic strategies for their inhibition
Engelman, A. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.rev119.006901 · Cited by 83
Nicod, C., Banaei‐Esfahani, A., & Collins, B. C. (2017) · Current Opinion in Microbiology · doi:10.1016/j.mib.2017.07.005 · Cited by 79
Behind the scenes of HIV-1 replication: Alternative splicing as the dependency factor on the quiet
Sertznig, H., Hillebrand, F., Erkelenz, S., Schaal, H., & Widera, M. (2018) · Virology · doi:10.1016/j.virol.2018.01.011 · Cited by 87
Common Nodes of Virus–Host Interaction Revealed Through an Integrated Network Analysis
Bösl, K., Ianevski, A., Than, T. T., Andersen, P. I., Kuivanen, S. H., Teppor, M., Žusinaite, E., Dumpis, U., Vitkauskienė, A., Cox, R. J., et al. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.02186 · Cited by 77
Li, C., Mousseau, G., & Valente, S. T. (2019) · Epigenetics & Chromatin · doi:10.1186/s13072-019-0267-8 · Cited by 74
Enterovirus pathogenesis requires the host methyltransferase SETD3
Diep, J., Ooi, Y. S., Wilkinson, A. W., Peters, C. E., Foy, E. M., Johnson, J. R., Zengel, J. R., Ding, S., Weng, K., Laufman, O., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0551-1 · Cited by 74
Self-citationNext-Generation Sequencing for Confronting Virus Pandemics
Quer, J., Colomer‐Castell, S., de Campos, C. F., Andrés, C., Piñana, M., Cortese, M. F., Gónzalez‐Sánchez, A., García‐Cehic, D., Ibañez‐Lligoña, M., Pumarola, T., et al. (2022) · Viruses · doi:10.3390/v14030600 · Cited by 78
Elwell, C. A., Czudnochowski, N., Dollen, J. V., Johnson, J. R., Nakagawa, R. M., Mirrashidi, K. M., Krogan, N. J., Engel, J. N., & Rosenberg, O. S. (2017) · eLife · doi:10.7554/elife.22709 · Cited by 75
Self-citationUnconventional RNA‐binding proteins step into the virus–host battlefront
García-Moreno, M., Järvelin, A. I., & Castelló, A. (2018) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1498 · Cited by 76
Klaus, J. P., Eisenhauer, P. L., Russo, J., Mason, A. B., Do, D. C., King, B. R., Taatjes, D. J., Cornillez-Ty, C. T., Boyson, J. E., Thali, M., et al. (2013) · Cell Host & Microbe · doi:10.1016/j.chom.2013.10.010 · Cited by 72
A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity
Swaney, D. L., Ramms, D. J., Wang, Z., Park, J., Goto, Y., Soucheray, M., Bhola, N. E., Kim, K., Zheng, F., Zeng, Y., et al. (2021) · Science · doi:10.1126/science.abf2911 · Cited by 72
Self-citationLigand-based receptor identification on living cells and tissues using TRICEPS
Frei, A. P., Moest, H., Novy, K., & Wollscheid, B. (2013) · Nature Protocols · doi:10.1038/nprot.2013.072 · Cited by 74
Reeder, J. E., Kwak, Y.-T., McNamara, R. P., Forst, C. V., & D’Orso, I. (2015) · eLife · doi:10.7554/elife.08955 · Cited by 74
Self-citationHow HIV Nef Proteins Hijack Membrane Traffic To Promote Infection
Buffalo, C. Z., Iwamoto, Y., Hurley, J. H., & Ren, X. (2019) · Journal of Virology · doi:10.1128/jvi.01322-19 · Cited by 76
Proteomic approaches to the study of papillomavirus–host interactions
White, E. A., & Howley, P. M. (2012) · Virology · doi:10.1016/j.virol.2012.09.046 · Cited by 71
Scoring Large‐Scale Affinity Purification Mass Spectrometry Datasets with MiST
Verschueren, E., Dollen, J. V., Cimermančič, P., Gulbahce, N., Šali, A., & Krogan, N. J. (2015) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0819s49 · Cited by 69
Self-citationJayaraman, B., Crosby, D. C., Homer, C. M., Ribeiro, I., Mavor, D., & Frankel, A. D. (2014) · eLife · doi:10.7554/elife.04120 · Cited by 74
Self-citationDing, S., Mooney, N. A., Li, B., Kelly, M. R., Feng, N., Loktev, A. V., Sen, A., Patton, J. T., Jackson, P. K., & Greenberg, H. B. (2016) · PLoS Pathogens · doi:10.1371/journal.ppat.1005929 · Cited by 72
Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication
Jin, D., & Musier-Forsyth, K. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.rev118.002957 · Cited by 67
“The MA domain of Gag is a major interaction partner of the MSC, and MA has also been reported to interact with a few non-MSC ARSs (Table 1) (122).”
BackgroundThe Impact of Mass Spectrometry–Based Proteomics on Fundamental Discoveries in Virology
Greco, T. M., Diner, B. A., & Cristea, I. M. (2014) · Annual Review of Virology · doi:10.1146/annurev-virology-031413-085527 · Cited by 67
Recruitment of RED-SMU1 Complex by Influenza A Virus RNA Polymerase to Control Viral mRNA Splicing
Fournier, G., Chiang, C., Munier, S., Tomoiu, A., Demeret, C., Vidalain, P., Jacob, Y., & Naffakh, N. (2014) · PLoS Pathogens · doi:10.1371/journal.ppat.1004164 · Cited by 66
Role of autophagy in HIV infection and pathogenesis
Nardacci, R., Ciccosanti, F., Marsella, C., Ippolito, G., Piacentini, M., & Fimia, G. M. (2017) · Journal of Internal Medicine · doi:10.1111/joim.12596 · Cited by 71
Two Accessory Proteins Govern MmpL3 Mycolic Acid Transport in Mycobacteria
Fay, A., Czudnochowski, N., Rock, J. M., Johnson, J. R., Krogan, N. J., Rosenberg, O., & Glickman, M. S. (2019) · mBio · doi:10.1128/mbio.00850-19 · Cited by 65
Self-citationRapid, optimized interactomic screening
Hakhverdyan, Z., Domanski, M., Hough, L. E., Oroskar, A. A., Oroskar, A. R., Keegan, S., Dilworth, D. J., Molloy, K. R., Sherman, V., Aitchison, J. D., et al. (2015) · Nature Methods · doi:10.1038/nmeth.3395 · Cited by 68
Inhibition of a NEDD8 Cascade Restores Restriction of HIV by APOBEC3G
Stanley, D. J., Bartholomeeusen, K., Crosby, D. C., Kim, D. Y., Kwon, E., Yen, L., Cartozo, N. C., Li, M., Jäger, S., Mason-Herr, J., et al. (2012) · PLoS Pathogens · doi:10.1371/journal.ppat.1003085 · Cited by 66
Self-citationARIH2 Is a Vif-Dependent Regulator of CUL5-Mediated APOBEC3G Degradation in HIV Infection
Hüttenhain, R., Xu, J., Burton, L. A., Gordon, D. E., Hultquist, J. F., Johnson, J. R., Satkamp, L., Hiatt, J. B., Rhee, D. Y., Baek, K., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.05.008 · Cited by 67
Self-citationProteomic and genetic analyses of influenza A viruses identify pan-viral host targets
Haas, K. M., McGregor, M., Bouhaddou, M., Polacco, B. J., Kim, E., Nguyen, T. T., Newton, B. W., Urbanowski, M., Kim, H. J., Williams, M. A. P., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-41442-z · Cited by 65
Self-citationHIV-1 Recruits UPF1 but Excludes UPF2 to Promote Nucleocytoplasmic Export of the Genomic RNA
Ajamian, L., Abel, K., Rao, S., Vyboh, K., García-de-Gracia, F., Soto‐Rifo, R., Kulozik, A. E., Gehring, N. H., & Mouland, A. J. (2015) · Biomolecules · doi:10.3390/biom5042808 · Cited by 68
Plank, T. M., Whitehurst, J., & Kieft, J. S. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt358 · Cited by 63
CDK11 in TREX/THOC Regulates HIV mRNA 3′ End Processing
Pak, V., Eifler, T., Jäger, S., Krogan, N. J., Fujinaga, K., & Peterlin, B. M. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.10.012 · Cited by 66
Self-citationDurmuş, S., & Ülgen, K. Ö. (2016) · FEBS Open Bio · doi:10.1002/2211-5463.12167 · Cited by 67
Influenza A Virus–Host Protein Interactions Control Viral Pathogenesis
Zhao, M., Wang, L., & Li, S. (2017) · International Journal of Molecular Sciences · doi:10.3390/ijms18081673 · Cited by 66
New horizons for antiviral drug discovery from virus–host protein interaction networks
de Chassey, B., Meyniel‐Schicklin, L., Aublin‐Gex, A., André, P., & Lotteau, V. (2012) · Current Opinion in Virology · doi:10.1016/j.coviro.2012.09.001 · Cited by 65
Bacon, C. W., Challa, A., Hyder, U., Shukla, A., Borkar, A. N., Bayo, J., Liu, J., Wu, S.-Y., Chiang, C., Kutateladze, T. G., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.04.024 · Cited by 63
Self-citationHIV-1 Replication and the Cellular Eukaryotic Translation Apparatus
Guerrero, S. X., Batisse, J., Libre, C., Bernacchi, S., Marquet, R., & Paillart, J. (2015) · Viruses · doi:10.3390/v7010199 · Cited by 61
KCNQ1OT1 promotes genome-wide transposon repression by guiding RNA–DNA triplexes and HP1 binding
Zhang, X., Jiang, Q., Li, J., Zhang, S., Cao, Y., Xia, X., Cai, D., Tan, J., Chen, J., & Han, J. J. (2022) · Nature Cell Biology · doi:10.1038/s41556-022-01008-5 · Cited by 60
Protein-protein interactions of human viruses
Goodacre, N., Devkota, P., Bae, E. H., Wuchty, S., & Uetz, P. (2018) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2018.07.018 · Cited by 60
Structure, function, and inhibitor targeting of HIV-1 Nef-effector kinase complexes
Staudt, R. P., Alvarado, J. J., Emert‐Sedlak, L. A., Shi, H., Shu, S. T., Wales, T. E., Engen, J. R., & Smithgall, T. E. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.rev120.012317 · Cited by 58
Zhu, J. K., Davoli, T., Perriera, J. M., Chin, C. R., Gaiha, G. D., John, S. P., Sigiollot, F. D., Gao, G., Xu, Q., Qu, H., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.09.031 · Cited by 61
Cheng, F., Murray, J. L., Zhao, J., Sheng, J., Zhao, Z., & Rubin, D. H. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005074 · Cited by 58
Armean, I. M., Lilley, K. S., & Trotter, M. W. B. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r112.019554 · Cited by 58
Shen, C., Jia, Y., Tian, R., Ding, M., Zhang, C., & Wang, J. (2012) · The FASEB Journal · doi:10.1096/fj.12-209023 · Cited by 57
The RNA Exosome Syncs IAV-RNAPII Transcription to Promote Viral Ribogenesis and Infectivity
Rialdi, A., Hultquist, J. F., Jimenez‐Morales, D., Peralta, Z., Campisi, L., Fenouil, R., Moshkina, N., Wang, Z. Z., Laffleur, B., Kaake, R. M., et al. (2017) · Cell · doi:10.1016/j.cell.2017.04.021 · Cited by 60
Self-citationSchulze‐Gahmen, U., Lu, H., Zhou, Q., & Alber, T. (2014) · eLife · doi:10.7554/elife.02375 · Cited by 58
Self-citationKim, M., Hosmane, N. N., Bullen, C. K., Capoferri, A. A., Yang, H., Siliciano, J. D., & Siliciano, R. F. (2014) · Nature Protocols · doi:10.1038/nprot.2014.188 · Cited by 56
Molecular principles of human virus protein–protein interactions
Halehalli, R. R., & Nagarajaram, H. A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu763 · Cited by 57
CRISPR-Based Tools in Immunity
Simeonov, D. R., & Marson, A. (2019) · Annual Review of Immunology · doi:10.1146/annurev-immunol-042718-041522 · Cited by 57
Contribution of the clathrin adaptor AP-1 subunit µ1 to acidic cluster protein sorting
Navarro Negredo, P., Edgar, J. R., Wrobel, A. G., Zaccai, N. R., Antrobus, R., Owen, D. J., & Robinson, M. S. (2017) · Journal of Cell Biology · doi:10.1083/jcb.201602058 · Cited by 50
Ghanam, R. H., Samal, A. B., Fernandez, T. F., & Saad, J. S. (2012) · Frontiers in Microbiology · doi:10.3389/fmicb.2012.00055 · Cited by 66
Carpp, L. N., Rogers, R. S., Moritz, R. L., & Aitchison, J. D. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.038984 · Cited by 58
Deep interactome profiling of membrane proteins by co-interacting protein identification technology
Pankow, S., Bamberger, C., Calzolari, D., Bamberger, A., & Yates, J. R. (2016) · Nature Protocols · doi:10.1038/nprot.2016.140 · Cited by 56
Proteome analysis of the HIV-1 Gag interactome
Engeland, C. E., Brown, N. P., Börner, K., Schümann, M., Krause, E., Kaderali, L., Müller, G. A., & Kräusslich, H.-G. (2014) · Virology · doi:10.1016/j.virol.2014.04.038 · Cited by 55
HIV protease cleaves the antiviral m6A reader protein YTHDF3 in the viral particle
Jurczyszak, D., Zhang, W., Terry, S. N., Kehrer, T., González, M. C. B., McGregor, E., Mulder, L. C. F., Eckwahl, M. J., Pan, T., & Simon, V. R. (2020) · PLoS Pathogens · doi:10.1371/journal.ppat.1008305 · Cited by 54
Analysis of HIV-1 Gag Protein Interactions via Biotin Ligase Tagging
Ritchie, C., Cylinder, I., Platt, E. J., & Barklis, E. (2015) · Journal of Virology · doi:10.1128/jvi.03584-14 · Cited by 57
Elucidating the in vivo interactome of HIV-1 RNA by hybridization capture and mass spectrometry
Knoener, R. A., Becker, J. T., Scalf, M., Sherer, N. M., & Smith, L. M. (2017) · Scientific Reports · doi:10.1038/s41598-017-16793-5 · Cited by 54
Yang, S., Chen, F., Lian, X., Dong, X., & Zhang, Z. (2019) · mSystems · doi:10.1128/msystems.00303-18 · Cited by 54
Positive selection of primate genes that promote HIV-1 replication
Meyerson, N. R., Rowley, P. A., Swan, C. H., Le, D. T., Wilkerson, G. K., & Sawyer, S. L. (2014) · Virology · doi:10.1016/j.virol.2014.02.029 · Cited by 54
HIV–host interactome revealed directly from infected cells
Luo, Y., Jacobs, E. Y., Greco, T. M., Mohammed, K., Tong, T., Keegan, S., Binley, J. Μ., Cristea, I. M., Fenyö, D., Rout, M. P., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.68 · Cited by 55
Proteomics Tracing the Footsteps of Infectious Disease
Greco, T. M., & Cristea, I. M. (2017) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o116.066001 · Cited by 54
An inter‐species protein–protein interaction network across vast evolutionary distance
Zhong, Q., Pevzner, S. J., Hao, T., Wang, Y., Mosca, R., Menche, J., Taipale, M., Taşan, M., Fan, C., Yang, X., et al. (2016) · Molecular Systems Biology · doi:10.15252/msb.20156484 · Cited by 54
Assembly of eIF3 Mediated by Mutually Dependent Subunit Insertion
Smith, M. D., de Tacca, L. A., Nitido, A. D., Montabana, E. A., Park, A., & Cate, J. H. D. (2016) · Structure · doi:10.1016/j.str.2016.02.024 · Cited by 54
Structural host-microbiota interaction networks
Guven‐Maiorov, E., Tsai, C., & Nussinov, R. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005579 · Cited by 55
Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy
Martin‐Sancho, L., Tripathi, S., Rodríguez-Frandsen, A., Pache, L., Sánchez-Aparicio, M. T., McGregor, M., Haas, K. M., Swaney, D. L., Nguyen, T. T., Mamede, J. I., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00964-2 · Cited by 55
Self-citationPoulsen, J. W., Madsen, C. T., Young, C., Poulsen, F. M., & Nielsen, M. L. (2012) · Journal of Proteome Research · doi:10.1021/pr300883y · Cited by 55
Zhang, Y., Sun, H., Zhang, J., Brasier, A. R., & Zhao, Y. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00432 · Cited by 52
Zhuang, S., & Torbett, B. E. (2021) · Viruses · doi:10.3390/v13030417 · Cited by 53
Milev, M. P., Ravichandran, M., Khan, M. F., Schriemer, D. C., & Mouland, A. J. (2012) · Frontiers in Microbiology · doi:10.3389/fmicb.2012.00367 · Cited by 51
Zhou, X., Evans, S. L., Han, X., Liu, Y., & Yu, X.-F. (2012) · PLoS ONE · doi:10.1371/journal.pone.0033495 · Cited by 55
HIV-1 Nef hijacks clathrin coats by stabilizing AP-1:Arf1 polygons
Shen, Q.-T., Ren, X., Zhang, R., Lee, I., & Hurley, J. H. (2015) · Science · doi:10.1126/science.aac5137 · Cited by 50
Heat Shock Factor 1 Mediates Latent HIV Reactivation
Pan, X., Zhao, W., Zeng, X., Lin, J., Li, M., Shen, X., & Liu, S. (2016) · Scientific Reports · doi:10.1038/srep26294 · Cited by 50
Huang, H., Kong, W., Jean, M. J., Fiches, G. N., Zhou, D., Hayashi, T., Que, J., Santoso, N. G., & Zhu, J. K. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz493 · Cited by 51
A functional map of HIV-host interactions in primary human T cells
Hiatt, J. B., Hultquist, J. F., McGregor, M., Bouhaddou, M., Leenay, R. T., Simons, L. M., Young, J. M., Haas, P., Roth, T. L., Tobin, V. R., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29346-w · Cited by 53
Self-citationEfficient SIVcpz replication in human lymphoid tissue requires viral matrix protein adaptation
Bibollet‐Ruche, F., Heigele, A., Keele, B. F., Easlick, J. L., Decker, J. M., Takehisa, J., Learn, G. H., Sharp, P. M., Hahn, B. H., & Kirchhoff, F. (2012) · Journal of Clinical Investigation · doi:10.1172/jci61429 · Cited by 50
Celona, B., Dollen, J. V., Vatsavayai, S. C., Kashima, R., Johnson, J. R., Tang, A. A., Hata, A., Miller, B. L., Huang, E. J., Krogan, N. J., et al. (2017) · eLife · doi:10.7554/elife.19032 · Cited by 50
Self-citationThe role of exosomal transport of viral agents in persistent HIV pathogenesis
Patters, B. J., & Kumar, S. (2018) · Retrovirology · doi:10.1186/s12977-018-0462-x · Cited by 49
Mapping protein–protein interactions by mass spectrometry
Liu, X., Abad, L., Chatterjee, L., Cristea, I. M., & Varjosalo, M. T. (2024) · Mass Spectrometry Reviews · doi:10.1002/mas.21887 · Cited by 54
Kane, J. R., Stanley, D. J., Hultquist, J. F., Johnson, J. R., Mietrach, N., Binning, J. M., Jönsson, S., Barelier, S., Newton, B. W., Johnson, T. L., et al. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.04.038 · Cited by 49
Self-citationBocharov, G. A., Черешнев, В. А., Gainova, I., Bazhan, S. I., Bachmetyev, B. A., Argilaguet, J. M., Martínez, J. P., & Meyerhans, A. (2012) · Mathematical Modelling of Natural Phenomena · doi:10.1051/mmnp/20127507 · Cited by 48
HIV-1 Proviral Transcription and Latency in the New Era
Shukla, A., Ramirez, N.-G. P., & D’Orso, I. (2020) · Viruses · doi:10.3390/v12050555 · Cited by 52
Self-citationHIV-1 protease-induced apoptosis
Rumlová, M., Křížová, I., Keprová, A., Hadravová, R., Doležal, M., Strohalmová, K., Pichová, I., Hájek, M., & Ruml, T. (2014) · Retrovirology · doi:10.1186/1742-4690-11-37 · Cited by 47
Filleton, F., Filleton, F., Gérossier, L., Paturel, A., Hall, J. A., Strubin, M., & Etienne, L. (2018) · Journal of Virology · doi:10.1128/jvi.00769-18 · Cited by 48
Aggresome assembly at the centrosome is driven by CP110–CEP97–CEP290 and centriolar satellites
Prosser, S. L., Tkach, J. M., Gheiratmand, L., Kim, J., Raught, B., Morrison, C. G., & Pelletier, L. (2022) · Nature Cell Biology · doi:10.1038/s41556-022-00869-0 · Cited by 50
From Systems to Structure: Bridging Networks and Mechanism
Fraser, J. S., Gross, J. D., & Krogan, N. J. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.01.003 · Cited by 47
Self-citationAwasthi, S., Verma, M., Mahesh, A., Khan, M. I. K., Govindaraju, G., Rajavelu, A., Chavali, P. L., Chavali, S., & Dhayalan, A. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky231 · Cited by 46
Terracciano, R., Preianò, M., Fregola, A., Pelaia, C., Montalcini, T., & Savino, R. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22020532 · Cited by 46
Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs
Mihalič, F., Simonetti, L., Giudice, G., Sander, M. R., Lindqvist, R., Peters, M. B. A., Benz, C., Kassa, E., Badgujar, D. C., Inturi, R., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-38015-5 · Cited by 51
Metadata
- Authors
- Jäger, S., Cimermancic, P., Gulbahce, N., Johnson, J. R., McGovern, K. E., Clarke, S. C., Shales, M., Mercenne, G., Pache, L., Li, K., Hernandez, H., Jang, G. M., Roth, S. L., Akiva, E., Marlett, J., Stephens, M., D’Orso, I., Fernandes, J., Fahey, M., Mahon, C., O’Donoghue, A. J., Todorovic, A., Morris, J. H., Maltby, D. A., Alber, T., Cagney, G., Bushman, F. D., Young, J. A., Chanda, S. K., Sundquist, W. I., Kortemme, T., Hernandez, R. D., Craik, C. S., Burlingame, A., Sali, A., Frankel, A. D., & Krogan, N. J.
- Affiliations
- University of California, San Francisco (US)
- QB3 (US)
- Sanford Burnham Prebys Medical Discovery Institute (US)
- University of Pennsylvania (US)
- Salk Institute for Biological Studies (US)
- University of California, Berkeley (US)
- University College Dublin (IE)
- University of Utah (US)
- Corresponding author
- Krogan, Nevan J.
- ORCID
- Jäger, Stefanie
- Gulbahce, Natali
- Johnson, Jeffrey R.
- McGovern, Kathryn E.
- Clarke, Starlynn C.
- Pache, Lars
- Li, Kathy
- Akiva, Eyal
- D’Orso, Iván
- Fernandes, Jason
- Fahey, Marie
- Mahon, Cathal
- O’Donoghue, Anthony J.
- Morris, John H.
- Cagney, Gerard
- Bushman, Frederic D.
- Young, John A.
- Chanda, Sumit K.
- Sundquist, Wesley I.
- Kortemme, Tanja
- Hernandez, Ryan D.
- Craik, Charles S.
- Burlingame, Alma
- Frankel, Alan D.
- Krogan, Nevan J.
- Venue
- Nature
- Published
- 2011-12-21
- Volume
- 481
- Issue
- 7381
- Pages
- 365-370
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3310911
- OpenAlex
- W1996076856
- Cited by
- 731
- References
- 29
- Citations by year
- 2026: 22 · 2025: 25 · 2024: 37 · 2023: 41 · 2022: 46 · 2021: 59 · 2020: 44 · 2019: 51 · 2018: 50 · 2017: 47 · 2016: 59 · 2015: 62 · 2014: 67 · 2013: 58 · 2012: 62
- FWCI
- 23.80
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Institute of General Medical Sciences (P50GM082250, P50GM081879, P50GM082545, P41GM103481, P01GM073732)
- National Institute of Allergy and Infectious Diseases (P01AI090935)
- National Center for Research Resources (P41RR001614, P41RR001081, U54RR022220)
- Topics
- Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Health Sciences › Medicine › Infectious Diseases › HIV/AIDS drug development and treatment
- Keywords
- HIV-1, host-virus protein interaction, protein-protein interaction, HIV replication, integrase, eIF3, primate conservation
- MeSH terms
- Affinity Labels, Amino Acid Sequence, Humans, Protein Binding, Mass Spectrometry, Virus Replication, Reproducibility of Results, HIV-1, HIV Infections, HIV Protease, Conserved Sequence, Jurkat Cells, Protein Interaction Mapping, Eukaryotic Initiation Factor-3, Immunoprecipitation, Human Immunodeficiency Virus Proteins, Host-Pathogen Interactions, HEK293 Cells, Protein Interaction Maps
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
