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 2,969
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
Cited by
Sorted by citations
A SARS-CoV-2 protein interaction map reveals targets for drug repurposing
Gordon, D. E., Jang, G. M., Bouhaddou, M., Xu, J., Obernier, K., White, K. M., O’Meara, M. J., Rezelj, V. V., Guo, J. Z., Swaney, D. L., et al. (2020) · Nature · doi:10.1038/s41586-020-2286-9 · Cited by 4,405
Self-citationTOX transcriptionally and epigenetically programs CD8+ T cell exhaustion
Khan, O., Giles, J. R., McDonald, S., Manne, S., Ngiow, S. F., Patel, K. P., Werner, M. T., Huang, A. C., Alexander, K. A., Wu, J. E., et al. (2019) · Nature · doi:10.1038/s41586-019-1325-x · Cited by 1,646
Deciphering cell–cell interactions and communication from gene expression
Armingol, E., Officer, A., Harismendy, O., & Lewis, N. E. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-020-00292-x · Cited by 1,267
The BioGRID interaction database: 2013 update
Chatr‐aryamontri, A., Breitkreutz, B., Heinicke, S., Boucher, L., Winter, A. G., Stark, C., Nixon, J., Ramage, L., Kolas, N. K., O’Donnell, L., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1158 · Cited by 1,021
Meta- and Orthogonal Integration of Influenza “OMICs” Data Defines a Role for UBR4 in Virus Budding
Tripathi, S., Pohl, M. O., Zhou, Y., Rodríguez-Frandsen, A., Wang, G., Stein, D. A., Moulton, H. M., DeJesus, P., Che, J., Mulder, L. C. F., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.11.002 · Cited by 856
Self-citationIdeker, T., & Krogan, N. J. (2012) · Molecular Systems Biology · doi:10.1038/msb.2011.99 · Cited by 795
Self-citationNext-generation proteomics: towards an integrative view of proteome dynamics
Altelaar, M. A. F., Muñoz, J., & Heck, A. J. R. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3356 · Cited by 802
Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms
Gordon, D. E., Hiatt, J. B., Bouhaddou, M., Rezelj, V. V., Ulferts, S., Braberg, H., Jureka, A. S., Obernier, K., Guo, J. Z., Batra, J., et al. (2020) · Science · doi:10.1126/science.abe9403 · Cited by 747
Self-citationRules of engagement: molecular insights from host–virus arms races
Daugherty, M. D., & Malik, H. S. (2012) · Annual Review of Genetics · doi:10.1146/annurev-genet-110711-155522 · Cited by 515
A “Candidate-Interactome” Aggregate Analysis of Genome-Wide Association Data in Multiple Sclerosis
Mechelli, R., Umeton, R., Policano, C., Annibali, V., Coarelli, G., Ricigliano, V. A. G., Vittori, D., Fornasiero, A., Buscarinu, M. C., Romano, S., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0063300 · Cited by 513
The functional landscape of the human phosphoproteome
Ochoa, D., Jarnuczak, A. F., Viéitez, C., Gehre, M., Soucheray, M., Mateus, A., Kleefeldt, A. A., Hill, A., Garcia-Alonso, L., Stein, F., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-019-0344-3 · Cited by 491
Self-citationMolecular dynamics simulations of large macromolecular complexes
Perilla, J. R., Goh, B. C., Cassidy, C. K., Liu, B., Bernardi, R. C., Rudack, T., Yu, H., Wu, Z., & Schulten, K. J. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.03.007 · Cited by 431
Multidimensional proteomics for cell biology
Larance, M., & Lamond, A. I. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3970 · Cited by 420
An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells
Lobingier, B. T., Hüttenhain, R., Eichel, K., Miller, K. B., Ting, A. Y., von Zastrow, M., & Krogan, N. J. (2017) · Cell · doi:10.1016/j.cell.2017.03.022 · Cited by 417
Self-citationMutational and fitness landscapes of an RNA virus revealed through population sequencing
Acevedo, A., Brodsky, L., & Andino, R. (2013) · Nature · doi:10.1038/nature12861 · Cited by 389
Shah, P. S., Link, N., Jang, G. Μ., Sharp, P. P., Zhu, T., Swaney, D. L., Johnson, J. R., Dollen, J. V., Ramage, H. R., Satkamp, L., et al. (2018) · Cell · doi:10.1016/j.cell.2018.11.028 · Cited by 382
Self-citationPredicting Protein–Protein Interactions from the Molecular to the Proteome Level
Keskin, O., Tuncbag, N., & Gursoy, A. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00683 · Cited by 369
PP2A as a master regulator of the cell cycle
Wlodarchak, N., & Xing, Y. (2016) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409238.2016.1143913 · Cited by 380
Viruses are a dominant driver of protein adaptation in mammals
Enard, D., Cai, L., Gwennap, C., & Petrov, D. A. (2016) · eLife · doi:10.7554/elife.12469 · Cited by 370
Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection
Jäger, S., Kim, D. Y., Hultquist, J. F., Shindo, K., LaRue, R. S., Kwon, E., Li, M., Anderson, B. D., Yen, L., Stanley, D., et al. (2012) · Nature · doi:10.1038/nature10693 · Cited by 352
Self-citationHIV-1 transcription and latency: an update
Lint, C. M. V., Bouchat, S., & Marcello, A. (2013) · Retrovirology · doi:10.1186/1742-4690-10-67 · Cited by 352
A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors
Park, R. J.-H., Wang, T., Koundakjian, D., Hultquist, J. F., Lamothe, P. A., Monel, B., Schumann, K., Yu, H., Krupzcak, K. M., García-Beltrán, W. F., et al. (2016) · Nature Genetics · doi:10.1038/ng.3741 · Cited by 329
Self-citationViral immune modulators perturb the human molecular network by common and unique strategies
Pichlmair, A., Kandasamy, K., Alvisi, G., Mulhern, O., Sacco, R., Habjan, M., Binder, M., Stefanovic, A., Eberle, C.-A., Goncalves, A., et al. (2012) · Nature · doi:10.1038/nature11289 · Cited by 262
Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function
Floyd, B. J., Wilkerson, E., Veling, M. T., Minogue, C. E., Xia, C., Beebe, E. T., Wrobel, R. L., Cho, H., Kremer, L. S., Alston, C. L., et al. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.06.033 · Cited by 264
Vinayagam, A., Gibson, T. E., Lee, H., Yilmazel, B., Roesel, C. L., Hu, Y., Kwon, Y. V., Sharma, A., Liu, Y., Perrimon, N., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1603992113 · Cited by 255
Sun, L., Li, P., Ju, X., Rao, J. Y., Huang, W., Ren, L., Zhang, S., Xiong, T., Xu, K., Zhou, X., et al. (2021) · Cell · doi:10.1016/j.cell.2021.02.008 · Cited by 229
Beltran, P. M. J., Federspiel, J. D., Sheng, X., & Cristea, I. M. (2017) · Molecular Systems Biology · doi:10.15252/msb.20167062 · Cited by 218
The APOBEC3 Family of Retroelement Restriction Factors
Refsland, E. W., & Harris, R. S. (2013) · Current topics in microbiology and immunology · doi:10.1007/978-3-642-37765-5_1 · Cited by 216
Global Mapping of Herpesvirus-Host Protein Complexes Reveals a Transcription Strategy for Late Genes
Davis, Z. H., Verschueren, E., Jang, G. Μ., Kleffman, K., Johnson, J. R., Park, J., Dollen, J. V., Maher, M. C., Johnson, T. L., Newton, W., et al. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.11.026 · Cited by 211
Self-citationMorris, J. H., Knudsen, G. M., Verschueren, E., Johnson, J. R., Cimermančič, P., Greninger, A. L., & Pico, A. R. (2014) · Nature Protocols · doi:10.1038/nprot.2014.164 · Cited by 210
Self-citationMass spectrometry‐based protein–protein interaction networks for the study of human diseases
Richards, A., Eckhardt, M., & Krogan, N. J. (2021) · Molecular Systems Biology · doi:10.15252/msb.20188792 · Cited by 205
Self-citationWhite, E. A., Kramer, R. E., Tan, M. J. A., Hayes, S. D., Harper, J. W., & Howley, P. M. (2012) · Journal of Virology · doi:10.1128/jvi.02172-12 · Cited by 198
The Dengue Virus NS5 Protein Intrudes in the Cellular Spliceosome and Modulates Splicing
Maio, F. A. D., Risso, G., Iglesias, N. G., Shah, P. S., Pozzi, B., Gebhard, L. G., Mammi, P., Mancini, E., Yanovsky, M. J., Andino, R., et al. (2016) · PLoS Pathogens · doi:10.1371/journal.ppat.1005841 · Cited by 205
Self-citationProtein-protein interaction networks: probing disease mechanisms using model systems
Kuzmanov, U., & Emili, A. (2013) · Genome Medicine · doi:10.1186/gm441 · Cited by 197
Global Mapping of the Inc-Human Interactome Reveals that Retromer Restricts Chlamydia Infection
Mirrashidi, K. M., Elwell, C. A., Verschueren, E., Johnson, J. R., Frando, A., Dollen, J. V., Rosenberg, O. S., Gulbahce, N., Jang, G. Μ., Johnson, T. L., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.06.004 · Cited by 187
Self-citationThe Mechanism and Function of Group II Chaperonins
Lopez, T., Dalton, K. M., & Frydman, J. (2015) · Journal of Molecular Biology · doi:10.1016/j.jmb.2015.04.013 · Cited by 179
Hultquist, J. F., Schumann, K., Woo, J. M., Manganaro, L., McGregor, M. J., Doudna, J., Simon, V., Krogan, N. J., & Marson, A. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.09.080 · Cited by 170
Self-citationDiscovery and significance of protein-protein interactions in health and disease
Greenblatt, J. F., Alberts, B., & Krogan, N. J. (2024) · Cell · doi:10.1016/j.cell.2024.10.038 · Cited by 181
Self-citationValášek, L. S., Zeman, J., Wagner, S., Beznosková, P., Pavlíková, Z., Mohammad, M. P., Hronová, V., Herrmannová, A., Hashem, Y., & Gunišová, S. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx805 · Cited by 163
24 hours in the life of HIV-1 in a T cell line
Mohammadi, P., Desfarges, S., Bartha, I., Joos, B., Zangger, N., Muñoz, M., Günthard, H. F., Beerenwinkel, N., Telenti, A., & Ciuffi, A. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003161 · Cited by 155
Viral internal ribosomal entry sites: four classes for one goal
Mailliot, J., & Martin, F. (2017) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1458 · Cited by 174
The Cancer Cell Map Initiative: Defining the Hallmark Networks of Cancer
Krogan, N. J., Lippman, S. M., Agard, D. A., Ashworth, A., & Ideker, T. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.05.008 · Cited by 154
Self-citationProtein Interaction Mapping Identifies RBBP6 as a Negative Regulator of Ebola Virus Replication
Batra, J., Hultquist, J. F., Liu, D., Shtanko, O., Dollen, J. V., Satkamp, L., Jang, G. Μ., Luthra, P., Schwarz, T. M., Small, G. I., et al. (2018) · Cell · doi:10.1016/j.cell.2018.08.044 · Cited by 155
Self-citationThe Structural Basis of Substrate Recognition by the Eukaryotic Chaperonin TRiC/CCT
Joachimiak, Ł. A., Walzthoeni, T., Liu, C. W., Aebersold, R. H., & Frydman, J. (2014) · Cell · doi:10.1016/j.cell.2014.10.042 · Cited by 149
The impact of host genetic variation on infection with HIV-1
McLaren, P. J., & Carrington, M. N. (2015) · Nature Immunology · doi:10.1038/ni.3147 · Cited by 147
Edgotype: a fundamental link between genotype and phenotype
Sahni, N., Yi, S. S., Zhong, Q., Jailkhani, N., Charloteaux, B., Cusick, M. E., & Vidal, M. (2013) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2013.11.002 · Cited by 150
Exploring the human diseasome: the human disease network
Goh, K.-I., & Choi, I. (2012) · Briefings in Functional Genomics · doi:10.1093/bfgp/els032 · Cited by 146
Ramage, H. R., Kumar, G. R., Verschueren, E., Johnson, J. R., Dollen, J. V., Johnson, T. L., Newton, B. W., Shah, P. S., Horner, J. A., Krogan, N. J., et al. (2015) · Molecular Cell · doi:10.1016/j.molcel.2014.12.028 · Cited by 146
Self-citationA decade of RNA virus metagenomics is (not) enough
Greninger, A. L. (2017) · Virus Research · doi:10.1016/j.virusres.2017.10.014 · Cited by 138
Host-Microbe Protein Interactions during Bacterial Infection
Schweppe, D. K., Harding, C. L., Chavez, J. D., Wu, X., Ramage, E. R., Singh, P. K., Manoil, C., & Bruce, J. E. (2015) · Chemistry & Biology · doi:10.1016/j.chembiol.2015.09.015 · Cited by 137
A structure-informed atlas of human-virus interactions
Lasso, G., Mayer, S. V., Winkelmann, E. R., Chu, T., Elliot, O., Patino-Galindo, J. A., Park, K., Rabadan, R., Honig, B., & Shapira, S. D. (2019) · Cell · doi:10.1016/j.cell.2019.08.005 · Cited by 133
Targeting Viral Proteostasis Limits Influenza Virus, HIV, and Dengue Virus Infection
Heaton, N. S., Moshkina, N., Fenouil, R., Gardner, T. J., Aguirre, S., Shah, P. S., Zhao, N., Manganaro, L., Hultquist, J. F., Noel, J. C., et al. (2016) · Immunity · doi:10.1016/j.immuni.2015.12.017 · Cited by 133
Self-citationGenotype to phenotype via network analysis
Carter, H., Hofree, M., & Ideker, T. (2013) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2013.10.003 · Cited by 132
Hafirassou, M. L., Meertens, L., Umaña-Diaz, C., Labeau, A., Dejarnac, O., Bonnet‐Madin, L., Kümmerer, B. M., Delaugerre, C., Roingeard, P., Vidalain, P., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.11.094 · Cited by 141
HIV ‐1 Nef: Taking Control of Protein Trafficking
Pereira, E. A., & daSilva, L. L. P. (2016) · Traffic · doi:10.1111/tra.12412 · Cited by 141
Willsey, A. J., Morris, M. T., Wang, S., Willsey, H. R., Sun, N., Teerikorpi, N., Baum, T., Cagney, G., Bender, K. J., Desai, T. A., et al. (2018) · Cell · doi:10.1016/j.cell.2018.06.016 · Cited by 129
Self-citationProtein–protein interactions and genetic diseases: The interactome
Lage, K. (2014) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2014.05.028 · Cited by 125
An integrated map of HIV genome-wide variation from a population perspective
Li, G., Piampongsant, S., Faria, N. R., Voet, A. R. D., Pineda-Peña, A.-C., Khouri, R., Lemey, P., Vandamme, A., & Theys, K. (2015) · Retrovirology · doi:10.1186/s12977-015-0148-6 · Cited by 138
Beyond Paralogs: The Multiple Layers of Redundancy in Bacterial Pathogenesis
Ghosh, S., & O’Connor, T. J. (2017) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2017.00467 · Cited by 128
Dynamics and regulation of nuclear import and nuclear movements of HIV-1 complexes
Burdick, R. C., Delviks‐Frankenberry, K. A., Chen, J., Janaka, S. K., Sastri, J., Hu, W.-S., & Pathak, V. K. (2017) · PLoS Pathogens · doi:10.1371/journal.ppat.1006570 · Cited by 117
CBFβ Stabilizes HIV Vif to Counteract APOBEC3 at the Expense of RUNX1 Target Gene Expression
Kim, D. Y., Kwon, E., Hartley, P. D., Crosby, D. C., Mann, S., Krogan, N. J., & Gross, J. D. (2013) · Molecular Cell · doi:10.1016/j.molcel.2012.12.012 · Cited by 119
Self-citationAdvances in Zika Virus Research: Stem Cell Models, Challenges, and Opportunities
Ming, G., Tang, H., & Song, H. (2016) · Cell stem cell · doi:10.1016/j.stem.2016.11.014 · Cited by 121
SARS-CoV-2 variants evolve convergent strategies to remodel the host response
Bouhaddou, M., Reuschl, A., Polacco, B. J., Thorne, L., Ummadi, M. R., Ye, C., Rosales, R., Pelin, A., Batra, J., Jang, G. Μ., et al. (2023) · Cell · doi:10.1016/j.cell.2023.08.026 · Cited by 120
Self-citationUsing biological networks to integrate, visualize and analyze genomics data
Charitou, T., Bryan, K. R., & Lynn, D. J. (2016) · Genetics Selection Evolution · doi:10.1186/s12711-016-0205-1 · Cited by 121
Dynamics of IRES-mediated translation
Johnson, A. G., Grosely, R., Petrov, A. N., & Puglisi, J. D. (2017) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2016.0177 · Cited by 124
Lamper, A. M., Fleming, R. H., Ladd, K. M., & Lee, A. S. Y. (2020) · Science · doi:10.1126/science.abb0993 · Cited by 115
Zhang, S., Huang, W., Ren, L., Ju, X., Gong, M., Rao, J. Y., Sun, L., Li, P., Ding, Q., Wang, J., et al. (2021) · Cell Research · doi:10.1038/s41422-021-00581-y · Cited by 119
Penn, B. H., Netter, Z., Johnson, J. R., Dollen, J. V., Jang, G. Μ., Johnson, T. L., Ohol, Y. M., Maher, C., Bell, S. L., Geiger, K. M., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.07.010 · Cited by 118
Self-citationLum, K. K., & Cristea, I. M. (2016) · Expert Review of Proteomics · doi:10.1586/14789450.2016.1147353 · Cited by 113
Suppression of APOBEC3-mediated restriction of HIV-1 by Vif
Feng, Y., Baig, T. T., Love, R. P., & Chelico, L. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00450 · Cited by 113
The activity of Nef on HIV-1 infectivity
Basmaciogullari, S., & Pizzato, M. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00232 · Cited by 110
A systems approach to infectious disease
Eckhardt, M., Hultquist, J. F., Kaake, R. M., Hüttenhain, R., & Krogan, N. J. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0212-5 · Cited by 111
Self-citationMcNamara, R. P., Costantini, L. M., Myers, T. A., Schouest, B., Maness, N. J., Griffith, J. D., Damania, B. A., MacLean, A. G., & Dittmer, D. P. (2018) · mBio · doi:10.1128/mbio.02344-17 · Cited by 109
Curing a viral infection by targeting the host: The example of cyclophilin inhibitors
Lin, K. W., & Gallay, P. A. (2013) · Antiviral Research · doi:10.1016/j.antiviral.2013.03.020 · Cited by 108
Improving Viral Protease Inhibitors to Counter Drug Resistance
Yılmaz, N. K., Swanstrom, R. I., & Schiffer, C. A. (2016) · Trends in Microbiology · doi:10.1016/j.tim.2016.03.010 · Cited by 107
An Atlas of Protein-Protein Interactions Across Mouse Tissues
Skinnider, M. A., Scott, N. E., Prudova, A., Kerr, C. H., Stoynov, N., Stacey, R. G., Chan, Q. W. T., Rattray, D., Gsponer, J. A., & Foster, L. J. (2021) · Cell · doi:10.1016/j.cell.2021.06.003 · Cited by 108
How HIV-1 Nef hijacks the AP-2 clathrin adaptor to downregulate CD4
Ren, X., Park, S., Bonifacino, J. S., & Hurley, J. H. (2014) · eLife · doi:10.7554/elife.01754 · Cited by 106
Miteva, Y. V., Budayeva, H. G., & Cristea, I. M. (2013) · Analytical Chemistry · doi:10.1021/ac3033257 · Cited by 105
Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite
Deutsch, E. W., Mendoza, L., Shteynberg, D. D., Hoopmann, M. R., Sun, Z., Eng, J. K., & Moritz, R. L. (2023) · Journal of Proteome Research · doi:10.1021/acs.jproteome.2c00624 · Cited by 105
Chen, Z., Wang, C., Feng, X., Nie, L., Tang, M., Zhang, H., Xiong, Y., Swisher, S. K., Srivastava, M., & Chen, J. (2021) · The EMBO Journal · doi:10.15252/embj.2021107776 · Cited by 103
Cullin E3 Ligases and Their Rewiring by Viral Factors
Mahon, C., Krogan, N., Craik, C., & Pick, E. (2014) · Biomolecules · doi:10.3390/biom4040897 · Cited by 101
Self-citationMultiple roles of the capsid protein in the early steps of HIV-1 infection
Fassati, A. (2012) · Virus Research · doi:10.1016/j.virusres.2012.09.012 · Cited by 108
How pathogens use linear motifs to perturb host cell networks
Via, A., Uyar, B., Brun, C., & Zanzoni, A. (2014) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2014.11.001 · Cited by 99
High-resolution network biology: connecting sequence with function
Ryan, C. J., Cimermančič, P., Szpiech, Z. A., Šali, A., Hernandez, R. D., & Krogan, N. J. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3574 · Cited by 98
Self-citationViral journeys on the intracellular highways
Robinson, M., Schor, S., Barouch‐Bentov, R., & Einav, S. (2018) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-018-2882-0 · Cited by 101
Host restriction factors in retroviral infection: promises in virus-host interaction
Zheng, Y., Jeang, K.-T., & Tokunaga, K. (2012) · Retrovirology · doi:10.1186/1742-4690-9-112 · Cited by 106
Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus–Host Protein Network
Eckhardt, M., Zhang, W., Gross, A. M., Dollen, J. V., Johnson, J. R., Franks-Skiba, K. E., Swaney, D. L., Johnson, T. L., Jang, G. Μ., Shah, P. S., et al. (2018) · Cancer Discovery · doi:10.1158/2159-8290.cd-17-1018 · Cited by 97
Self-citationA review on computational systems biology of pathogen–host interactions
DurmuÅŸ, S., Çakır, T., Özgür, A., & Guthke, R. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00235 · Cited by 93
Cullin-RING E3 Ubiquitin Ligases: Bridges to Destruction
Nguyen, H. C., Wang, W., & Xiong, Y. (2017) · Sub-cellular biochemistry/Subcellular biochemistry · doi:10.1007/978-3-319-46503-6_12 · Cited by 102
Mukerji, J., Olivieri, K. C., Misra, V., Agopian, K. A., & Gabuzda, D. H. (2012) · Retrovirology · doi:10.1186/1742-4690-9-33 · Cited by 97
Greenwood, E. J. D., Williamson, J. C., Sienkiewicz, A., Naamati, A., Matheson, N. J., & Lehner, P. J. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.04.025 · Cited by 95
Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2
Gao, K., Wang, R., Chen, J., Cheng, L., Frishcosy, J., Huzumi, Y., Qiu, Y., Schluckbier, T., Wei, X., & Wei, G. (2022) · Chemical Reviews · doi:10.1021/acs.chemrev.1c00965 · Cited by 93
HIV-1 Vpr Modulates Macrophage Metabolic Pathways: A SILAC-Based Quantitative Analysis
Barrero, C. A., Datta, P. K., Sen, S., Deshmane, S. L., Amini, S., Khalili, K., & Merali, S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0068376 · Cited by 98
McLaren, P. J., Gawanbacht, A., Pyndiah, N., Krapp, C., Hotter, D., Kluge, S. F., Götz, N., Heilmann, J., Mack, K., Sauter, D., et al. (2015) · Retrovirology · doi:10.1186/s12977-015-0165-5 · Cited by 95
Virus-Like Particles as an Instrument of Vaccine Production
Syomin, B. V., & Ilyin, Y. V. (2019) · Molecular Biology · doi:10.1134/s0026893319030154 · Cited by 90
HIV-1 Gag co-opts a cellular complex containing DDX6, a helicase that facilitates capsid assembly
Reed, J. C., Molter, B., Geary, C. D., McNevin, J. P., McElrath, J., Giri, S., Klein, K. C., & Lingappa, J. R. (2012) · The Journal of Cell Biology · doi:10.1083/jcb.201111012 · Cited by 95
HIV Genome-Wide Protein Associations: a Review of 30 Years of Research
Li, G., & Clercq, E. D. (2016) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00065-15 · Cited by 105
Gupta, M., Azumaya, C. M., Moritz, M., Pourmal, S., Diallo, A., Merz, G. E., Jang, G., Bouhaddou, M., Fossati, A., Brilot, A. F., et al. (2021) · doi:10.1101/2021.05.10.443524 · Cited by 89
Self-citationCellular and molecular mechanisms of HIV-1 integration targeting
Engelman, A., & Singh, P. K. (2018) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-018-2772-5 · Cited by 102
Autophagy plays an important role in the containment of HIV-1 in nonprogressor-infected patients
Nardacci, R., Amendola, A., Ciccosanti, F., Corazzari, M., Esposito, V., Vlassi, C., Taibi, C., Fimia, G. M., Nonno, F. D., Ippolito, G., et al. (2014) · Autophagy · doi:10.4161/auto.28678 · Cited by 90
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
