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    Structured Review

    GraphPad Software Inc graphpad prism 10.1
    Graphpad Prism 10.1, supplied by GraphPad Software Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/prism+for+statistical+analysis%2C+v+10%2E1/graphpad+prism+software/pm40456378-99-0-10
    Average 90 stars, based on 1 article reviews
    graphpad prism 10.1 - by Bioz Stars, 2026-09
    90/100 stars

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    Virus:

    Article Title: PROTAC-mediated degradation of HIV-1 Nef efficiently restores cell-surface CD4 and MHC-I expression and blocks HIV-1 replication.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-CD4-APC conjugate BD Biosciences Cat# 555349; RRID: AB_398593 Mouse monoclonal anti-MHC-I-PE conjugate Santa Cruz Biotechnology Cat# sc-32235 PE; RRID: AB_627934 Mouse monoclonal anti-Actin, clone C4 Millipore Sigma Cat# MAB1501R: RRID: AB_2223041 Rabbit polyclonal Anti-HIV-1 Nef antiserum HIV Reagent Program Cat# ARP-2949 Bacterial and virus strains E. coli DH5a Thermo Fisher Cat# 18265017 E. coli Rosetta2(DE3) pLysS Millipore Sigma Cat# 71403 Human immunodeficiency virus 1 (HIV-1) HIV Reagent Program Cat# ARP-114 Biological samples Peripheral blood mononuclear cells Miltenyi Biotec Cat# 150-000-450 Chemicals, peptides, and recombinant proteins G418 Thermo Fisher Cat# 10131027 Puromycin Millipore Sigma Cat# P9620 Doxycycline Takara Bio USA Cat# 631311 Cell Lysis Buffer Cell Signaling Cat# 9803 Protease Inhibitor Cocktail Millipore Sigma Cat# P8340 ImmunoCult human CD3/CD28 T cell activator STEMCELL Technologies Cat# 10971 Interleukin-2 BD Biosciences Cat# 40043B Critical commercial assays NanoBRET Ubiquitination Kit Promega Cat# ND2690 Lenti-XTM Tet-One System Takara Bio USA Cat# 631847 StraightFrom Leukopak PBMC Isolation Kit Miltenyi Biotec Cat# 130-123-456 HIV-1 p24 AlphaLISA Assay Revvity Cat# AL332C CellTiter-Blue Cell Viability Assay Promega Cat# G8080 Experimental models: Cell lines CEM-T4 Lymphoblasts HIV Reagent Program Cat# ARP-117 293T Cells ATCC Cat# CRL-3216 TZM-bl Reporter Cells HIV Reagent Program Cat# ARP-8129 Recombinant DNA pET-28a bacterial expression plasmid Sigma Millipore Cat# 69864 Software and algorithms Prism for statistical analysis, v 10.1 GraphPad https://www.graphpad.com/ TraceDrawer for SPR curve fitting TraceDrawer https://tracedrawer.com/ Image Studio for immunoblot quantitation LI-COR Biosciences https://www.licor.com/bio/image-studio/ BioRender for illustrations BioRender https://www.biorender.com/ Other HisTrap HP column Cytiva Cat# 17524802 HiLoad 16/600 Superdex 75 column Cytiva Cat# 28989333 Superdex 75 Increase 10/300 GL Cytiva Cat# 29148721 Reichert 4SPR Instrument Reichert Technologies https://www.reichertspr.com/en/products/ reichert-4spr (Continued on next page) Cell Chemical Biology 31, 658–668.e1–e14, April 18, 2024 e1

    Recombinant:

    Article Title: PROTAC-mediated degradation of HIV-1 Nef efficiently restores cell-surface CD4 and MHC-I expression and blocks HIV-1 replication.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-CD4-APC conjugate BD Biosciences Cat# 555349; RRID: AB_398593 Mouse monoclonal anti-MHC-I-PE conjugate Santa Cruz Biotechnology Cat# sc-32235 PE; RRID: AB_627934 Mouse monoclonal anti-Actin, clone C4 Millipore Sigma Cat# MAB1501R: RRID: AB_2223041 Rabbit polyclonal Anti-HIV-1 Nef antiserum HIV Reagent Program Cat# ARP-2949 Bacterial and virus strains E. coli DH5a Thermo Fisher Cat# 18265017 E. coli Rosetta2(DE3) pLysS Millipore Sigma Cat# 71403 Human immunodeficiency virus 1 (HIV-1) HIV Reagent Program Cat# ARP-114 Biological samples Peripheral blood mononuclear cells Miltenyi Biotec Cat# 150-000-450 Chemicals, peptides, and recombinant proteins G418 Thermo Fisher Cat# 10131027 Puromycin Millipore Sigma Cat# P9620 Doxycycline Takara Bio USA Cat# 631311 Cell Lysis Buffer Cell Signaling Cat# 9803 Protease Inhibitor Cocktail Millipore Sigma Cat# P8340 ImmunoCult human CD3/CD28 T cell activator STEMCELL Technologies Cat# 10971 Interleukin-2 BD Biosciences Cat# 40043B Critical commercial assays NanoBRET Ubiquitination Kit Promega Cat# ND2690 Lenti-XTM Tet-One System Takara Bio USA Cat# 631847 StraightFrom Leukopak PBMC Isolation Kit Miltenyi Biotec Cat# 130-123-456 HIV-1 p24 AlphaLISA Assay Revvity Cat# AL332C CellTiter-Blue Cell Viability Assay Promega Cat# G8080 Experimental models: Cell lines CEM-T4 Lymphoblasts HIV Reagent Program Cat# ARP-117 293T Cells ATCC Cat# CRL-3216 TZM-bl Reporter Cells HIV Reagent Program Cat# ARP-8129 Recombinant DNA pET-28a bacterial expression plasmid Sigma Millipore Cat# 69864 Software and algorithms Prism for statistical analysis, v 10.1 GraphPad https://www.graphpad.com/ TraceDrawer for SPR curve fitting TraceDrawer https://tracedrawer.com/ Image Studio for immunoblot quantitation LI-COR Biosciences https://www.licor.com/bio/image-studio/ BioRender for illustrations BioRender https://www.biorender.com/ Other HisTrap HP column Cytiva Cat# 17524802 HiLoad 16/600 Superdex 75 column Cytiva Cat# 28989333 Superdex 75 Increase 10/300 GL Cytiva Cat# 29148721 Reichert 4SPR Instrument Reichert Technologies https://www.reichertspr.com/en/products/ reichert-4spr (Continued on next page) Cell Chemical Biology 31, 658–668.e1–e14, April 18, 2024 e1

    Lysis:

    Article Title: PROTAC-mediated degradation of HIV-1 Nef efficiently restores cell-surface CD4 and MHC-I expression and blocks HIV-1 replication.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-CD4-APC conjugate BD Biosciences Cat# 555349; RRID: AB_398593 Mouse monoclonal anti-MHC-I-PE conjugate Santa Cruz Biotechnology Cat# sc-32235 PE; RRID: AB_627934 Mouse monoclonal anti-Actin, clone C4 Millipore Sigma Cat# MAB1501R: RRID: AB_2223041 Rabbit polyclonal Anti-HIV-1 Nef antiserum HIV Reagent Program Cat# ARP-2949 Bacterial and virus strains E. coli DH5a Thermo Fisher Cat# 18265017 E. coli Rosetta2(DE3) pLysS Millipore Sigma Cat# 71403 Human immunodeficiency virus 1 (HIV-1) HIV Reagent Program Cat# ARP-114 Biological samples Peripheral blood mononuclear cells Miltenyi Biotec Cat# 150-000-450 Chemicals, peptides, and recombinant proteins G418 Thermo Fisher Cat# 10131027 Puromycin Millipore Sigma Cat# P9620 Doxycycline Takara Bio USA Cat# 631311 Cell Lysis Buffer Cell Signaling Cat# 9803 Protease Inhibitor Cocktail Millipore Sigma Cat# P8340 ImmunoCult human CD3/CD28 T cell activator STEMCELL Technologies Cat# 10971 Interleukin-2 BD Biosciences Cat# 40043B Critical commercial assays NanoBRET Ubiquitination Kit Promega Cat# ND2690 Lenti-XTM Tet-One System Takara Bio USA Cat# 631847 StraightFrom Leukopak PBMC Isolation Kit Miltenyi Biotec Cat# 130-123-456 HIV-1 p24 AlphaLISA Assay Revvity Cat# AL332C CellTiter-Blue Cell Viability Assay Promega Cat# G8080 Experimental models: Cell lines CEM-T4 Lymphoblasts HIV Reagent Program Cat# ARP-117 293T Cells ATCC Cat# CRL-3216 TZM-bl Reporter Cells HIV Reagent Program Cat# ARP-8129 Recombinant DNA pET-28a bacterial expression plasmid Sigma Millipore Cat# 69864 Software and algorithms Prism for statistical analysis, v 10.1 GraphPad https://www.graphpad.com/ TraceDrawer for SPR curve fitting TraceDrawer https://tracedrawer.com/ Image Studio for immunoblot quantitation LI-COR Biosciences https://www.licor.com/bio/image-studio/ BioRender for illustrations BioRender https://www.biorender.com/ Other HisTrap HP column Cytiva Cat# 17524802 HiLoad 16/600 Superdex 75 column Cytiva Cat# 28989333 Superdex 75 Increase 10/300 GL Cytiva Cat# 29148721 Reichert 4SPR Instrument Reichert Technologies https://www.reichertspr.com/en/products/ reichert-4spr (Continued on next page) Cell Chemical Biology 31, 658–668.e1–e14, April 18, 2024 e1

    Protease Inhibitor:

    Article Title: PROTAC-mediated degradation of HIV-1 Nef efficiently restores cell-surface CD4 and MHC-I expression and blocks HIV-1 replication.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-CD4-APC conjugate BD Biosciences Cat# 555349; RRID: AB_398593 Mouse monoclonal anti-MHC-I-PE conjugate Santa Cruz Biotechnology Cat# sc-32235 PE; RRID: AB_627934 Mouse monoclonal anti-Actin, clone C4 Millipore Sigma Cat# MAB1501R: RRID: AB_2223041 Rabbit polyclonal Anti-HIV-1 Nef antiserum HIV Reagent Program Cat# ARP-2949 Bacterial and virus strains E. coli DH5a Thermo Fisher Cat# 18265017 E. coli Rosetta2(DE3) pLysS Millipore Sigma Cat# 71403 Human immunodeficiency virus 1 (HIV-1) HIV Reagent Program Cat# ARP-114 Biological samples Peripheral blood mononuclear cells Miltenyi Biotec Cat# 150-000-450 Chemicals, peptides, and recombinant proteins G418 Thermo Fisher Cat# 10131027 Puromycin Millipore Sigma Cat# P9620 Doxycycline Takara Bio USA Cat# 631311 Cell Lysis Buffer Cell Signaling Cat# 9803 Protease Inhibitor Cocktail Millipore Sigma Cat# P8340 ImmunoCult human CD3/CD28 T cell activator STEMCELL Technologies Cat# 10971 Interleukin-2 BD Biosciences Cat# 40043B Critical commercial assays NanoBRET Ubiquitination Kit Promega Cat# ND2690 Lenti-XTM Tet-One System Takara Bio USA Cat# 631847 StraightFrom Leukopak PBMC Isolation Kit Miltenyi Biotec Cat# 130-123-456 HIV-1 p24 AlphaLISA Assay Revvity Cat# AL332C CellTiter-Blue Cell Viability Assay Promega Cat# G8080 Experimental models: Cell lines CEM-T4 Lymphoblasts HIV Reagent Program Cat# ARP-117 293T Cells ATCC Cat# CRL-3216 TZM-bl Reporter Cells HIV Reagent Program Cat# ARP-8129 Recombinant DNA pET-28a bacterial expression plasmid Sigma Millipore Cat# 69864 Software and algorithms Prism for statistical analysis, v 10.1 GraphPad https://www.graphpad.com/ TraceDrawer for SPR curve fitting TraceDrawer https://tracedrawer.com/ Image Studio for immunoblot quantitation LI-COR Biosciences https://www.licor.com/bio/image-studio/ BioRender for illustrations BioRender https://www.biorender.com/ Other HisTrap HP column Cytiva Cat# 17524802 HiLoad 16/600 Superdex 75 column Cytiva Cat# 28989333 Superdex 75 Increase 10/300 GL Cytiva Cat# 29148721 Reichert 4SPR Instrument Reichert Technologies https://www.reichertspr.com/en/products/ reichert-4spr (Continued on next page) Cell Chemical Biology 31, 658–668.e1–e14, April 18, 2024 e1

    Ubiquitin Proteomics:

    Article Title: PROTAC-mediated degradation of HIV-1 Nef efficiently restores cell-surface CD4 and MHC-I expression and blocks HIV-1 replication.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-CD4-APC conjugate BD Biosciences Cat# 555349; RRID: AB_398593 Mouse monoclonal anti-MHC-I-PE conjugate Santa Cruz Biotechnology Cat# sc-32235 PE; RRID: AB_627934 Mouse monoclonal anti-Actin, clone C4 Millipore Sigma Cat# MAB1501R: RRID: AB_2223041 Rabbit polyclonal Anti-HIV-1 Nef antiserum HIV Reagent Program Cat# ARP-2949 Bacterial and virus strains E. coli DH5a Thermo Fisher Cat# 18265017 E. coli Rosetta2(DE3) pLysS Millipore Sigma Cat# 71403 Human immunodeficiency virus 1 (HIV-1) HIV Reagent Program Cat# ARP-114 Biological samples Peripheral blood mononuclear cells Miltenyi Biotec Cat# 150-000-450 Chemicals, peptides, and recombinant proteins G418 Thermo Fisher Cat# 10131027 Puromycin Millipore Sigma Cat# P9620 Doxycycline Takara Bio USA Cat# 631311 Cell Lysis Buffer Cell Signaling Cat# 9803 Protease Inhibitor Cocktail Millipore Sigma Cat# P8340 ImmunoCult human CD3/CD28 T cell activator STEMCELL Technologies Cat# 10971 Interleukin-2 BD Biosciences Cat# 40043B Critical commercial assays NanoBRET Ubiquitination Kit Promega Cat# ND2690 Lenti-XTM Tet-One System Takara Bio USA Cat# 631847 StraightFrom Leukopak PBMC Isolation Kit Miltenyi Biotec Cat# 130-123-456 HIV-1 p24 AlphaLISA Assay Revvity Cat# AL332C CellTiter-Blue Cell Viability Assay Promega Cat# G8080 Experimental models: Cell lines CEM-T4 Lymphoblasts HIV Reagent Program Cat# ARP-117 293T Cells ATCC Cat# CRL-3216 TZM-bl Reporter Cells HIV Reagent Program Cat# ARP-8129 Recombinant DNA pET-28a bacterial expression plasmid Sigma Millipore Cat# 69864 Software and algorithms Prism for statistical analysis, v 10.1 GraphPad https://www.graphpad.com/ TraceDrawer for SPR curve fitting TraceDrawer https://tracedrawer.com/ Image Studio for immunoblot quantitation LI-COR Biosciences https://www.licor.com/bio/image-studio/ BioRender for illustrations BioRender https://www.biorender.com/ Other HisTrap HP column Cytiva Cat# 17524802 HiLoad 16/600 Superdex 75 column Cytiva Cat# 28989333 Superdex 75 Increase 10/300 GL Cytiva Cat# 29148721 Reichert 4SPR Instrument Reichert Technologies https://www.reichertspr.com/en/products/ reichert-4spr (Continued on next page) Cell Chemical Biology 31, 658–668.e1–e14, April 18, 2024 e1

    Isolation:

    Article Title: PROTAC-mediated degradation of HIV-1 Nef efficiently restores cell-surface CD4 and MHC-I expression and blocks HIV-1 replication.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-CD4-APC conjugate BD Biosciences Cat# 555349; RRID: AB_398593 Mouse monoclonal anti-MHC-I-PE conjugate Santa Cruz Biotechnology Cat# sc-32235 PE; RRID: AB_627934 Mouse monoclonal anti-Actin, clone C4 Millipore Sigma Cat# MAB1501R: RRID: AB_2223041 Rabbit polyclonal Anti-HIV-1 Nef antiserum HIV Reagent Program Cat# ARP-2949 Bacterial and virus strains E. coli DH5a Thermo Fisher Cat# 18265017 E. coli Rosetta2(DE3) pLysS Millipore Sigma Cat# 71403 Human immunodeficiency virus 1 (HIV-1) HIV Reagent Program Cat# ARP-114 Biological samples Peripheral blood mononuclear cells Miltenyi Biotec Cat# 150-000-450 Chemicals, peptides, and recombinant proteins G418 Thermo Fisher Cat# 10131027 Puromycin Millipore Sigma Cat# P9620 Doxycycline Takara Bio USA Cat# 631311 Cell Lysis Buffer Cell Signaling Cat# 9803 Protease Inhibitor Cocktail Millipore Sigma Cat# P8340 ImmunoCult human CD3/CD28 T cell activator STEMCELL Technologies Cat# 10971 Interleukin-2 BD Biosciences Cat# 40043B Critical commercial assays NanoBRET Ubiquitination Kit Promega Cat# ND2690 Lenti-XTM Tet-One System Takara Bio USA Cat# 631847 StraightFrom Leukopak PBMC Isolation Kit Miltenyi Biotec Cat# 130-123-456 HIV-1 p24 AlphaLISA Assay Revvity Cat# AL332C CellTiter-Blue Cell Viability Assay Promega Cat# G8080 Experimental models: Cell lines CEM-T4 Lymphoblasts HIV Reagent Program Cat# ARP-117 293T Cells ATCC Cat# CRL-3216 TZM-bl Reporter Cells HIV Reagent Program Cat# ARP-8129 Recombinant DNA pET-28a bacterial expression plasmid Sigma Millipore Cat# 69864 Software and algorithms Prism for statistical analysis, v 10.1 GraphPad https://www.graphpad.com/ TraceDrawer for SPR curve fitting TraceDrawer https://tracedrawer.com/ Image Studio for immunoblot quantitation LI-COR Biosciences https://www.licor.com/bio/image-studio/ BioRender for illustrations BioRender https://www.biorender.com/ Other HisTrap HP column Cytiva Cat# 17524802 HiLoad 16/600 Superdex 75 column Cytiva Cat# 28989333 Superdex 75 Increase 10/300 GL Cytiva Cat# 29148721 Reichert 4SPR Instrument Reichert Technologies https://www.reichertspr.com/en/products/ reichert-4spr (Continued on next page) Cell Chemical Biology 31, 658–668.e1–e14, April 18, 2024 e1

    Viability Assay:

    Article Title: PROTAC-mediated degradation of HIV-1 Nef efficiently restores cell-surface CD4 and MHC-I expression and blocks HIV-1 replication.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-CD4-APC conjugate BD Biosciences Cat# 555349; RRID: AB_398593 Mouse monoclonal anti-MHC-I-PE conjugate Santa Cruz Biotechnology Cat# sc-32235 PE; RRID: AB_627934 Mouse monoclonal anti-Actin, clone C4 Millipore Sigma Cat# MAB1501R: RRID: AB_2223041 Rabbit polyclonal Anti-HIV-1 Nef antiserum HIV Reagent Program Cat# ARP-2949 Bacterial and virus strains E. coli DH5a Thermo Fisher Cat# 18265017 E. coli Rosetta2(DE3) pLysS Millipore Sigma Cat# 71403 Human immunodeficiency virus 1 (HIV-1) HIV Reagent Program Cat# ARP-114 Biological samples Peripheral blood mononuclear cells Miltenyi Biotec Cat# 150-000-450 Chemicals, peptides, and recombinant proteins G418 Thermo Fisher Cat# 10131027 Puromycin Millipore Sigma Cat# P9620 Doxycycline Takara Bio USA Cat# 631311 Cell Lysis Buffer Cell Signaling Cat# 9803 Protease Inhibitor Cocktail Millipore Sigma Cat# P8340 ImmunoCult human CD3/CD28 T cell activator STEMCELL Technologies Cat# 10971 Interleukin-2 BD Biosciences Cat# 40043B Critical commercial assays NanoBRET Ubiquitination Kit Promega Cat# ND2690 Lenti-XTM Tet-One System Takara Bio USA Cat# 631847 StraightFrom Leukopak PBMC Isolation Kit Miltenyi Biotec Cat# 130-123-456 HIV-1 p24 AlphaLISA Assay Revvity Cat# AL332C CellTiter-Blue Cell Viability Assay Promega Cat# G8080 Experimental models: Cell lines CEM-T4 Lymphoblasts HIV Reagent Program Cat# ARP-117 293T Cells ATCC Cat# CRL-3216 TZM-bl Reporter Cells HIV Reagent Program Cat# ARP-8129 Recombinant DNA pET-28a bacterial expression plasmid Sigma Millipore Cat# 69864 Software and algorithms Prism for statistical analysis, v 10.1 GraphPad https://www.graphpad.com/ TraceDrawer for SPR curve fitting TraceDrawer https://tracedrawer.com/ Image Studio for immunoblot quantitation LI-COR Biosciences https://www.licor.com/bio/image-studio/ BioRender for illustrations BioRender https://www.biorender.com/ Other HisTrap HP column Cytiva Cat# 17524802 HiLoad 16/600 Superdex 75 column Cytiva Cat# 28989333 Superdex 75 Increase 10/300 GL Cytiva Cat# 29148721 Reichert 4SPR Instrument Reichert Technologies https://www.reichertspr.com/en/products/ reichert-4spr (Continued on next page) Cell Chemical Biology 31, 658–668.e1–e14, April 18, 2024 e1

    Expressing:

    Article Title: PROTAC-mediated degradation of HIV-1 Nef efficiently restores cell-surface CD4 and MHC-I expression and blocks HIV-1 replication.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-CD4-APC conjugate BD Biosciences Cat# 555349; RRID: AB_398593 Mouse monoclonal anti-MHC-I-PE conjugate Santa Cruz Biotechnology Cat# sc-32235 PE; RRID: AB_627934 Mouse monoclonal anti-Actin, clone C4 Millipore Sigma Cat# MAB1501R: RRID: AB_2223041 Rabbit polyclonal Anti-HIV-1 Nef antiserum HIV Reagent Program Cat# ARP-2949 Bacterial and virus strains E. coli DH5a Thermo Fisher Cat# 18265017 E. coli Rosetta2(DE3) pLysS Millipore Sigma Cat# 71403 Human immunodeficiency virus 1 (HIV-1) HIV Reagent Program Cat# ARP-114 Biological samples Peripheral blood mononuclear cells Miltenyi Biotec Cat# 150-000-450 Chemicals, peptides, and recombinant proteins G418 Thermo Fisher Cat# 10131027 Puromycin Millipore Sigma Cat# P9620 Doxycycline Takara Bio USA Cat# 631311 Cell Lysis Buffer Cell Signaling Cat# 9803 Protease Inhibitor Cocktail Millipore Sigma Cat# P8340 ImmunoCult human CD3/CD28 T cell activator STEMCELL Technologies Cat# 10971 Interleukin-2 BD Biosciences Cat# 40043B Critical commercial assays NanoBRET Ubiquitination Kit Promega Cat# ND2690 Lenti-XTM Tet-One System Takara Bio USA Cat# 631847 StraightFrom Leukopak PBMC Isolation Kit Miltenyi Biotec Cat# 130-123-456 HIV-1 p24 AlphaLISA Assay Revvity Cat# AL332C CellTiter-Blue Cell Viability Assay Promega Cat# G8080 Experimental models: Cell lines CEM-T4 Lymphoblasts HIV Reagent Program Cat# ARP-117 293T Cells ATCC Cat# CRL-3216 TZM-bl Reporter Cells HIV Reagent Program Cat# ARP-8129 Recombinant DNA pET-28a bacterial expression plasmid Sigma Millipore Cat# 69864 Software and algorithms Prism for statistical analysis, v 10.1 GraphPad https://www.graphpad.com/ TraceDrawer for SPR curve fitting TraceDrawer https://tracedrawer.com/ Image Studio for immunoblot quantitation LI-COR Biosciences https://www.licor.com/bio/image-studio/ BioRender for illustrations BioRender https://www.biorender.com/ Other HisTrap HP column Cytiva Cat# 17524802 HiLoad 16/600 Superdex 75 column Cytiva Cat# 28989333 Superdex 75 Increase 10/300 GL Cytiva Cat# 29148721 Reichert 4SPR Instrument Reichert Technologies https://www.reichertspr.com/en/products/ reichert-4spr (Continued on next page) Cell Chemical Biology 31, 658–668.e1–e14, April 18, 2024 e1

    Plasmid Preparation:

    Article Title: PROTAC-mediated degradation of HIV-1 Nef efficiently restores cell-surface CD4 and MHC-I expression and blocks HIV-1 replication.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-CD4-APC conjugate BD Biosciences Cat# 555349; RRID: AB_398593 Mouse monoclonal anti-MHC-I-PE conjugate Santa Cruz Biotechnology Cat# sc-32235 PE; RRID: AB_627934 Mouse monoclonal anti-Actin, clone C4 Millipore Sigma Cat# MAB1501R: RRID: AB_2223041 Rabbit polyclonal Anti-HIV-1 Nef antiserum HIV Reagent Program Cat# ARP-2949 Bacterial and virus strains E. coli DH5a Thermo Fisher Cat# 18265017 E. coli Rosetta2(DE3) pLysS Millipore Sigma Cat# 71403 Human immunodeficiency virus 1 (HIV-1) HIV Reagent Program Cat# ARP-114 Biological samples Peripheral blood mononuclear cells Miltenyi Biotec Cat# 150-000-450 Chemicals, peptides, and recombinant proteins G418 Thermo Fisher Cat# 10131027 Puromycin Millipore Sigma Cat# P9620 Doxycycline Takara Bio USA Cat# 631311 Cell Lysis Buffer Cell Signaling Cat# 9803 Protease Inhibitor Cocktail Millipore Sigma Cat# P8340 ImmunoCult human CD3/CD28 T cell activator STEMCELL Technologies Cat# 10971 Interleukin-2 BD Biosciences Cat# 40043B Critical commercial assays NanoBRET Ubiquitination Kit Promega Cat# ND2690 Lenti-XTM Tet-One System Takara Bio USA Cat# 631847 StraightFrom Leukopak PBMC Isolation Kit Miltenyi Biotec Cat# 130-123-456 HIV-1 p24 AlphaLISA Assay Revvity Cat# AL332C CellTiter-Blue Cell Viability Assay Promega Cat# G8080 Experimental models: Cell lines CEM-T4 Lymphoblasts HIV Reagent Program Cat# ARP-117 293T Cells ATCC Cat# CRL-3216 TZM-bl Reporter Cells HIV Reagent Program Cat# ARP-8129 Recombinant DNA pET-28a bacterial expression plasmid Sigma Millipore Cat# 69864 Software and algorithms Prism for statistical analysis, v 10.1 GraphPad https://www.graphpad.com/ TraceDrawer for SPR curve fitting TraceDrawer https://tracedrawer.com/ Image Studio for immunoblot quantitation LI-COR Biosciences https://www.licor.com/bio/image-studio/ BioRender for illustrations BioRender https://www.biorender.com/ Other HisTrap HP column Cytiva Cat# 17524802 HiLoad 16/600 Superdex 75 column Cytiva Cat# 28989333 Superdex 75 Increase 10/300 GL Cytiva Cat# 29148721 Reichert 4SPR Instrument Reichert Technologies https://www.reichertspr.com/en/products/ reichert-4spr (Continued on next page) Cell Chemical Biology 31, 658–668.e1–e14, April 18, 2024 e1

    Software:

    Article Title: PROTAC-mediated degradation of HIV-1 Nef efficiently restores cell-surface CD4 and MHC-I expression and blocks HIV-1 replication.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-CD4-APC conjugate BD Biosciences Cat# 555349; RRID: AB_398593 Mouse monoclonal anti-MHC-I-PE conjugate Santa Cruz Biotechnology Cat# sc-32235 PE; RRID: AB_627934 Mouse monoclonal anti-Actin, clone C4 Millipore Sigma Cat# MAB1501R: RRID: AB_2223041 Rabbit polyclonal Anti-HIV-1 Nef antiserum HIV Reagent Program Cat# ARP-2949 Bacterial and virus strains E. coli DH5a Thermo Fisher Cat# 18265017 E. coli Rosetta2(DE3) pLysS Millipore Sigma Cat# 71403 Human immunodeficiency virus 1 (HIV-1) HIV Reagent Program Cat# ARP-114 Biological samples Peripheral blood mononuclear cells Miltenyi Biotec Cat# 150-000-450 Chemicals, peptides, and recombinant proteins G418 Thermo Fisher Cat# 10131027 Puromycin Millipore Sigma Cat# P9620 Doxycycline Takara Bio USA Cat# 631311 Cell Lysis Buffer Cell Signaling Cat# 9803 Protease Inhibitor Cocktail Millipore Sigma Cat# P8340 ImmunoCult human CD3/CD28 T cell activator STEMCELL Technologies Cat# 10971 Interleukin-2 BD Biosciences Cat# 40043B Critical commercial assays NanoBRET Ubiquitination Kit Promega Cat# ND2690 Lenti-XTM Tet-One System Takara Bio USA Cat# 631847 StraightFrom Leukopak PBMC Isolation Kit Miltenyi Biotec Cat# 130-123-456 HIV-1 p24 AlphaLISA Assay Revvity Cat# AL332C CellTiter-Blue Cell Viability Assay Promega Cat# G8080 Experimental models: Cell lines CEM-T4 Lymphoblasts HIV Reagent Program Cat# ARP-117 293T Cells ATCC Cat# CRL-3216 TZM-bl Reporter Cells HIV Reagent Program Cat# ARP-8129 Recombinant DNA pET-28a bacterial expression plasmid Sigma Millipore Cat# 69864 Software and algorithms Prism for statistical analysis, v 10.1 GraphPad https://www.graphpad.com/ TraceDrawer for SPR curve fitting TraceDrawer https://tracedrawer.com/ Image Studio for immunoblot quantitation LI-COR Biosciences https://www.licor.com/bio/image-studio/ BioRender for illustrations BioRender https://www.biorender.com/ Other HisTrap HP column Cytiva Cat# 17524802 HiLoad 16/600 Superdex 75 column Cytiva Cat# 28989333 Superdex 75 Increase 10/300 GL Cytiva Cat# 29148721 Reichert 4SPR Instrument Reichert Technologies https://www.reichertspr.com/en/products/ reichert-4spr (Continued on next page) Cell Chemical Biology 31, 658–668.e1–e14, April 18, 2024 e1

    SPR Assay:

    Article Title: PROTAC-mediated degradation of HIV-1 Nef efficiently restores cell-surface CD4 and MHC-I expression and blocks HIV-1 replication.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-CD4-APC conjugate BD Biosciences Cat# 555349; RRID: AB_398593 Mouse monoclonal anti-MHC-I-PE conjugate Santa Cruz Biotechnology Cat# sc-32235 PE; RRID: AB_627934 Mouse monoclonal anti-Actin, clone C4 Millipore Sigma Cat# MAB1501R: RRID: AB_2223041 Rabbit polyclonal Anti-HIV-1 Nef antiserum HIV Reagent Program Cat# ARP-2949 Bacterial and virus strains E. coli DH5a Thermo Fisher Cat# 18265017 E. coli Rosetta2(DE3) pLysS Millipore Sigma Cat# 71403 Human immunodeficiency virus 1 (HIV-1) HIV Reagent Program Cat# ARP-114 Biological samples Peripheral blood mononuclear cells Miltenyi Biotec Cat# 150-000-450 Chemicals, peptides, and recombinant proteins G418 Thermo Fisher Cat# 10131027 Puromycin Millipore Sigma Cat# P9620 Doxycycline Takara Bio USA Cat# 631311 Cell Lysis Buffer Cell Signaling Cat# 9803 Protease Inhibitor Cocktail Millipore Sigma Cat# P8340 ImmunoCult human CD3/CD28 T cell activator STEMCELL Technologies Cat# 10971 Interleukin-2 BD Biosciences Cat# 40043B Critical commercial assays NanoBRET Ubiquitination Kit Promega Cat# ND2690 Lenti-XTM Tet-One System Takara Bio USA Cat# 631847 StraightFrom Leukopak PBMC Isolation Kit Miltenyi Biotec Cat# 130-123-456 HIV-1 p24 AlphaLISA Assay Revvity Cat# AL332C CellTiter-Blue Cell Viability Assay Promega Cat# G8080 Experimental models: Cell lines CEM-T4 Lymphoblasts HIV Reagent Program Cat# ARP-117 293T Cells ATCC Cat# CRL-3216 TZM-bl Reporter Cells HIV Reagent Program Cat# ARP-8129 Recombinant DNA pET-28a bacterial expression plasmid Sigma Millipore Cat# 69864 Software and algorithms Prism for statistical analysis, v 10.1 GraphPad https://www.graphpad.com/ TraceDrawer for SPR curve fitting TraceDrawer https://tracedrawer.com/ Image Studio for immunoblot quantitation LI-COR Biosciences https://www.licor.com/bio/image-studio/ BioRender for illustrations BioRender https://www.biorender.com/ Other HisTrap HP column Cytiva Cat# 17524802 HiLoad 16/600 Superdex 75 column Cytiva Cat# 28989333 Superdex 75 Increase 10/300 GL Cytiva Cat# 29148721 Reichert 4SPR Instrument Reichert Technologies https://www.reichertspr.com/en/products/ reichert-4spr (Continued on next page) Cell Chemical Biology 31, 658–668.e1–e14, April 18, 2024 e1

    Western Blot:

    Article Title: PROTAC-mediated degradation of HIV-1 Nef efficiently restores cell-surface CD4 and MHC-I expression and blocks HIV-1 replication.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-CD4-APC conjugate BD Biosciences Cat# 555349; RRID: AB_398593 Mouse monoclonal anti-MHC-I-PE conjugate Santa Cruz Biotechnology Cat# sc-32235 PE; RRID: AB_627934 Mouse monoclonal anti-Actin, clone C4 Millipore Sigma Cat# MAB1501R: RRID: AB_2223041 Rabbit polyclonal Anti-HIV-1 Nef antiserum HIV Reagent Program Cat# ARP-2949 Bacterial and virus strains E. coli DH5a Thermo Fisher Cat# 18265017 E. coli Rosetta2(DE3) pLysS Millipore Sigma Cat# 71403 Human immunodeficiency virus 1 (HIV-1) HIV Reagent Program Cat# ARP-114 Biological samples Peripheral blood mononuclear cells Miltenyi Biotec Cat# 150-000-450 Chemicals, peptides, and recombinant proteins G418 Thermo Fisher Cat# 10131027 Puromycin Millipore Sigma Cat# P9620 Doxycycline Takara Bio USA Cat# 631311 Cell Lysis Buffer Cell Signaling Cat# 9803 Protease Inhibitor Cocktail Millipore Sigma Cat# P8340 ImmunoCult human CD3/CD28 T cell activator STEMCELL Technologies Cat# 10971 Interleukin-2 BD Biosciences Cat# 40043B Critical commercial assays NanoBRET Ubiquitination Kit Promega Cat# ND2690 Lenti-XTM Tet-One System Takara Bio USA Cat# 631847 StraightFrom Leukopak PBMC Isolation Kit Miltenyi Biotec Cat# 130-123-456 HIV-1 p24 AlphaLISA Assay Revvity Cat# AL332C CellTiter-Blue Cell Viability Assay Promega Cat# G8080 Experimental models: Cell lines CEM-T4 Lymphoblasts HIV Reagent Program Cat# ARP-117 293T Cells ATCC Cat# CRL-3216 TZM-bl Reporter Cells HIV Reagent Program Cat# ARP-8129 Recombinant DNA pET-28a bacterial expression plasmid Sigma Millipore Cat# 69864 Software and algorithms Prism for statistical analysis, v 10.1 GraphPad https://www.graphpad.com/ TraceDrawer for SPR curve fitting TraceDrawer https://tracedrawer.com/ Image Studio for immunoblot quantitation LI-COR Biosciences https://www.licor.com/bio/image-studio/ BioRender for illustrations BioRender https://www.biorender.com/ Other HisTrap HP column Cytiva Cat# 17524802 HiLoad 16/600 Superdex 75 column Cytiva Cat# 28989333 Superdex 75 Increase 10/300 GL Cytiva Cat# 29148721 Reichert 4SPR Instrument Reichert Technologies https://www.reichertspr.com/en/products/ reichert-4spr (Continued on next page) Cell Chemical Biology 31, 658–668.e1–e14, April 18, 2024 e1

    Quantitation Assay:

    Article Title: PROTAC-mediated degradation of HIV-1 Nef efficiently restores cell-surface CD4 and MHC-I expression and blocks HIV-1 replication.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-CD4-APC conjugate BD Biosciences Cat# 555349; RRID: AB_398593 Mouse monoclonal anti-MHC-I-PE conjugate Santa Cruz Biotechnology Cat# sc-32235 PE; RRID: AB_627934 Mouse monoclonal anti-Actin, clone C4 Millipore Sigma Cat# MAB1501R: RRID: AB_2223041 Rabbit polyclonal Anti-HIV-1 Nef antiserum HIV Reagent Program Cat# ARP-2949 Bacterial and virus strains E. coli DH5a Thermo Fisher Cat# 18265017 E. coli Rosetta2(DE3) pLysS Millipore Sigma Cat# 71403 Human immunodeficiency virus 1 (HIV-1) HIV Reagent Program Cat# ARP-114 Biological samples Peripheral blood mononuclear cells Miltenyi Biotec Cat# 150-000-450 Chemicals, peptides, and recombinant proteins G418 Thermo Fisher Cat# 10131027 Puromycin Millipore Sigma Cat# P9620 Doxycycline Takara Bio USA Cat# 631311 Cell Lysis Buffer Cell Signaling Cat# 9803 Protease Inhibitor Cocktail Millipore Sigma Cat# P8340 ImmunoCult human CD3/CD28 T cell activator STEMCELL Technologies Cat# 10971 Interleukin-2 BD Biosciences Cat# 40043B Critical commercial assays NanoBRET Ubiquitination Kit Promega Cat# ND2690 Lenti-XTM Tet-One System Takara Bio USA Cat# 631847 StraightFrom Leukopak PBMC Isolation Kit Miltenyi Biotec Cat# 130-123-456 HIV-1 p24 AlphaLISA Assay Revvity Cat# AL332C CellTiter-Blue Cell Viability Assay Promega Cat# G8080 Experimental models: Cell lines CEM-T4 Lymphoblasts HIV Reagent Program Cat# ARP-117 293T Cells ATCC Cat# CRL-3216 TZM-bl Reporter Cells HIV Reagent Program Cat# ARP-8129 Recombinant DNA pET-28a bacterial expression plasmid Sigma Millipore Cat# 69864 Software and algorithms Prism for statistical analysis, v 10.1 GraphPad https://www.graphpad.com/ TraceDrawer for SPR curve fitting TraceDrawer https://tracedrawer.com/ Image Studio for immunoblot quantitation LI-COR Biosciences https://www.licor.com/bio/image-studio/ BioRender for illustrations BioRender https://www.biorender.com/ Other HisTrap HP column Cytiva Cat# 17524802 HiLoad 16/600 Superdex 75 column Cytiva Cat# 28989333 Superdex 75 Increase 10/300 GL Cytiva Cat# 29148721 Reichert 4SPR Instrument Reichert Technologies https://www.reichertspr.com/en/products/ reichert-4spr (Continued on next page) Cell Chemical Biology 31, 658–668.e1–e14, April 18, 2024 e1



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