2023 Publications

B-HIVE Member Presentations at the 2023 Retroviral Meeting at Cold Spring Harbor

Quantitative full-length sequencing of the HIV-1 transcriptome in primary cell derived resting CD4+ T-cells and T-cell subsets

Christian M. Gallardo, Nadejda Beliakova-Bethell, Bruce E. Torbett.

HIV-1 uncoating in the nucleus progresses through a distinct step of small defect formation in the capsid lattice prior to terminal uncoating

Levi Gifford, Gregory B. Melikian.

Mutations outside integrase lead to high-level resistance to integrase strand transfer inhibitors

Yuta Hikichi, Jonathan Grover, Walther Mothes, Eric Freed.

Structural insights into PPP2R5A degradation by HIV-1 Vif

Yingxia Hu, Krista A. Delviks-Frankenberry, Fidel Arizarga, Chunxiang Wu, Vinay Pathak, Yong Xiong.

Lenacapavir inhibits virion maturation by blocking formation of capsid pentamers

Szu-Wei Huang, Lorenzo Briganti, Guochao Wei, Arun Annamalai, Stephanie Bester, Reed Haney, Lauren Schope, Nikoloz Shkriabai, Ashwanth Francis, Daniel Adu-Ampratwum, James Fuchs, Alan Engelman, Mamuka Kvaratskhelia.

A critical role for the C-terminal mixed-charge domain of CPSF6 in nuclear HIV incursion and integration targeting

Sooin Jang, Hyun Jae Yu, Parmit K. Singh, Gregory J. Bedwell, Zachary M. Ingram, Satya P. Singh, AidanDarian Douglas, Zandrea Ambrose, Ashwanth C. Francis, Vineet N. KewalRamani, Alan N. Engelman.

Implications for integrase functional plasticity from the structure of the HIV-1 integrase tetramer

Tao Jing, Zelin Shan, Tung Dinh, Juliet Greenwood, Min Li, Terry Zhang, Bo Zhou, Sriram Aiyer, Robert Craigie, Alan N. Engelman, Mamuka Kvaratskhelia, Dmitry Lyumkis.

Lenacapavir disrupts HIV-1 core integrity while stabilizing the capsid lattice

Chenglei Li, Ryan C. Burdick, Sanath K. Janaka, Wei-Shau Hu, Vinay K. Pathak.

Intasomes assembled with full-length HIV-1 integrase and CTD facilitate structural studies by cryo-EM and reveal the role of the integrase C-terminal tail

Min Li, Xuemin Chen, Yanxiang Cui, Robert Craigie.

HIV-1 usurps transcription start site heterogeneity of host RNA polymerase II to maximize replication fitness

Olga Nikolaitchik, Saiful Islam, Jonathan Kitzrow, Alice Duchon, Zetao Cheng, Wei Shao, Maria Nikolaitchik, Mary Kearney, Frank Maldarelli, Karin Musier-Forsyth, Vinay K. Pathak, Wei-Shau Hu.

The role of LEDGF in transcription is intertwined with its function in HIV-1 integration

Rakesh Pathak, Parmit K. Singh, Hongen N. Zhang, Seyed Z. Rabi, Sahand Hormoz, Alan N. Engelman, Henry L. Levin.

Regulation of the timing of HIV-1 uncoating by nucleocapsid protein

Ioulia Rouzina, Helena Gien, Michael Morse, Micah McCauley, Jonathan Kitzrow, Karin Musier-Forsyth, Robert Gorelick, Mark Williams.

HIV-1 preintegration complex preferentially integrates the viral DNA into nucleosomes containing trimethylated histone 3-lysine36 modification and flanking linker DNA.

Nicklas Sapp, Nathaniel Burge, Khan Cox, Prem Prakash, Muthukumar Balasubramaniam, Devin Christenson, Min Li, Jared Linderberger, Mamuka Kvaratskhelia, Jui Pandhare, Robert Craigie, Michael Poirier, Chandravanu Dash.

Identification of host dependency factors that modulate nuclear import of HIV-1 cores

Rokeya Siddiqui, Sushila Kumari, Ryan C. Burdick, Gianluca Pegoraro, Wei-Shau Hu, Vinay K. Pathak.

CPSF6 licenses HIV-1 integration into Pol II-paused genes regulated by P-TEFb and U2 snRNP

Parmit K. Singh, Arun S. Annamalai, Mamuka Kvaratskhelia, Alan N. Engelman.

Live-cell and superresolution microscopy studies of HIV-1 restriction by MX2

Dariana Torres-Rivera, Gilberto Betancor, Michael H. Malim, Gregory B. Melikyan.

Antagonism of viral glycoproteins by guanylate binding protein 5

Hana Veler, Geraldine Vilmen, Abdul Waheed, Cheng Man Lun, Eric O. Freed.

Reactive Docking: A computational method for high-throughput virtual screenings of reactive species

B-HIVE researchers develop a new method for discovering covalent inhibitors.

Bianco G, Holcomb M, Santos-Martins D, Tillack A, Hansel-Harris A, Forli S. J Chem Inf Model. 2023 Sep 11;63(17):5631-5640. doi: 10.1021/acs.jcim.3c00832. Epub 2023 Aug 28.

PubMed PMID: 37639635

Halo Library, a tool for rapid identification of ligand binding sites on proteins using crystallographic fragment screening

B-HIVE researchers show that halogenated compounds are an effective way to screen for new druggable sites on target proteins

Chopra A, Bauman JD, Ruiz FX, Arnold E. J Med Chem. 2023 May 11;66(9):6013-6024. doi: 10.1021/acs.jmedchem.2c01681. Epub 2023 Apr 28.

PubMed PMID: 37115705

PubMedCentralPMCID: PMC10184123

Near-physiological in vitro assembly of 50S ribosomes involves parallel pathways

Ribosomes are a model system for profiling of complex ribonucleoprotein assembly.

Dong X, Doerfel LK, Sheng K, Rabuck-Gibbons JN, Popova AM, Lyumkis D, Williamson JR. Nucleic Acids Res. 2023 Apr 11;51(6):2862-2876. doi: 10.1093/nar/gkad082.

PubMed PMID: 36864669

PubMedCentral PMCID: PMC10085682

Reversible phase separation of ESCRT protein ALIX through tyrosine phosphorylation

ALIX protein, which plays important roles in HIV budding, forms phase-separated condensates.

Elias RD, Zhu Y, Su Q, Ghirlando R, Zhang J, Deshmukh L. Sci Adv. 2023 Jul 14;9(28):eadg3913. doi: 10.1126/sciadv.adg3913. Epub 2023 Jul 14.

PubMed PMID: 37450591

PubMedCentral PMCID: PMC10348681

Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization

By combining structural, biophysical and biochemical experiments, B-HIVE researchers reveal the role of key amino acids in HIV-1 capsid stability.

Gres AT, Kirby KA, McFadden WM, Du H, Liu D, Xu C, Bryer AJ, Perilla JR, Shi J, Aiken C, Fu X, Zhang P, Francis AC, Melikyan GB, Sarafianos SG. Nat Commun. 2023 Sep 12;14(1):5614. doi: 10.1038/s41467-023-41197-7.

PubMed PMID: 37699872

PubMedCentral PMCID: PMC10497533

Critical mechanistic features of HIV-1 viral capsid assembly

B-HIVE researchers simulate the assembly of HIV capsid in the presence of IP6.

Gupta M, Pak AJ, Voth GA. Sci Adv. 2023 Jan 6;9(1):eadd7434. doi: 10.1126/sciadv.add7434. Epub 2023 Jan 6.

PubMed PMID: 36608139

PubMedCentral PMCID: PMC9821859

Structural insights into HIV-1 polyanion-dependent capsid lattice formation revealed by single particle cryo-EM

Cryo-EM structures of capsid in lattice assemblies reveal a critical role for inositol hexakisphosphate in the formation of pentamers.

Highland CM, Tan A, Ricaña CL, Briggs JAG, Dick RA. Proc Natl Acad Sci U S A. 2023 May 2;120(18):e2220545120. doi: 10.1073/pnas.2220545120. Epub 2023 Apr 24. Erratum in: Proc Natl Acad Sci U S A. 2023 Aug 29;120(35):e2312510120.

PubMed PMID: 37094124

PubMedCentral PMCID: PMC10160977

Dynamics of upstream ESCRT organization at the HIV-1 budding site

Simulation is used to explore the role of cellular ESCRT proteins in the budding of HIV.

Hudait A, Hurley JH, Voth GA. Biophys J. 2023 Jul 11;122(13):2655-2674. doi: 10.1016/j.bpj.2023.05.020. Epub 2023 May 22.

PubMed PMID: 37218128

PubMedCentral PMCID: PMC10397573 (available on )

Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants

B_HIVE researchers study the mechanism of drug resistance in HIV-1 integrase and how some drugs evade resistance.

Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke TR Jr, Levy RM, Hughes SH, Craigie R, Lyumkis D. Sci Adv. 2023 Jul 21;9(29):eadg5953. doi: 10.1126/sciadv.adg5953. Epub 2023 Jul 21.

PubMed PMID: 37478179

Targeting the HIV-1 and HBV Capsids, an EnCore

B-HIVE researchers discuss the targeting of capsid in antiviral therapy.

McFadden WM, Sarafianos SG. Viruses. 2023 Mar 31;15(4):896. doi: 10.3390/v15040896.

PubMed PMID: 37112877

PubMedCentral PMCID: PMC10146275

HIV-1 usurps transcription start site heterogeneity of host RNA polymerase II to maximize replication fitness

HIV-1 uses host-cell RNA polymerase II to create several slightly different viral RNAs with different specialized roles in viral replication.

Nikolaitchik OA, Islam S, Kitzrow JP, Duchon A, Cheng Z, Liu Y, Rawson JMO, Shao W, Nikolaitchik M, Kearney MF, Maldarelli F, Musier-Forsyth K, Pathak VK, Hu WS.  Proc Natl Acad Sci U S A. 2023 Jun 6;120(23):e2305103120. doi: 10.1073/pnas.2305103120. Epub 2023 May 30.

PubMed PMID: 37252967

PubMedCentral PMCID: PMC10266039 (available on )

A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase

RNA polymerases can successfully transcribe an expanded set of non-standard bases.

Oh J, Shan Z, Hoshika S, Xu J, Chong J, Benner SA, Lyumkis D, Wang D. Nat Commun. 2023 Dec 12;14(1):8219. doi: 10.1038/s41467-023-43735-9.

PubMed PMID: 38086811

PubMedCentral PMCID: PMC10716388

Hydrogen-deuterium exchange epitope mapping of glycosylated epitopes enabled by online immobilized glycosidase

Removing glycosylation can improve study of antibody binding epitopes by hydrogen-deuterium exchange and mass spectrometry.

O’Leary TR, Balasubramaniam D, Hughes K, Foster D, Boyles J, Coleman K, Griffin PR. Anal Chem. 2023 Jul 11;95(27):10204-10210. doi: 10.1021/acs.analchem.3c00374. Epub 2023 Jun 28.

PubMed PMID: 37379434

Assembly landscape for the bacterial large ribosomal subunit

The hierarchy of cooperative folding units is revealed in ribosome assembly.

Sheng K, Li N, Rabuck-Gibbons JN, Dong X, Lyumkis D, Williamson JR. Nat Commun. 2023 Aug 26;14(1):5220. doi: 10.1038/s41467-023-40859-w.

PubMed PMID: 37633970

PubMedCentral PMCID: PMC10460392

The drug-induced interface that drives HIV-1 integrase hypermultimerization and loss of function

Atomic structures reveal the mechanism of integrase condensation by allosteric HIV-1 integrase inhibitors (ALLINIs).

Singer MR, Dinh T, Levintov L, Annamalai AS, Rey JS, Briganti L, Cook NJ, Pye VE, Taylor IA, Kim K, Engelman AN, Kim B, Perilla JR, Kvaratskhelia M, Cherepanov P. mBio. 2023 Feb 28;14(1):e0356022. doi: 10.1128/mbio.03560-22.

PubMed PMID: 36744954

PubMedCentral PMCID: PMC9973045

ViReMa: a virus recombination mapper of next-generation sequencing data characterizes diverse recombinant viral nucleic acids

An improved method is presented for identifying recombination events in long read sequences of viral genomes.

Sotcheff S, Zhou Y, Yeung J, Sun Y, Johnson JE, Torbett BE, Routh AL.  Gigascience. 2023 Mar 20;12:giad009. doi: 10.1093/gigascience/giad009.

PubMed PMID: 36939008

PubMed Central PMCID: PMC10025937

Two structural switches in HIV-1 capsid regulate capsid curvature and host factor binding

The inner mechanics of HIV-1 capsid are explored using single-particle cryoelectron microscopy.

Stacey JCV, Tan A, Lu JM, James LC, Dick RA, Briggs JAG. Proc Natl Acad Sci U S A. 2023 Apr 18;120(16):e2220557120. doi: 10.1073/pnas.2220557120. Epub 2023 Apr 11.

PubMed PMID: 37040417

PubMedCentralPMCID: PMC10120081

Label-free imaging of nuclear membrane for analysis of nuclear import of viral complexes

Individual HIV-1 replication complexes are visualized as they enter the cell nucleus.

Ten Eyck A, Chen YC, Gifford L, Torres-Rivera D, Dyer EL, Melikyan GB. J Virol Methods. 2023 Dec;322:114834. doi: 10.1016/j.jviromet.2023.114834. Epub 2023 Oct 22.

PubMed PMID: 37875225

Neutral sphingomyelinase 2 is required for HIV-1 maturation

Neutral sphingomyelinase 2 plays important roles in HIV budding and maturation.

Waheed AA, Zhu Y, Agostino E, Naing L, Hikichi Y, Soheilian F, Yoo SW, Song Y, Zhang P, Slusher BS, Haughey NJ, Freed EO. Proc Natl Acad Sci U S A. 2023 Jul 11;120(28):e2219475120. doi: 10.1073/pnas.2219475120. Epub 2023 Jul 5.

PubMed PMID: 37406093

PubMedCentral PMCID: PMC10334776 (available on )

Inhibition of neutral sphingomyelinase 2 impairs HIV-1 envelope formation and substantially delays or eliminates viral rebound

Inhibitors of neutral sphingomyelinase 2 block HIV replication and kill HIV-infected cells.

Yoo SW, Waheed AA, Deme P, Tohumeken S, Rais R, Smith MD, DeMarino C, Calabresi PA, Kashanchi F, Freed EO, Slusher BS, Haughey NJ. Proc Natl Acad Sci U S A. 2023 Jul 11;120(28):e2219543120. doi: 10.1073/pnas.2219543120. Epub 2023 Jul 5.

PubMed PMID: 37406092

PubMedCentral PMCID: PMC10334757