2021 Research Highlights

HIVE Members Presentations at the 2021 Retroviral Meeting at Cold Spring Harbor

INTERACTIONS BETWEEN HIV-1 REVERSE TRANSCRIPTASE AND HUMAN APOBEC3G

Ryan L. Slack, Darja Pollpeter, Scott J. Novick, Seongmi Kim, Kamlendra Singh, Eddy Arnold, Patrick R. Griffin, Michael H. Malim, Stefan G. Sarafianos.

A NOVEL BIS(ARYL FLUOROSULFATE) COMPOUND COVALENTLY BINDS TO THE HIV-1 CAPSID PROTEIN

Mary C. Casey, Karen A. Kirby, Hua Wang, Theresa Tiefenbrunn Sample, Philip R. Tedbury, John R. Cappiello, Bruce E. Torbett, Arthur J. Olson, K Barry Sharpless, Stefan G. Sarafianos.

ADAPTATION OF CHIMERIC HIV—INSIGHTS INTO GAG-RNA INTERACTIONS THAT LEAD TO GENOME PACKAGING

Jonathan M. Rawson, Olga A. Nikolaitchik, Jennifer A. Yoo, Xayathed Somoulay, Vinay K. Pathak, Ryan L. Slack, Stefan G. Sarafianos, Wei-Shau Hu.

MULTIOMICS PROFILING OF HIV-INFECTED CELLS REVEALS UNIQUE CHROMATIN ‘SIGNATURE’ ASSOCIATED WITH ACTIVE INTEGRATED PROVIRUSES

Raven Shah, Christian M. Gallardo, Yoonhee H. Jung, Victor G. Corces, Bruce E. Torbett, Philip R. Tedbury, Stefan G. Sarafianos.

IDENTIFY HOST FACTORS INVOLVED IN GAG TRAFFICKING AND ASSEMBLY BY USING SPLIT-APEX2 SYSTEM COUPLED WITH QUANTITATIVE MS

Shentian Zhuang, Bruce Torbett

MRHAMER YIELDS HIGHLY ACCURATE SINGLE MOLECULE VIRAL SEQUENCES ENABLING ANALYSIS OF INTRA-HOST EVOLUTION

Christian M. Gallardo, Shiyi Wang, Daniel J. Montiel-Garcia, Susan J. Little, Davey M. Smith, Andrew L. Routh, Bruce E. Torbett.

SHAPE PROBING OF THE HIV-1 REVERSE TRANSCRIPTASE INITIATION COMPLEX REVEALS RNA FLEXIBILITY CHANGES ADJACENT TO THE PRIMERBINDING SITE

Chathuri Pathirage, William Cantara, Steven Tuske, Eddy Arnold, Karin Musier-Forsyth.

ROLE OF HIV-1 5’UTR RNA STRUCTURE AND CONFORMATIONAL DYNAMICS IN GENOME PACKAGING

Jonathan P. Kitzrow, Shuohui Lui, Shiqin Miao, Kevin Jamison, Dennis Bong, Michael Poirier, Karin Musier-Forsyth.

ANALYSIS OF HTLV-1 GAG INTERACTOME AND CHARACTERIZATION OF ITS CHAPERONE ACTIVITY

Yu-Ci Syu, Joshua Hatterschide, Yingke Tang, Jacob Al-Saleem, Amanda R. Panfil, Patrick L. Green, Karin Musier-Forsyth.

STRUCTURE OF HIV-1 POL POLYPROTEIN REVEALS REVERSE TRANSCRIPTASE P66/P51 HETERODIMER-LIKE CORE: IMPLICATIONS FOR PROTEASE ACTIVATION

Jerry J Harrison, Dario Oliveira Passos, Jessica Bruhn, Joseph Bauman, Lynda Tuberty, Jeffrey DeStefano, Dmitry Lyumkis, Eddy Arnold.

HIGH RESOLUTION MAPPING OF GENIC TARGETING PREFERENCES DURING HIV-1 INTEGRATION IN VITRO AND IN VIVO

Gregory J. Bedwell, Sooin Jang, Wen Li, Parmit K. Singh, Alan N. Engelman.

STRUCTURAL BASIS FOR THE EVOLUTION OF VIRAL RESISTANCE TO LONG-ACTING HIV-1 CAPSID INHIBITOR GS-6207

Stephanie M. Bester, Arun S. Annamalai, Daniel Adu-Ampratwum, Reed Haney, James R. Fuchs, Mamuka Kvaratskhelia.

PRE-MRNA SPLICING AND GENE DENSITY ARE SIGNIFICANT DETERMINANTS OF LENTIVIRAL INTEGRATION

Parmit K. Singh, Vidya Chivukula, Peter Cherepanov, Alan N. Engelman.

GFP-TAGGED HIV-1 CAPSID PROTEIN IS SELECTIVELY PACKAGED WITH VIRAL RIBONUCLEOPROTEIN COMPLEX INSIDE THE CONICAL SHELL OF INFECTIOUS VIRIONS

Ashwanth C Francis, Parmit K Singh, Jiong Shi, Anna Cereseto, Alan Engelman, Christopher R Aiken, Gregory B Melikyan

HIV-1 INTEGRATION FAVORS GENES ASSOCIATED WITH PROMOTER-PROXIMAL POL II PAUSING

Parmit K Singh, Arun Annamalai, Mamuka Kvaratkshelia, Alan N. Engelman

UNVEILING THE GENETIC FRAGILITY OF HIV-1 THROUGH DEEP LEARNING

Juan S. Rey, Wen Li, Hagan Beatson, Christian Lantz, Alexander Bryer, Alan N. Engelman, Juan R. Perilla.

HIV-1 PIC-MEDIATED INTEGRATION IS SELECTIVELY AFFECTED BY NUCLEOSOME STRUCTURE

Nicklas Sapp, Nathan Burge, Khan Cox, Muthukumar Balasubramaniam, Jui Pandhare, Min Li, Jared Lindenberger, Mamuka Kvaratskhelia, Robert Craigie, Michael Poirier, Chandravanu Dash

DDX3 AND EIF4G1 INFLUENCE HIV-1 TRAFFICKING TO NUCLEAR SPECKLES

Szu-Wei Huang, KyeongEun Lee, Hyun Jae Yu, Stephanie V. Rebensburg, Mamuka Kvaratskhelia, Vineet N. KewalRamani.

Evaluating local and directional resolution of cryo-EM density maps

Methods are presented for evaluating and improving cryo-EM maps.

Aiyer S, Zhang C, Baldwin PR, Lyumkis D. Methods Mol Biol. 2021;2215:161-187.

PubMed PMID: 33368004

Tools for visualizing and analyzing Fourier space sampling in Cryo-EM

Tools are presented for understanding how molecular orientation impacts structure determination by cryoelectron microscopy.

Baldwin PR, Lyumkis D. Prog Biophys Mol Biol. 2021 Mar;160:53-65.

PubMed PMID: 32645314

PubMedCentral PMCID: PMC7785567

rigrag: high-resolution mapping of genic targeting preferences during HIV-1 integration in vitro and in vivo

A method is presented for identifying genes that are recurrently targeted by HIV integrase, and genes that are recurrently avoided.

Bedwell GJ, Jang S, Li W, Singh PK, Engelman AN. Nucleic Acids Res. 2021 Jul 21;49(13):7330-7346.

PubMed PMID: 34165568

PubMedCentral PMCID: PMC8287940

MX2-mediated innate immunity against HIV-1 is regulated by serine phosphorylation

Several cellular proteins are identified that interact with MX2 as part of its antiviral action.

Betancor G, Jimenez-Guardeño JM, Lynham S, Antrobus R, Khan H, Sobala A, Dicks MDJ, Malim MH. Nat Microbiol. 2021 Aug;6(8):1031-1042. Erratum in: Nat Microbiol. 2021 Sep;6(9):1211.

PubMed PMID: 34282309

PubMedCentral PMCID: PMC7611661 

Drugs that inhibit TMEM16 proteins block SARS-CoV-2 spike-induced syncytia

Avoiding drug resistance in HIV reverse transcriptase

HIVE Center researchers review the biology of HIV reverse transcriptase and discuss approaches to fight drug resistance.

Cilento ME, Kirby KA, Sarafianos SG.  Chem Rev. 2021 Mar 24;121(6):3271-3296.

PubMed PMID: 33507067

PubMedCentral PMCID: PMC8149104 

Revealing the structural plasticity of SARS-CoV-2 nsp7 and nsp8 using structural proteomics

Solution-based structural proteomics techniques reveal that two coronavirus non-structural proteins may form multiple oligomeric states.

Courouble VV, Dey SK, Yadav R, Timm J, Harrison JJEK, Ruiz FX, Arnold E, Griffin PR. J Am Soc Mass Spectrom. 2021 Jul 7;32(7):1618-1630.

PubMed PMID: 34121407

PubMedCentral PMCID: PMC8231661

Discrimination between functional and non-functional cellular Gag complexes involved in HIV-1 assembly

The SMC5/6 complex compacts and silences unintegrated HIV-1 DNA and is antagonized by Vpr

Researchers explore how HIV protein Vpr blocks the natural defenses against integration of the viral genome.

Dupont L, Bloor S, Williamson JC, Cuesta SM, Shah R, Teixeira-Silva A, Naamati A, Greenwood EJD, Sarafianos SG, Matheson NJ, Lehner PJ. Cell Host Microbe. 2021 May 12;29(5):792-805.

PubMed PMID: 33811831

PubMedCentral PMCID: PMC8118623

Neutralizing antibody activity in convalescent sera from infection in humans with SARS-CoV-2 and variants of concern

Mechanistic roles of tyrosine phosphorylation in reversible amyloids, autoinhibition, and endosomal membrane association of ALIX

An autoinhibition mechanism relocates ALIX to the cytosol and tyrosine phosphorylation plays many roles in its functions.

Elias RD, Ramaraju B, Deshmukh L. J Biol Chem. 2021 Nov;297(5):101328.

PubMed PMID: 34688656

PubMedCentral PMCID: PMC8577116

MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution

A new nanopore-based method allows long-range sequencing of thousands of viral genomes from clinical samples.

Gallardo CM, Wang S, Montiel-Garcia DJ, Little SJ, Smith DM, Routh AL, Torbett BE.  Nucleic Acids Res. 2021 Jul 9;49(12):e70.

PubMed PMID: 33849057

PubMedCentral PMCID: PMC8266615

Neutralization potency of monoclonal antibodies recognizing dominant and subdominant epitopes on SARS-CoV-2 Spike is impacted by the B.1.1.7 variant

Mi3-GPU: MCMC-based Inverse Ising Inference on GPUs for protein covariation analysis

HIVE Center members improve methods for predicting interactions between amino acids based on observed mutational covariations.

Haldane A, Levy RM. Comput Phys Commun. 2021 Mar;260:107312.

PubMed PMID: 33716309

PubMedCentral PMCID: PMC7944406 

Crystal structure of a retroviral polyprotein: Prototype foamy virus protease-reverse transcriptase (PR-RT)

The structure of a monomeric precursor of PFV protease-reverse transcriptase is presented.

Harrison JJEK, Tuske S, Das K, Ruiz FX, Bauman JD, Boyer PL, DeStefano JJ, Hughes SH, Arnold E. Viruses. 2021 Jul 29;13(8):1495. doi: 10.3390/v13081495.

PubMed PMID: 34452360

PubMedCentral PMCID: PMC8402755

Icosahedral virus structures and the Protein Data Bank

The history of structural studies of icosahedral viruses is reviewed.

Johnson JE, Olson AJ.  J Biol Chem. 2021 Jan-Jun;296:100554.

PubMed PMID: 33744290

PubMedCentral PMCID: PMC8081926

TMPRSS2 promotes SARS-CoV-2 evasion from NCOA7-mediated restriction

Resilient SARS-CoV-2 diagnostics workflows including viral heat inactivation

HIV-1 integrase binding to genomic RNA 5′-UTR induces local structural changes in vitro and in virio

HIVE Center researchers find that nucleocapsid and integrase bind differently to HIV genomic RNA

Liu S, Koneru PC, Li W, Pathirage C, Engelman AN, Kvaratskhelia M, Musier-Forsyth K. Retrovirology. 2021 Nov 22;18(1):37.

PubMed PMID: 34809662

PubMedCentral PMCID: PMC8609798

Rotten to the core: antivirals targeting the HIV-1 capsid core

The role of HIV-1 capsid in the viral life cycle and the mechanisms of capsid inhibitors are reviewed.

McFadden WM, Snyder AA, Kirby KA, Tedbury PR, Raj M, Wang Z, Sarafianos SG. Retrovirology. 2021 Dec 22;18(1):41. doi: 10.1186/s12977-021-00583-z.

PubMed PMID: 34937567

PubMedCentral PMCID: PMC8693499

The generative capacity of probabilistic protein sequence models

Several methods for predicting evolutionary sequence covariation in viral populations are tested and compared.

McGee F, Hauri S, Novinger Q, Vucetic S, Levy RM, Carnevale V, Haldane A. Nat Commun. 2021 Nov 2;12(1):6302.

PMID: 34728624

PMCID: PMC8563988

Selective packaging of HIV-1 RNA genome is guided by the stability of 5′ untranslated region polyA stem

Retroviral integrase: Structure, mechanism, and inhibition

The function, structure, and inhibition of retroviral integrases are reviewed.

Passos DO, Li M, Craigie R, Lyumkis D. Enzymes. 2021;50:249-300. doi: 10.1016/bs.enz.2021.06.007. Epub 2021 Aug 23.

PubMed PMID: 34861940

PubMedCentral PMCID: PMC8732146

Quantitative NMR study of insulin-degrading enzyme using amyloid-β and HIV-1 p6 elucidates its chaperone activity

Insulin-degrading enzyme forms a single productive complex with HIV p6 and a more complex set of interactions with amyloids.

Ramaraju B, Nelson SL, Zheng W, Ghirlando R, Deshmukh L. Biochemistry. 2021 Aug 24;60(33):2519-2523.

PubMedCentral PubMed PMID: 34342986

Sec24C is an HIV-1 host dependency factor crucial for virus replication

Integrase strand transfer inhibitors are effective anti-HIV drugs

HIV Center members and collaborators review the current stated of clinically-relevant integrase strand transfer inhibitors.

Smith SJ, Zhao XZ, Passos DO, Lyumkis D, Burke TR Jr, Hughes SH. Integrase Strand Transfer Inhibitors Are Effective Anti-HIV Drugs. Viruses. 2021 Jan 29;13(2):205.

PubMed PMID: 33572956

PubMedCentral PMCID: PMC7912079

HIV-1 integrase inhibitors with modifications that affect their potencies against drug resistant integrase mutants

Based on structures of HIV-1 and SIV integrases, new integrase strand transfer inhibitors are designed and tested for their ability to block drug-resistant mutants of the enzyme.

Smith SJ, Zhao XZ, Passos DO, Pye VE, Cherepanov P, Lyumkis D, Burke TR Jr, Hughes SH. ACS Infect Dis. 2021 Jun 11;7(6):1469-1482.

PubMed PMID: 33686850

PubMedCentral PMCID: PMC8205226

Molecular dynamics free energy simulations reveal the mechanism for the antiviral resistance of the M66I HIV-1 capsid mutation

The free energy cost of protein side chain reorganization is largely responsible for drug resistance of a capsid inhibitor.

Sun Q, Levy RM, Kirby KA, Wang Z, Sarafianos SG, Deng N.  Viruses. 2021 May 15;13(5):920.

PMID: 34063519

PMCID: PMC8156065

Computational design of small molecular modulators of protein-protein interactions with a novel thermodynamic cycle: Allosteric inhibitors of HIV-1 integrase

A new method for targeting protein-protein interfaces is applied to design of integrase inhibitors

Sun Q, Ramaswamy VSK, Levy R, Deng N. Protein Sci. 2021 Feb;30(2):438-447.

PubMed PMID: 33244804

PubMedCentral PMCID: PMC7784772

Cleavage and Polyadenylation Specificity Factor 6 is required for efficient HIV-1 latency reversal

The cellular protein CPSF6 plays a novel role in HIV-1 transcription and latency of the virus.

Zheng Y, Schubert HL, Singh PK, Martins LJ, Engelman AN, D’Orso I, Hill CP, Planelles V.  mBio. 2021 Jun 29;12(3):e0109821.

PubMed PMID: 34154414

Interactions of HIV-1 Capsid with host factors and their implications for developing novel therapeutics

The structure and function of HIV-1 capsid and its interactions with host factors and drugs are reviewed.

Zhuang S, Torbett BE. Viruses. 2021 Mar 5;13(3):417.

PubMed PMID: 33807824

PubMedCentral PMCID: PMC8001122