2024

Patterns of Evolution of TRIM Genes Highlight the Evolutionary Plasticity of Antiviral Effectors in Mammals.

Fernandes AP, OhAinle M, Esteves PJ. (2024) Genome Biol Evol. 1;15(12):evad209. PMCID: PMC10709114

FIND-seq: high-throughput nucleic acid cytometry for rare single-cell transcriptomics.

Shin SW, Mudvari P, Thaploo S, Wheeler MA, Douek DC, Quintana FJ, Boritz EA, Abate AR, Clark IC, (2024) Nature Protocols.

Molecular Determinants of PQBP1 Binding to the HIV-1 Capsid Lattice.

Piacentini J, Allen DS, Ganser-Pornillos BK, Chanda SK, Yoh SM, Pornillos O. (2024) J Mol Biol. 15;436(4):168409. PMCID: PMC10885737

3D animation as a tool for integrative modeling of dynamic molecular mechanisms.

Riggi M, Torrez RM, Iwasa JH. (2024) Structure. 1;32(2):122-130. PMCID: PMC10872329

2023

Single-cell epigenetic, transcriptional, and protein profiling of latent and active HIV-1 reservoir revealed that IKZF3 promotes HIV-1 persistence.

Wei Y, Davenport TC, Collora JA, Ma HK, Pinto-Santini D, Lama J, Alfaro R, Duerr A, Ho YC. (2023) Immunity. 14;56(11):2584-2601.e7. PMCID: PMC10843106

Human immunodeficiency virus 1 5'-leader mutations in plasma viruses before and after the development of reverse transcriptase inhibitor-resistance mutations.

Nouhin J, Tzou PL, Rhee SY, Sahoo MK, Pinsky BA, Krupkin M, Puglisi JD, Puglisi EV, Shafer RW.(2023) J Gen Virol. 104(10):001898. PMCID: PMC10721937

In vivo selection of synthetic nucleocapsids for tissue targeting.

Olshefsky A, Benasutti H, Sylvestre M, Butterfield GL, Rocklin GJ, Richardson C, Hicks DR, Lajoie MJ, Song K, Leaf E, Treichel C, Decarreau J, Ke S, Kher G, Carter L, Chamberlain JS, Baker D, King NP, Pun SH. (2023) Proc Natl Acad Sci U S A. 120(46):e2306129120. PMCID: PMC10655225

Genome Integration site-dependent HIV-1 promoter activity shapes host chromatin conformation.

Collora JA, Ho YC. (2023) Genome Res. 33(6):891-906. PMCID: PMC10519397

Single-cell multiomic understanding of HIV-1 reservoir at epigenetic, transcriptional, and protein levels.

Wong M, Wei Y, Ho YC. (2023) Curr Opin HIV AIDS. 1;18(5):246-256. PMCID: PMC10442869

Pressure pushes tRNALys3 into excited conformational states.

Wang J, Koduru T, Harish B, McCallum SA, Larsen KP, Patel KS, Peters EV, Gillilan RE, Puglisi EV, Puglisi JD, Makhatadze G, Royer CA. (2023). Proc Natl Acad Sci U S A. 120(26):e2215556120. PMCID: 10293818

CD4 binding site immunogens elicit heterologous anti-HIV-1 neutralizing antibodies in transgenic and wild-type animals.

Gristick HB, Hartweger H, Loewe M, van Schooten J, Ramos V, Oliveira TY, Nishimura Y, Koranda NS, Wall A, Yao KH, Poston D, Gazumyan A, Wiatr M, Horning M, Keeffe JR, Hoffmann MAG, Yang Z, Abernathy ME, Dam KA, Gao H, Gnanapragasam PNP, Kakutani LM, Pavlovitch-Bedzyk AJ, Seaman MS, Howarth M, McGuire AT, Stamatatos L, Martin MA, West AP Jr, Nussenzweig MC, Bjorkman PJ. (2023) Sci Immunol. 17;8(80):eade6364. PMCID: PMC10202037

Virology under the Microscope-a Call for Rational Discourse.

Goodrum F, …. Sundquist WI…(156 authors) (2023). mSphere 8(2):e000034-23. PMCID: 10117089

Primate TRIM34 is a broadly-acting, TRIM5-dependent lentiviral restriction factor.

Twentyman J, Khalifeh A, Felton AL, Emerman M, OhAinle M. (2023) Retrovirology. 20(1):15.. PMCID: PMC10464172

The HIV-1 capsid core is an opportunistic nuclear import receptor.

Xue G, Yu HJ, Goh SL, Gres AT, Guney MH, Sarafianos SG, Luban J, KewalRamani VN. (2023) Nat Commun. 14(1):3782. PMCID: PMC10290713

Reducing the inherent auto-inhibitory interaction within the pegRNA enhances prime editing efficiency.

Ponnienselvan K, Liu P, Nyalile T, Oikemus S, Maitland S, Lawson ND, Luban J, and Wolfe SA. (2023) Nucleic Acids Res. 51(13):6966-6980. PMCID: PMC10359601

Transcriptional and chromatin profiling of human blood innate lymphoid cell subsets sheds light on HIV-1 pathogenesis.

Wang Y, Lifshitz L, Silverstein NJ, Mintzer E, Luk K, StLouis P, Brehm MA, Wolfe SA, Deeks SG, Luban J. (2023) EMBO J. 15;42(16):e114153. PMID: 37382276; PMCID: PMC10425848

Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock.

Sheffler W, Yang EC,  Dowling Q,  Hsia Y,  Fries CN, Stanislaw J , Langowski M, Brandys M,  Khmelinskaia A, King NP, Baker D (2023) PLoS Comput Biol. 22;19(5):e1010680. PMCID: PMC10237659

Intermediate conformations of CD4-bound HIV-1 Env heterotrimers.

Dam K-MA, Fan, C, Yang, Z, Bjorkman,PJ (2023) Nature. 623(7989):1017-1025.  PMCID: PMC9900888

HIV-1 Gag Binds the Multi-Aminoacyl-tRNA Synthetase Complex via the EPRS Subunit.

Jin D, Zhu Y, Schubert HL, Goff SP, Musier-Forsyth K. (2023). Viruses 2023, 15(2), 474. PMCID: PMC9967848

A Virus-Packageable CRISPR System Identifies Host Dependency Factors Co-Opted by Multiple HIV-1 Strains.

Montoya VR, Ready TM, Felton A, Fine SR, OhAinle M, Emerman M. (2023) mBio. PMID: 36744886

Communicating science through visual means.

Lyall K, Iwasa JH, Goodsell DS, Holt L. (2023) Trends Biochem Sci. 48(1):2-4. PMID: 36563656

A molecular switch modulates assembly and host factor binding of the HIV-1 capsid.

Schirra RT, dos Santos NFB, Zadrozny KK, Kucharska I, Ganser-Pornillos BK, Pornillos O. (2023) Nat Struct Mol Biol. PMID: 36759579

A modular CRISPR screen identifies individual and combination pathways contributing to HIV-1 latency.

Hsieh E, Janssens DH, Paddison PJ, Browne EP, Henikoff S, OhAinle M, Emerman M. (2023) PLoS Pathog. 19(1) PMCID: PMC9907829

Reversible phase separation of ESCRT protein ALIX through tyrosine phosphorylation.

Elias RD, Zhu Y, Su Q, Ghirlando R, Zhang J, Deshmukh L. (2023) Sci Adv. 9(28):eadg3913. PMID: 37450591; PMCID: PMC10348681

2022

Optimization of NLS Composition Improves CRISPR-Cas12a Editing Rates in Human Primary Cells.

Luk K, Liu P, Zeng J, Wang Y, Maitland SA, Idrizi F, Ponnienselvan K, Zhu LJ, Luban J, Bauer DE, Wolfe SA. (2022) Gen Biotech. PMCID: PMC10887433

Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains.

Wang JY, Khmelinskaia A, Sheffler W, Marcos C, Antanasijevic A, Borst AJ, Vazquez Torres S, Shu C, Yang H, Nattermann U, Ellis D, Walkey C, Ahlrichs M, Chan S, Kang A, Nguyen H, Syderman C, Sankaran B, Wu M, Bera AK, Carter L, Fiala B, Murphy M, Baker D, Ward AB, King NP (2022) Proc Natl Acad Sci U S A. 120(11):e2214556120. PMCID: PMC10089191

Interferon opens up: HIV-induced inflammation reconfigures 3D chromatin conformation and affects where HIV integrates.

Wei Y, Ho YC. (2022) Mol Cell. 82(24); 4585-4587. PMCID: PMC9925257. 

Uncovering translation roadblocks during the development of a synthetic tRNA.

Prabhakar A, Krahn N, Zhang J, Vargas-Rodriguez O, Krupkin M, Fu Z, Acosta-Reyes FJ, Ge X, Choi J, Crnkovic, Ehrenberg M, Puglisi EV, Soll D, Puglisi J. (2022) Nucleic Acids Res.14;50(18) PMCID: PMC9561287 

Recognition of HIV-1 capsid by PQBP1 licenses an innate immune sensing of nascent HIV-1 DNA.

Yoh SM, Mamede JI, Lau D, Ahn N, Sanchez-Aparicio MT, Temple J, Tuckwell A, Fuchs NV, Cianci GC, Riva I, Hope TJ et al (2022) Mol Cell. 82(15):2871-2884.e6. PMCID: PMC9552964 (available on 2023-08-04)

HIV-1 Vpu restricts Fc-mediated effector functions in vivo.

Prevost J, Anand AP, Krishnaswamy J, Richard J, Goyette G, Mejahed H, Gendron-Lepage G, Chen HC, Chen Y, Horwitz JA, Grunst MW, Zolla-Pazner S, Haynes BF, Burton DR, Flavell RA, Kirchoff F, Hahn BH, Smith III AB, Pazgier M, Nussenzweig MC, Kumar P, Finzi A. (2022) Cell Rep. 41(6):111624. PMID: 36351384

Organization  of  Upstream  ESCRT  Machinery  at the HIV-1 Budding Site.

Hudait A, Hurley JH, Voth GA. (2022) Biophys J. 122(13):2655-2674. PMCID: PMC10397573

A molecular switch modulates assembly and host factor binding of the HIV-1 capsid.

Schirra RT, dos Santos NFB, Zadrozny KK, Kucharska I, Ganser-Pornillos BK, Pornillos O. (2023) Nat Struct Mol Biol. 30(3):383-390. PMCID: PMC10023569

Nanoscale details of mitochondrial constriction revealed by cryoelectron tomography.

Mageswaran SK, Grotjahn DA, Zeng X, Barad BA, Medina M, Hoang MH, Dobro MJ, Chang YW, Xu M, Yang WY, Jensen GJ. (2022) Biophys J. 122(18):3768-3782. PMID: 37533259; PMCID: PMC10541493.

Brominated Lipid Probes Expose Structural Asymmetries in Constricted Membranes.

Moss III FR, Lincoff J, Tucker M, Mohammed A, Grabe M, Frost A. (2022). bioRxiv. (under revision at NSMB)

Antibody recognition of CD4-induced open HIV-1 Env trimers.

Yang Z, Dam KMA, Gershoni JM, Zolla-Pazner S, Bjorkman PJ. (2022) J Virol. 96(24) PMCID: PMC9769388

HIV-1 CD4-binding site germline antibody–Env structures inform vaccine design.

Dam KMA, Barnes CO, Gristick HB, Schoofs T, Gnanapragasam PNP, Nussenzweig MC, Bjorkman PJ. (2022) Nat Commun. PMCID: PMC9576718

A naturally arising broad and potent CD4-binding site antibody with low somatic mutation.

Barnes CO, Schoofs T, Gnanapragasam PNP, Golijanin J, Huey-Tubman KE, Gruell H, Schommers P, Suh-Toma N, Lee YE, Cetrulo Lorenzi JC, Piechocka-Trocha A, Scheid JF, West AP Jr, Walker BD, Seaman MS, Klein F, Nussenzweig MC, Bjorkman PJ. (2022) Sci Adv. 2022 Aug 12;8(32):eabp8155. PMID: 35960796 PMCID: PMC9374330

Improved Handling of Peptide Segments Using Side Chain-Based "Helping Hand" Solubilizing Tools.

Jacobsen MT, Spaltenstein P, Giesler RJ, Chou DH, Kay MS. (2022) Methods Mol Biol. 2022;2530:81-107. PMID: 35761044

Engineering Self-Assembling Protein Nanoparticles for Therapeutic Delivery.

Olshefsky A, Richardson C, Pun SH, King NP. (2022) Bioconjug Chem. 2022 Nov 16;33(11):2018-2034. PMID: 35487503

Uncovering translation roadblocks during the development of a synthetic tRNA.

Prabhakar A, Krahn N, Zhang J, Vargas-Rodriguez O, Krupkin M, Fu Z, Acosta-Reyes FJ, Ge X, Choi J, Crnković A, Ehrenberg M, Puglisi EV, Puglisi JD. (2022) Nucleic Acids Res. 2022 Oct 14;50(18):10201-10211. PMID: 35882385 PMCID: PMC9561287

Genetic Modification of Primary Human Myeloid Cells to Study Cell Migration, Activation, and Organelle Dynamics.

Greiner D, Scott TM, Olson GS, Aderem A, Roh-Johnson M, Johnson JS. (2022) Curr Protoc. 2022 Aug;2(8):e514. PMID: 36018279 PMCID: PMC9476234 (available on 2023-08-01)

Inhibition of a Chromatin and Transcription Modulator, SLTM, Increases HIV-1 Reactivation Identified by a CRISPR Inhibition Screen.

Pedersen SF, Collora JA, KimRN, Yang K, Razmi A, Catalano AA, Yeh YJ, Mounzer K, Tebas P, Montaner LJ, Ho YC. (2022) J Virol. 2022 Jul 13;96(13):e0057722. PMID: 35730977 PMCID: PMC9278143

Recognition of HIV-1 capsid licenses innate immune response to viral infection.

Yoh SM, Mamede, JI, Lau D, Sánchez-Aparicio MT, Temple J, Fuchs NV, Tuckwell A,  Cianci GC, Riva L, Curry H, König N, Xiong Y, García-Sastre A, Böcking T, Hope TJ, Chanda SK. (2022). Mol Cell. 2022 Aug 4;82(15):2871-2884.e6. Epub 2022 Jul 8. PMID: 35809572 PMCID: PMC9552964 (available on 2023-08-04)

Single-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic T cell clones.

Collora JA, Liu R, Pinto-Santini D, Ravindra N, Ganoza C, Lama JR, Alfaro R, Chiarella J, Spudich S, Mounzer K, Tebas P, Montaner LJ, van Dijk D, Duerr A, Ho YC. (2022). Immunity. 2022 Jun 14;55(6):1013-1031.e7. Epub 2022 Mar 22. PMID: 35320704; PMCID: PMC9203927 

Active conformation of the p97-p47 unfoldase complex.

Xu Y, Han H, Cooney I, Guo Y, Moran NG, Zuniga NR, Price JC, Hill CP, Shen PS. Nat Commun. 2022 May 12;13(1):2640. PMID: 35552390  PMCID: PMC9098461

Recurrent evolution of an inhibitor of ESCRT-dependent virus budding and LINE-1 retrotransposition in primates.

Rheinemann L, Downhour DM, Davenport KA, McKeown AN, Sundquist WI, Elde NC. (2022) Curr Biol. 2022 Apr 11;32(7):1511-1522.e6. PMID: 35245459 PMCID: PMC9007875

Strain and rupture of HIV-1 capsids during uncoating.

Yu A, Lee EMY, Briggs JAG, Ganser-Pornillos BK, Pornillos O, Voth GA. (2022) Proc Natl Acad Sci U S A. 2022 Mar 8;119(10):e2117781119. PMID: 35238630 PMCID: PMC8915963

Neutralizing antibodies induced in immunized macaques recognize the CD4-binding site on an occluded-open HIV-1 envelope trimer.

Yang Z, Dam K-MA, Bridges MD, Hoffmann MAG, DeLaitsch AT, Gristick HB, Escolano A, Gautam R, Martin MA, Nussenzweig MC, Hubbell WL, Bjorkman PJ. (2022) Nat Commun. 2022 Feb 8;13(1):732. PMID: 35136084 PMCID: PMC8826976

The interaction between the Spt6-tSH2 domain and Rpb1 affects multiple functions of RNA Polymerase II.

Connell Z, Parnell TJ, McCullough LL, Hill CP, Formosa T. (2022) Nucleic Acids Res. 2022 Jan 25;50(2):784-802. PMID: 34967414 PMCID: PMC8789061

UVC inactivation of pathogenic samples suitable for cryo-EM analysis.

Depelteau, JS, Renault L, Athof N, Cassidy CK, Mendonca LM, Jensen GJ, Resch GP, Briegel A. (2022). Commun Biol. 2022 Jan 11;5(1):29. PMID: 35017666 PMCID: PMC8752862

2021

Hallmarks of icosahedral virus capsids emerged during laboratory evolution of a bacterial enzyme.

Olshefsky A, King NP. (2021). Trends Biochem Sci. 2021 Nov;46(11):863-865. PMID: 34456123

Sequential immunization of macaques elicits heterologous neutralizing antibodies targeting the V3-glycan patch of HIV-1 Env.

Escolano A, Gristick HB, Gautam R, DeLaitsch AT, Abernathy ME, Yang Z, Wang H, Hoffmann MAG Nishimura Y, Wang Z, Koranda N, Kakutani LM, Gao H, Gnanapragasam PNP, Raina H, Gazumyan A, Cipolla M, Oliveria TY, Ramos V, Irvine DJ, Silva M, West AP, Keeffe JR, Barnes CO, Seaman MS, Nussenzweig MC, Martin MA, Bjorkman PJ. (2021) Sci Transl Med. 2021 Nov 24;13(621):eabk1533. PMID: 34818054 PMCID: PMC8932345

Development of a universal nanobody-binding Fab module for fiducial-assisted cryo-EM studies of membrane proteins.

Bloch JS, Mukherjee S, Kowal J, Filippova EV, Niederer M, Pardon E, Steyaert J, Kossiakoff AA, Locher KP. (2021) Proc Natl Acad Sci U S A. 2021 Nov 23;118(47):e2115435118. PMID: 34782475 PMCID: PMC8617411

A glutamic acid-based traceless linker to address challenging chemical protein syntheses.

Giesler RJ, Spaltenstein P, Jacobsen MT, Xu W, Maqueda M, Kay MS. (2021) Org Biomol Chem. 2021 Oct 20;19(40):8821-8829. PMID: 34585207 PMCID: PMC8605459

How Antibodies Recognize Pathogenic Viruses: Structural Correlates of Antibody Neutralization of HIV-1, SARS-CoV-2, and Zika.

Abernathy ME, Dam KMA, Esswein SR, Jette,CA, Bjorkman PJ. (2021) Viruses. 2021 Oct 19;13(10):2106. PMID: 34696536 PMCID: PMC8537525

CycFlowDec: A Python module for decomposing flow networks using simple cycles.

Bernardi A, Swanson JMJ. (2021) SoftwareX. 2021 Jun;14:100676. PMID: 34703873 PMCID: PMC8545271

Diarrheal pathogens trigger rapid evolution of the guanylate cyclase-C signaling axis in bats.

Carey CM, Apple SE, Hilbert ZA, Kay MS, Elde NC. (2021) Cell Host Microbe. 2021 Sep 8;29(9):1342-1350.e5. PMID: 34358433 PMCID: PMC8429143

The Evolution of Interdependence in a Four-Way Mealybug Symbiosis.

Garber AI, Kupper M, Laetsch DR, Weldon SR, Ladinsky MS, Bjorkman PJ, McCutcheon JP. (2021) Genome Biol Evol. 2021 Aug 3;13(8):evab123. PMID: 34061185 PMCID: PMC8331144

Modulating HIV-1 envelope glycoprotein conformation to decrease the HIV-1 reservoir.

Rajashekar JK, Richard J, Beloor J, Prévost J, Anand SP, Beaudoin-Bussières G, Shan L, Herndler-Brandstetter D, Gendron-Lepage G, Medjahed H, Bourassa C, Gaudette F, Ullah I, Symmes K, Peric A, Lindemuth E, Bibollet-Ruche F, Park J, Chen HC, Kaufmann DE, Hahn BH, Sodroski J, Pazgier M, Flavell RA, Smith AB 3rd, Finzi A, Kumar P. (2021) Cell Host Microbe. 2021 Jun 9;29(6):904-916.e6. PMID: 34019804 PMCIDD: PMC8214472

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

Elias RD, Ramaraju B, Deshmukh L. (2021) J Biol Chem. 2021 Nov;297(5):101328. PMID: 34688656 PMCID: PMC8577116

The stress-sensing domain of activated IRE1α forms helical filaments in narrow ER membrane tubes.

Tran NH, Carter SD, De Maziére A, Ashkenazi A, Klumperman J, Walter P, Jensen GJ. (2021) Science. 2021 Oct;374(6563):52-57. PMID: 34591618 PMCID: PMC9041316

Traceless Click-Assisted Native Chemical Ligation Enabled by Protecting Dibenzocyclooctyne from Acid-Mediated Rearrangement with Copper(I).

Erickson PW, Fulcher JM, Spaltenstein P, Kay MS. (2021) Bioconjug Chem. 2021 Oct 20;32(10):2233-2244. PMID: 34619957

Anatomic Distribution of Intravenously Injected IgG Takes Approximately 1 Week to Achieve Stratum Corneum Saturation in Vaginal Tissues.

Carias AM, Schneider JR, Madden P, Lorenzo-Redondo R, Arainga M, Pegu A, Cianci GC, Maric D, Villinger F, Mascola JR, Veazey RS, Hope TJ. (2021) J Immunol. 2021 Jul 15;207(2):505-511. PMID: 34162723 PMCID: PMC8516693

RetroCHMP3 blocks budding of enveloped viruses without blocking cytokinesis.

Rheinemann L, Downhour DM, Bredbenner K, Mercenne G, Davenport KA, Schmitt PT, Necessary CR, McCullough J, Schmitt AP, Simon SM, Sundquist WI, Elde NC. (2021) Cell. 2021 Oct 14;184(21):5419-5431.e16. Epub 2021 Sep 30. PMID: 34597582 PMCID: PMC8929533

In vivo imaging of retrovirus infection reveals a role for Siglec-1/CD169 in multiple routes of transmission.

Haugh KA, Ladinsky MS, Ullah I, Pi R, Gilardet A, Kumar P, Bjorkman PJ, Mothes W. (2021) Uchil PD. Elife. 2021 Jul 5;10:e64179. PMID: 34223819 PMCID: PMC8298093

Antibody elicited by HIV-1 immunogen vaccination in macaques displaces Env fusion peptide and destroys a neutralizing epitope.

Abernathy ME, Gristick HB, Vielmetter J, Keeffe JR, Gnanapragasam PNP, Lee YE, Escolano A, Gautam R, Seaman MS, Martin MA, Nussenzweig MC, Bjorkman, PJ. (2021). NPJ Vaccines. 2021 Oct 25;6(1):126. PMID: 34697307 PMCID: PMC8545924

Cleavage and polyadenylation specificity factor 6 is required for efficient HIV-1 latency reversal.

Zheng Y, Schubert HL, Parmit K, Singh PK, Martins LJ, Engelman AN, D’Orso I, Hill CP, Planelles V. (2021). mBio. 2021 Jun 29;12(3):e0109821. PMCID: PMC8262898

Generation of ordered protein assemblies using rigid three-body fusion.

Vulovic I, Yao Q, Park Y-J, Courbet A, Norris A, Busch F, Sahasrabuddhe A, Merten H, Sahtoe DD, Ueda G, Fallas JA, Weaver SJ, Hsia Y, Langan RA, Puckthun A, Wysocki VH, Veesler D, Jensen GJ, Baker D. (2021). Proc Natl Acad Sci U S A. 2021 Jun 8;118(23):e2015037118. PMID: 34074752 PMCID: PMC8201882

PET/CT targeted tissue sampling reveals virus specific dIgA can alter the distribution and localization of HIV after rectal exposure.

  Taylor RA, Xiao S, Carias AM, McRaven MD, Thakker DN, Araínga AJ, Allen EJ, Rogers KA, Kumarapperuma SC, Gong S, Fought AJ, Anderson MR, Thomas Y, Schneider JR, Goins B, Fox P, Villinger FJ, Ruprecht RM, Hope TJ. (2021). PLoS Pathogens. 2021 Jun 1;17(6):e1009632. eCollection 2021 Jun. PMID: 34061907 PMCID: PMC8195437

ILF3 Is a Negative Transcriptional Regulator of Innate Immune Responses and Myeloid Dendritic Cell Maturation.

Nazitto R, Amon LM, Mast FD, Aitchison JD, Aderem A, Johnson JS, Diercks A. (2021). J Immunol. 2021 Jun 15;206(12):2949-2965. Epub 2021 May 24. PMID: 34031149 PMCID:PMC8611108

Structure-based design of novel polyhedral protein nanomaterials.

Khmelinskaia A, Wargacki A, King NP. (2021). Curr Opin Microbiol. 2021 Jun;61:51-57. Epub 2021 Mar 27. PMID: 33784513 PMCID: PMC8231309

SIV susceptibility, immunology and microbiome in the female genital tract of adolescent versus adult pigtail macaques. AIDS Res Hum Retroviruses.

Berard AR, Miller C, Araínga M, Broedlow CA, Noël-Romas L, Schifanella L, Hensley-McBain T, Roederer A, Driscoll C, Coronado E, Manuzak J, McKinnon LR, Villinger FJ, Hope TJ, Burgener AD, Klatt NR. (2021). AIDS Res Hum Retroviruses. 2021 Jul;37(7):510-522. Epub 2021 Jun 22. PMID: 33446027 PMCID PMC8260895

In situ imaging and structure determination of biomolecular complexes using cryo-electron tomography.

Kaplan M, Nicolas WJ, Zhao W, Carter SD, Metskas LA, Chreifi G, Ghosal D, Jensen GJ. (2021). Methods Mol Biol. 2021;2215:83-111. PMID: 33368000 PMCID in process

The single-cell landscape of immunological responses of CD4+ T cells in HIV versus severe acute respiratory syndrome coronavirus.

Collora JA, Liu R, Albrecht K, Ho YC. (2021). Curr Opin HIV AIDS. 2021 Jan;16(1):36-47. PMID: 33165008 PMCID PMC8162470

Shock-and-kill versus block-and-lock: Targeting the fluctuating and heterogeneous HIV-1 gene expression.

Yeh YJ, Ho YC. (2021). Proc Natl Acad Sci USA. 2021 Apr 20;118(16):e2103692118. PMID: 33758027 PMCID: PMC8072369

High-resolution view of HIV-1 reverse transcriptase initiation complexes and inhibition by NNRTI drugs.

Ha B, Larsen KP, Zhang J, Fu Z, Montabana E, Jackson LN, Chen DH, Puglisi EV. (2021). Nat Commun. 2021 May 4;12(1):2500. PMID: 33947853 PMCID: PMC8096811

Intercellular Communication in the Nervous System Goes Viral.

Hantak MP, Einstein J, Kearns RB, Shepherd JD. (2021). Trends Neurosci. 2021 Apr;44(4):248-259. PMID: 33485691 PMCID: PMC8041237

A cryo-electron tomography workflow reveals protrusion-mediated shedding on injured plasma membrane.

Mageswaran SK, Yang WY, Chakrabarty Y, Oikonomou CM, Jensen GJ. (2021) Sci Adv. 2021 Mar 26;7(13):eabc6345. PMID: 33771860 PMCID: PMC7997517

Cryo-EM structures of HIV-1 trimer bound to CD4-mimetics BNM-III-170 and M48U1 adopt a CD4-bound open conformation.

Jette CA, Barnes CO, Kirk SM, Melillo B, Smith III AB, Bjorkman, PJ. (2021). Nat Commun. 2021 Mar 29;12(1):1950. PMID: 33782388 PMCID: PMC8007822

A new generation of functional tagged proteins for HIV fluorescence imaging.

Mamede JI, Griffin J, Gambut S, Hope TJ. (2021). Viruses. 2021 Feb 28;13(3):386.PMID: 33670986 PMCID: PMC7997544

Deep gene sequence cluster analyses of multi-virus-infected mucosal tissue reveal enhanced transmission of acute HIV-1.

Klein K, Nankya I, Nickel G, Ratcliff AN, Meadows AAJ, Hathaway N, Bailey JA, Stieh DJ, Cheeseman HM, Carias AM, Lobritz MA, Mann JFS, Gao Y, Hope TJ, Shattock RJ, Arts EJ. (2021). J Virol. 2021 Jan 13;95(3):e01737-20. Print 2021 Jan 13. PMID: 33177204 PMCID: PMC7925087

Complete and cooperative in vitro assembly of computationally designed self-assembling protein nanomaterials.

Wargacki AJ, Wörner TP, van de Waterbeemd M, Ellis D, Heck AJR, King NP. (2021). Nat Commun. 2021 Feb 9;12(1):883. PMID: 33563988 PMCID: PMC7873210

The XPB subunit of the TFIIH complex plays a critical role in HIV-1 transcription and XPB inhibition by spironolactone prevents HIV-1 reactivation from latency.

Mori L, Jenike K, Yeh YJ, Lacombe B, Li C, Getzler A, Mediouni S, Cameron M, Pipkin M, Ho YC, Ramirez BC, Valente, SJ. (2021). J Virol. 2020 Nov 25;95(4):e01247-20. Online ahead of print. PMID: 33239456 PMCID: PMC7851559

2020

Advances in understanding the initiation of HIV-1 reverse transcription.

Krupkin M, Jackson LN, Ha B, Puglisi EV. (2020). Curr Opin Struct Biol. 2020 Dec;65:175-183. Epub 2020 Sep 8. PMID: 32916568

Capsid lattice destabilization leads to premature loss of the viral genome and integrase enzyme during HIV-1 infection.

Eschbach JE, Elliott JL, Li W, Zadrozny KK, Davis K, Mohammed SJ, Lawson DQ, Pornillos O, Engelman AN, Kutluay SB. (2020). J Virol. 020 Dec 22;95(2):e00984-20. Print 2020 Dec 22. PMID: 33115869 PMCID: PMC7944438.

Recommendations for measuring HIV reservoir size in cure-directed clinical trials.

Abdel-Mohsen M, Richman D, Siliciano RF, Nussenzweig MC, Howell BJ, Martinez-Picado J, Chomont N, Bar KJ, Yu XG, Lichterfeld M, Alcami J, Hazuda D, Bushman F, Siliciano JD, Betts MR, Spivak AM, Planelles V, Hahn BH, Smith DM, Ho YC, Buzon MJ, Gaebler C, Paiardini M, Li Q, Estes JD, Hope TJ, Kostman J, Mounzer K, Caskey M, Fox L, Frank I, Riley JL, Tebas P, Montaner LJ; (2020). Nat Med. 2020 Sep;26(9):1339-1350. Epub 2020 Sep 7. PMID: 32895573 PMCID: PMC7703694

Proline-rich domain of human ALIX contains multiple TSG101-UEV interaction sites and forms phosphorylation-mediated reversible amyloids.

Elias RD, Ma W, Ghirlando R, Schwieters CD, Reddy VS, Deshmukh L. (2020). Proc Natl Acad Sci. 2020 Sep 29;117(39):24274-24284. Epub 2020 Sep 11. PMID: 32917811 PMCID: PMC7533887

Design and structure of two new protein cages illustrate successes and ongoing challenges in protein engineering.

Cannon KA, Park RU, Boyken SE, Nattermann U, Yi S, Baker D, King NP, Yeates TO.  (2020). Protein Sci. 29(4):919-929. PMID: 31840320 PMCID: PMC7096701

Convergent antibody responses to SARS-CoV-2 infection in convalescent individuals.

Robbiani DF, Gaebler C, Muecksch F, Cetrulo Lorenzi JC, Wang Z, Cho A, Agudelo M, Barnes CO, Finkin S, Hagglof T, Oliveira TY, Viant C, Hurley A, Hoffmann HH, Millard KG, Kost RG, Cipolla M, Gordon K, Bianchini F, Chen ST, Ramos V, Patel R, Dizon J, Shimeliovich I, Mendoza P, Hartweer H, Nogueria L, Pack M, Horowitz J, Schmidt F, Weisblum Y, Michalilidis E, Ashbrook AW, Waltari E, Pak JE, Huey-Tubman KE, Koranda N, Hoffmann PR, West AP, Rice CM, Hatziloannou T, Bjorkman PJ, Bieniasz PD, Caskey M, Nussenzweig MC. (2020). Nature. 2020 Aug;584(7821):437-442. Epub 2020 Jun 18. PMID: 32555388 PMCID: PMC7442695

HIV-cell membrane fusion intermediates are restricted by Serincs as revealed by cryo-electron and TIRF microscopy. 

Ward AE, Kiessling V, Pornillos O, White JM, Ganser-Pornillos BK, Tamm LK. (2020). J Biol Chem. 2020 Nov 6;295(45):15183-15195. Epub 2020 Aug 11. PMID: 32788212 PMCID: PMC7650252

Distinct conformational states underlie pausing during initiation of HIV-1 reverse transcription.

Larsen KP, Choi J, Jackson LN, Kappel K, Zhang J, Ha B, Chen DH, Puglisi EV. (2020). J Mol Biol. 2020 Jul 24;432(16):4499-4522. Epub 2020 Jun 6. PMID: 32512005 PMCID: PMC7387199

Reconstitution and visualization of HIV-1 capsid-dependent replication and integration in vitro.

Christensen D, Ganser-Pornillos BK, Johnson JS, Pornillos O, Sundquist WI. (2020). Science. 2020 Oct 9;370(6513):eabc8420. PMID: 33033190 PMCID: PMC8022914

Enhancing native chemical ligation for challenging chemical protein syntheses

Giesler RJ, Erickson PW, Kay MS. (2020). Curr Opin Chem Biol. 2020 Oct;58:37-44. Epub 2020 Jul 31. PMID: 32745915 PMCID: PMC8106950

Filgotinib suppresses HIV-1-driven gene transcription by inhibiting HIV-1 splicing and T cell activation.

Yeh YJ, Jenike KM, Calvi R, Chiarella J, Hoh R, Deeks SG, Ho YC. (2020). J Clin Invest. 2020 Sep 1;130(9):4969-4984. PMID: 32573496 PMCID: PMC7456222

Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies.

Barnes CO, West Jr AP, Huey-Tubman KE, Hoffmann MAG, Sharaf NG, Hoffman PR, Koranda N, Gristick HB, Gaebler C, Muecksch F, Cetrulo Lorenzi JC, Finkin S, Hägglöf T, Hurley A, Millard KG, Weisblum Y, Schmidt F, Hatziioannou T, Bieniasz PD, Caskey M, Robbiani DF, Nussenzweig MC, Bjorkman PJ. (2020). Cell. 2020 Aug 20;182(4):828-842.e16. Epub 2020 Jun 24. PMID: 32645326 PMCID: PMC7311918 

Atomic-scale characterization of mature HIV-1 capsid stabilization by inositol hexakisphosphate (IP6).

Yu A, Lee EMY, Jin J, Voth GA. (2020). Sci Adv. 2020 Sep 16;6(38):eabc6465. Print 2020 Sep. PMID: 32938668 PMCID: PMC7494349

Anisotropic ESCRT-III architecture governs helical membrane tube formation.

Von Filseck JM, Barberi L, Talledge N, Johnson I, Frost A, Lenz M, Roux A. (2020). Nat Commun. 2020 May 29;11(1):1516. PMID: 32471995 PMCID: PMC7260168

A Sec14-like phosphatidylinositol transfer protein paralog defines a novel class of heme-binding proteins with an unusual heme coordination mechanism.

Khan D, Lee D, Gulten G, Aggarwal A, Wofford J, Krieger I, Tripathi A, Patrick JW, Eckert DM, Laganowsky A, Sacchettini J, Lindahl P, Bankaitis VA. (2020). Elife. 2020 Aug 11;9:e57081. PMID: 32780017 PMCID: PMC7462610   

Prevention and treatment of SHIVAD8 infection in rhesus macaques by a potent D-peptide HIV entry inhibitor.

Nishimura Y, Francis JN, Donau O, Jesteadt E, Sadjadpour R, Smith AR, Seaman MS, Welch BD, Martin MA, Kay MS. (2020). Proc Natl Acad Sci. 2020 Sep 8;117(36):22436-22442. Epub 2020 Aug 20. PMID: 32820072 PMCID: PMC7486783

Electron tomography visualization of HIV-1 fusion with target cells using fusion inhibitors to trap the pre-hairpin intermediate.

  Ladinsky MS, Gnanapragasam NP, Yang Z, West AP Jr, Kay MS, Bjorkman PJ. (2020). Elife. 2020 Jul 22;9:e58411. PMID: 32697193 PMCID: PMC7394545

Clinical targeting of HIV capsid with a long-acting small molecule.

Link JO, Rhee MS, Tse WC, Zheng J, Somoza JR, Rowe W, Begley R, Chiu A, Mulato A,Hansen D, Singer E, Tsai LK, Bam RA, Chou CH, Canales E, Brizgys G, Zhang JR, Li J, Graupe M, Morganelli P, Liu Q, Wu Q, Halcomb RL, Saito RD, Schroeder SD, Lazerwith SE, Bondy S, Jin D, Hung M, Novikov N, Liu X, Villaseñor AG, Cannizzaro CE, Hu EY, Anderson RL, Appleby TC, Lu B, Mwangi J, Liclican A, Niedziela-Majka A, Papalia GA, Wong MH, Leavitt SA, Xu Y, Koditek D, Stepan GJ, Yu H, Pagratis N, Clancy S, Ahmadyar S, Cai T, Seller S, Wolckehauer S, Ling J, Callebaut C, Margot N, Ram R, Liu Y, Hyland R, Singlair G, Ruane P, Crofoot G, McDonald C, Brainard D, Lad L, Swaminathan S, Sundquist WI, Sakowicz R, Chester A, Lee W, Daar E, Cihlar T, Yant S. (2020). Nature. 2020 Aug;584(7822):614-618. Epub 2020 Jul 1.PMID: 32612233 PMCID PMC8188729

A helical assembly of human ESCRT-I scaffolds reverse-topology membrane scission.

Flower TG, Takahashi Y, Hudait A, Rose K, Tjahjono N, Pak AJ, Yokom AL, Liang X, Wang HG, Boumar F, Voth GA, Hurley JH. (2020). Nat Struct Mol Biol. 2020 Jun;27(6):570-580. Epub 2020 May 18. PMID: 32424346 PMCID PMC7339825

Single-cell transcriptional landscapes reveal HIV-1-driven aberrant host gene transcription as a potential therapeutic target.

Liu R, Yeh YJ, Varayou A, Collora JA, Sherrill-Mix S, Talbot Jr. C, Mehta S, Albrecht K, Hao H, Zhang H, Pollack RA, Beg SA, Calvi RM, Hu J, Durand CM, Ambinder RF, Hoh R, Deeks SG, Chiarella J, Spudich S, Douek DC, Bushman FD, Pertea M, Ho Y. (2020). Science Trans Med. 2020 May 13;12(543):eaaz0802. PMID: 32404504 PMCID: PMC7453882

Membrane constriction and thinning by sequential ESCRT-III polymerization.

Nguyen HC, Talledge N, McCullough J, Sharma A, Moss FR 3rd, Iwasa JH, Vershinin MD, Sundquist WI, Frost A. (2020). Nat Struct Mol Biol. 2020 Apr;27(4):392-399. Epub 2020 Apr 6. PMID: 32251413 PMCID: PMC7343221

Challenges in solving structures from radiation-damaged tomograms of protein nanocrystals assessed by simulation.

Peck A, Ya Q, Brewster AS, Zwart PH, Heumann JM, Sauter NK, Jensen GJ. (2020). Acta Crystallogr D Struct Biol. 2021 May 1;77(Pt 5):572-586. Epub 2021 Apr 14. PMID: 33950014 PMCID: PMC8098477

Can we use structural knowledge to design a protective vaccine against HIV-1?

Bjorkman PJ. (2020). HLA. 2020 Feb;95(2):95-103. Epub 2019 Nov 27. PMID: 31721469. PMCID exempt.

In Vivo Imaging-Driven Approaches to Study Virus Dissemination and Pathogenesis.

Uchil PD, Haugh KA, Pi R, Mothes W. (2019). Annu Rev Virol. 2019 Sep 29;6(1):501-524. Epub 2019 Jul 5. PMID: 31283440 PCMID: PMC7217087

SARS-CoV-2: A storm is raging.

Pedersen SF, Ho YC. (2020). J Clin Invest. 2020 May 1;130(5):2202-2205. PMID: 32217834 PMCID: PMC7190904

Same structure, different mechanisms?

Tsai FT, Hill, CP. (2020). Elife. 2020 Apr 23;9:e56501. PMID: 32321627 PMCID: PMC7180051

TRIM34 restricts HIV-1 and SIV capsids in a TRIM5α-dependent manner.

Ohainle M, Kim K, Komurlu Keceli S, Felton A, Campbell E, Luban J, Emerman M. (2020). LoS Pathog. 2020 Apr 13;16(4):e1008507. eCollection 2020 Apr. PMID: 32282853 PMCID: PMC7179944

Visualizing Association of the Retroviral Gag Protein with Unspliced Viral RNA in the Nucleusm.

Maldonado RJK, Rice B, Chen EC, Tuffy KM, Chiari EF, Fahrbach KM, Hope TJ, Parent LJ. (2020). mBio. 2020 Apr 7;11(2):e00524-20. PMID: 32265329 PMCID: PMC7157774

Ribosome-associated vesicles: A dynamic subcompartment of the endoplasmic reticulum in secretory cells.

Carter SD, Hampton CM, Langlois R, Melero R, Farino ZJ, Calderon MJ, Li W, Wallace CT, Tran NH, Grassucci RA, Siegmund SE, Pemberton J, Morgenstern TJ, Eisenman L, Aguilar JI, Greenberg NL, Levy ES, Yi E, Mitchell WG, Rice WJ, Wigge C, Pilli J, George EW, Aslanoglou D, Courel M, Freyberg RJ, Javitch JA, Wills ZP, Area-Gomez E, Shiva S, Bartolini F, Volchuk A, Murray SA, Aridor M, Fish KN, Walter P, Balla T, Fass D, Wolf SG, Watkins SC, Carazo JM, Jensen GJ, Frank J, and Freyberg Z. (2020). Sci Adv. 2020 Apr 1;6(14):eaay9572. eCollection 2020 Apr. PMID: 32270040 PMCID: PMC7112762

Synthetic antibodies against BRIL as universal fiducial marks for single-particle cryoEM structure determination of membrane proteins.

Mukherjee S, Erramilli SK, Ammirati M, Alvarez FJD, Fennell KF, Purdy MD, Skrobek BM, Radziwon K, Coukos J, Kang Y, Dutka P, Gao X, Qiu X, Yeager M, Xu HE, Han S, Kossiakoff AA. (2020). Nature Commun. 2020 Mar 27;11(1):1598. PMID: 32221310 PMCID: PMC7101349

TRIM5α self-assembly and compartmentalization of the HIV-1 viral capsid.

Yu A, Skorupka KA, Pak AJ, Ganser-Pornillos BK, Pornillos O, Voth GA. (2020). Nat Commun. 2020 Mar 11;11(1):1307.PMID: 32161265 PMCID: PMC7066149

Restriction of HIV-1 Escape by a Highly Broad and Potent Neutralizing Antibody. 

Schommers, P, Gruell, H, Abernathy, ME, Tran, M-K, Dingens, AS, Gristick, HB, Barnes, CO, Schoofs, T, Schlotz, M. Vanshylla, K, Kreer, C, Weiland, D, Holtick U, Scheid, C, Valter, MM, van Gils, MJ, Sanders RW, Vehreschild, JJ, Cornely, OA, Lehmann, C, Fatkenheuer, G, Seaman, MS, Bloom, JD, Bjorkman PJ, Klein, F. (2020). Cell. 2020 Feb 6;180(3):471-489.e22. Epub 2020 Jan 30. PMID: 32004464 PMCID: PMC7042716

A Comprehensive Map of the Monocyte-Derived Dendritic Cell Transcriptional Network Engaged upon Innate Sensing of HIV.

Johnson JS, De Veaux N, Rives AW, Lahaye X, Lucas SY, Perot BP, Luka M, Garcia-Paredes V, Amon LM, Watters A, Abdessalem G, Aderem A, Manel N, Littman DR, Bonneau R, Ménager MM. (2020). Cell Rep. 2020 Jan 21;30(3):914-931.e9. PMID: 31968263 PMCID: PMC7039998

Structures of virus-like capsids formed by the Drosophila neuronal Arc proteins.

Erlendsson S, Morado DR, Cullen HB, Feschotte C, Shepherd JD, Briggs JAG. (2020). Nat Neurosci. 2020 Feb;23(2):172-175. Epub 2020 Jan 6. PMID: 31907439 PMCID: PMC7032958

Structure of spastin bound to a glutamate-rich peptide implies a hand-over-hand mechanism of substrate translocation.

Han, H., Schubert, H.L., McCullough, J., Monroe, N., Purdy, M.D., Yeager, M., Sundquist, W.I., Hill, C.P. (2020). J. Biol. Chem. 2020 Jan 10;295(2):435-443. Epub 2019 Nov 25. PMID: 31767681 PMCID: PMC6956536

The forces driving clonal expansion of the HIV-1 latent reservoir.

Liu R, Simonetti FR, Ho YC. (2020). Virol J. 2020 Jan 7;17(1):4. PMID: 31910871 PMCID: PMC6947923

2019

Editorial overview: Biophysical and computational methods, part B. 

Yeager, M. (2019). Curr. Opin. Struct. Biol. 2019 Oct;58:v-vi. Epub 2019 Aug 30. PMID: 31477340

Illuminating the virus life cycle with single-molecule FRET imaging.

Lu M, Ma X, Mothes W. (2019). Adv Virus Res. 2019;105:239-273. Epub 2019 Aug 20. PMID: 31522706 PMCID: PMC7246055.

Asymmetric opening of HIV-1 Env bound to CD4 and a coreceptor-mimicking antibody.

Yang Z, Wang H, Liu AZ, Gristick HB, Bjorkman PJ. (2019). Nat Struct Mol Biol. 2019 Dec;26(12):1167-1175. Epub 2019 Dec 2. PMID: 31792452 PMCID: PMC6899201

Multiple Pathways To Avoid Beta Interferon Sensitivity of HIV-1 by Mutations in Capsid.

Sultana T, Mamede JI, Saito A, Ode H, Nohata K, Cohen R, Nakayama EE, Iwatani Y, Yamashita M, Hope TJ, Shioda T. (2019). J Virol. 2019 Nov 13;93(23):e00986-19. Print 2019 Dec 1. PMCID: PMC6854511

Characterization of resistance to a potent D-peptide HIV entry inhibitor.

Smith AR, Weinstock MT, Siglin AE, Whitby FG, Francis JN, Hill CP, Eckert DM, Root MJ, Kay MS. (2019). Retrovirology 2019 Oct 22;16(1):28. PMID: 31640718 PMCID: PMC6805555

Murine Leukemia Virus Exploits Innate Sensing by Toll-Like Receptor 7 in B-1 Cells To Establish Infection and Locally Spread in Mice. 

Pi R, Iwasaki A, Sewald X, Mothes W, Uchil PD. (2019). J Virol. 2019 Oct 15;93(21):e00930-19. Print 2019 Nov 1. PMID: 31434732 PMCID: PMC6803250

Expanding single-molecule fluorescence spectroscopy to capture complexity in biology.

Choi J, Grosely R, Puglisi EV, Puglisi JD. (2019). Curr Opin Struct Biol. 2019 Oct;58:233-240. Epub 2019 Jun 15. PMID: 31213390 PMCID: PMC6778503

Endocytosis of commensal antigens by intestinal epithelial cells regulates mucosal T cell homeostasis.

Ladinsky MS, Araujo LP, Zhang X, Veltri J, Galan-Diez M, Soualhi S, Lee C, Irie K, Pinker EY, Narushima S, Bandyopadhyay S, Nagayama M, Elhenawy W, Coombes BK, Ferraris RP, Honda K, Iliev ID, Gao N, Bjorkman PJ, Ivanov II. (2019). Science. 2019 Mar 8;363(6431):eaat4042. PMID: 30846568 PMCID: PMC6708280

Relating Structure and Dynamics in RNA Biology.

Larsen KP, Choi J, Prabhakar A, Puglisi EV, Puglisi JD. (2019). Cold Spring Harb Perspect Biol. 2019 Jul 1;11(7):a032474. PMID: 31262948 PMCID: PMC6601459 

Broad and potent neutralizing antibodies recognize the silent face of the HIV envelope.

Schoofs T, Barnes CO, Suh-Toma N, Golijanin J, Schommers P, Gruell H, West AP, Back F, Lee YE, Nogueria L, Georgiev IS, Bailer RT, Czartoski J, Mascola JR, Seaman MS, McElrath MJ, Doria-Rose NA, Klein F, Nussenzweig MC, Bjorkman PJ. (2019). Immunity. 2019 Jun 18;50(6):1513-1529.e9. Epub 2019 May 21. PMID: 31126879 PMCID: PMC6591006

Activation of the Anti-Oxidative Stress Response Reactivates Latent HIV-1 Through the Mitochondrial Antiviral Signaling Protein Isoform MiniMAVS.  

Novis CL, Sarabia I, Macedo AB, Takata H, Nell R, Furler RL, Shakya B, Schubert HL, Hill CP, De Paula-Silva AB, Spivak AM, Trautmann L, Planelles P, Bosque A. (2019). Front Immunol. 2021 Jun 14;12:682182. eCollection 2021. PMID: 34194436 PMCID: PMC8236643

Structure of the Cdc48 segregase in the act of unfolding an authentic substrate.

Cooney I, Han H, Stewart MG, Carson RH, Hansen DY, Price JC, Hill CP, Shen PS. (2019). Science. 2019 Aug 2;365(6452):502-505. Epub 2019 Jun 27. PMID: 31249134 PMCID: PMC7362759

Mechanisms of virus dissemination in bone marrow of HIV-1-infected humanized BLT mice.

Ladinsky MS, Khamaikawin W, Jung Y, Lin S, Lam J, An DS, Bjorkman PJ, Kieffer C. (2019). Elife. 2019 Oct 28;8:e46916. PMID: 31657719 PMCID: PMC6839903

Qualitative Analyses of Polishing and Precoating FIB Milled Crystals for MicroED.

Martynowycz MW, Zhao W, Hattne J, Jensen GJ, Gonen T. (2019). Structure. 2019 Oct 1;27(10):1594-1600.e2. Epub 2019 Aug 15. PMID: 31422911 PMCID: PMC7145226

A highly potent long-acting small-molecule HIV-1 capsid inhibitor with efficacy in a humanized mouse model.

Yant SR, Mulato A, Hansen D, Tse WC, Niedziela-Majka A, Zhang JR, Stepan GJ, Jin D, Wong MH, Perreira JM, Singer E, Papalia G, Hu E, Zheng J, Lu B, Schroeder SD, Chou K, Ahmadyar S, Yu H Novikov N, Paoli E, Gonik D, Ram RR, Hung M, McDougall WM, Brass AL, Sundquist WI, Cihlar T, Link JO. (2019). Nature Medicine. 2019 Sep;25(9):1377-1384. Epub 2019 Sep 9. PMID: 31501601 PMCID PMC7396128

Longitudinal bioluminescent imaging of HIV-1 infection during antiretroviral therapy and treatment interruption in humanized mice.

Ventura JD, Beloor J, Allen E, Haugh KA, Matias E, Uchil PD, Ochsenbauer C, Kumar P, Hope TJ, Mothes WM. (2019). PLoS Pathogens. 2019 Dec 5;15(12):e1008161. eCollection 2019 Dec. PMID: 31805155 PMCID: PMC6917343

Off-Pathway Assembly: A Broad-Spectrum Mechanism of Action for Drugs That Undermine Controlled HIV-1 Viral Capsid Formation.

Pak A, Grime J, Yu A, Voth GA. (2019). J Am Chem Soc. 2019 Jul 3;141(26):10214-10224. doi: 10.1021/jacs.9b01413.Epub 2019 Jun 19. PMCID: PMC6739737

LEM2 phase separation promotes ESCRT-mediated nuclear envelope reformation.

Von Appen A, Lajoie D, Johnson IE, Trnka M, Pick AL, Ullman KS, Frost A. (2019). Nature. 582(7810):115-118. Epub 2020 Apr 29. PMID: 32494070. PMCID: PMC7321842

Hierarchical assembly governs TRIM5α recognition of HIV-1 and retroviral capsids.

Skorupka K, Roganowicz MD, Christensen DE, Wan Y, Pornillos O, Ganser-Pornillos BK. (2019). Sci Adv. 2019 Nov 27;5(11):eaaw3631. eCollection 2019 Nov. PMID: 31807695 PMCID: PMC6881174

Correlated cryogenic fluorescence microscopy and electron cryo-tomography shows that exogenous TRIM5α can form hexagonal lattices or autophagy aggregates in vivo.

 Carter SD, Mamede JI, Hope TJ, Jensen GJ. (2019). Proc Natl Acad Sci U S A. 2020 Nov 24;117(47):29702-29711. Epub 2020 Nov 5. PMID: 33154161 PMCID: PMC7703684

A Tunable Microfluidic Device Enables Cargo Encapsulation by Cell- or Organelle-Sized Lipid Vesicles Comprising Asymmetric Lipid Bilayers.

Romanov V, McCullough J, Sharma A, Vershinin M, Gale BK, Frost A. (2019). Advanced Biosystems. 2019 Jul;3(7):1900010. Epub 2019 May 27. PMID: 31428671 PMCID: PMC6699779

Selective Kinase Inhibition Shows That Bur1 (Cdk9) Phosphorylates the Rpb1 Linker In Vivo.

Chun Y, Joo YJ, Suh H, Batot G, Hill CP, Formosa T, Buratowski S. (2019). Mol Cell Biol. 39(15):e00602-18. Print 2019 Aug 1. PMID: 31085683 PMCID: PMC6639251

Immunization expands B cells specific to HIV-1 V3 glycan in mice and macaques.

Escolano A, Gristick HB, Abernathy ME, Merkenschlager J, Gautam R, Oliveira TY, Pai J, West AP Jr., Barnes CO, Cohen AA, Wang H, Golijanin J, Yost D, Keeffe JR, Wang Z, Zhao P, Yao K-H, Bauer J, Nogueira L, Gao H, Voll AV, Montefiori DC, Seaman MS, Gazumyan A, Silva M, McGuire AT, Stamatatos L, Irvine DJ, Wells L, Martin MA, Bjorkman PJ, Nussenzweig MC. (2019). Nature. 2019 Jun;570(7762):468-473. Epub 2019 May 29. PMID: 31142836 PMCID: PMC6657810

Cryo-EM maps are full of potential.

Marques MA, Purdy MD, Yeager M. (2019). Curr Opin Struct Biol. 2019 Oct;58:214-223. Epub 2019 Aug 7. PMID: 31400843 PMCID: PMC6778505

Restriction of HIV-1 and other retroviruses by TRIM5. 

Ganser-Pornillos BK, Pornillos O. (2019). Nature Rev Microbiol. 2019 Sep;17(9):546-556. Epub 2019 Jul 16. PMID: 31312031 PMCID: PMC6858284

Maturation of retroviruses.

Pornillos O, Ganser-Pornillos BK. (2019). Curr Opin Virol. 2019 Jun;36:47-55. Epub 2019 Jun 8. PMID: 31185449 PMCID: PMC6730672

Fusion of DARPin to aldolase enables visualization of small protein by cryoEM.

Yao Q, Weaver SJ, Mock J-Y, Jensen GJ. (2019). Structure. 2019 Jul 2;27(7):1148-1155.e3. Epub 2019 May 9. PMID: 31080120 PMCID PMC6610650

Collection of Continuous Rotation MicroED Data from Ion Beam-Milled Crystals of Any Size.

Martynowycz MW, Hattne J, Jensen GJ, Gonen T. (2019). Structure. 2019 Mar 5;27(3):545-548.e2. Epub 2019 Jan 17. PMID: 30661853 PMCID: PMC6476546

Structure and mechanism of the ESCRT Pathway AAA+ ATPase Vps4.

Han H, Hill CP. (2019). Biochem Soc Trans. 2019 Feb 28;47(1):37-45. Epub 2019 Jan 15. PMID: 30647138 PMCID: PMC6393862

A Protective Role for the Lectin CD169/Siglec-1 against a Pathogenic Murine Retrovirus.

Uchil PD, Pi R, Haugh KA, Ladinsky MS, Ventura JD, Barrett BS, Santiago ML, Bjorkman PJ, Kassiotis G, Sewald X, Mothes W. (2019). Cell Host Microbe. 2019 Jan 9;25(1):87-100.e10. Epub 2018 Dec 27. PMID: 30595553 PMCID: PMC6331384

Recurrent Loss-of-Function Mutations Reveal Costs to OAS1 Antiviral Activity in Primates.

Carey CM, Govande AA, Cooper JM, Hartley MK, Kranzusch PJ, Elde NC. (2019). Cell Host Microbe. 2019 Feb 13;25(2):336-343.e4. Epub 2019 Jan 31. PMID: 30713099 PMCID PMC6609161

2018

MicroED structures of HIV-1 Gag CTD-SP1 reveal binding interactions with the maturation inhibitor bevirimat.

Purdy MD, Shi D, Chrustowicz J, Hattne J, Gonen T, Yeager M. (2018). Proc Natl Acad Sci U S A. 2018 Dec 26;115(52):13258-13263. Epub 2018 Dec 10. PMID: 30530702 PMCID: PMC6310804

Advances in coarse-grained modeling of macromolecular complexes.

Pak AJ, Voth GA. (2018). Curr Opin Struct Biol. 2018 Oct;52:119-126. Epub 2018 Nov 30. PMID: 30508766 PMCID: PMC6296860

Inflammation weakens HIV prevention.

Hope TJ. (2018). Nature Medicine. 01 Apr 2018, 24(4):384-385. PMID: 29634687 (PMCID exempt).  

FDM 3D Printing of High-Pressure, Heat-Resistant, Transparent Microfluidic Devices.

 Romanov V, Samuel R, Chaharlang M, Jafek AR, Frost A, Gale BK. (2018). Anal Chem. 2018 Sep 4;90(17):10450-10456. Epub 2018 Aug 17. PMID: 30071717 PMCID: PMC6538390

Retrovirus Restriction by TRIM5α: RINGside at a Cage Fight.

  Sundquist WI, Pornillos O. (2018). Cell Host Microbe. 2018 Dec 12;24(6):751-753. PMID: 30543772 PMCID: PMC6464375

Partially Open HIV-1 Envelope Structures Exhibit Conformational Changes Relevant for Coreceptor Binding and Fusion.

  Wang H, Barnes CO, Yang Z, Nussenzweig MC, Bjorkman PJ. (2018). Cell Host Microbe. 2018 Oct 10;24(4):579-592.e4. PMID: 30308160 PMCID: PMC6185872

De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes.

  Kappel K, Liu S, Larsen KP, Puglisi, EV, Puglisi JD, Skiniotis J, Zhao R, Zhou ZH, Das R. (2018). Nature Methods. 2018 Nov;15(11):947-954. Epub 2018 Oct 30. PMID: 30377372 PMCID: PMC6636682

Dynamic Interplay of RNA and Protein in the Human Immunodeficiency Virus-1 Reverse Transcription Initiation Complex.

  Coey AT, Larsen KP, Barrero D, Puglisi JD, Puglisi, EV. (2018). J Mol Biol. 2018 Dec 7;430(24):5137-5150. Epub 2018 Sep 7. PMID: 30201267 PCMID: PMC6289658

Structures, Functions, and Dynamics of ESCRT-III/Vps4 Membrane Remodeling and Fission Complexes.

  McCullough J, Frost A, Sundquist WI. (2018). Annu Rev Cell Dev Biol. 2018 Oct 6;34:85-109. Epub 2018 Aug 10. PMID: 30095293 PMCID: PMC6241870

Gut microbiota utilize immunoglobulin A for mucosal colonization.

Donaldson GP, Ladinsky MS, Yu KB, Sanders JG, Yoo BB, Chou WC, Conner ME, Earl AM, Knight R, Bjorkman PJ, Mazmanian SK. (2018). Science. 2018 May 18;360(6390):795-800. Epub 2018 May 3. PMID: 29724905 PMCID: PMC5973787

Architecture of an HIV-1 reverse transcriptase initiation complex.

Larsen KP, Mathiharan YK, Kappel K, Coey AT, Chen DH, Barrero D, Madigan L, Puglisi JD, Skiniotis G, Puglisi EV. (2018). Nature 2018 May;557(7703):118-122. Epub 2018 Apr 25. PMID: 29695867 PMCID: PMC5934294

The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer.

  Pastuzyn ED, Day CE, Kearns RB, Kyrke-Smith M, Taibi AV, McCormick J, Yoder N, Belnap DM, Erlendsson S, Morado DR, Briggs JAG, Feschotte C, Shepherd JD. (2018). Cell. 2018 Jan 11;172(1-2):275-288.e18. PMID: 29328916 PMCID: PMC5884693

Structural characterization of a highly-potent V3-glycan broadly neutralizing antibody bound to natively-glycosylated HIV-1 envelope.

  Barnes, CO, Gristick, HB, Freund, NT, Escolano, A, Lyubimov, AY, Hartweger, H, West Jr, AP, Cohen, AE, Nussenzweig, MC, Bjorkman, PJ. (2018). Nat Commun. 2018 Mar 28;9(1):1251. PMID: 29593217 PMCID: PMC5871869

Arc - An endogenous neuronal retrovirus?

  Sheperd JD. (2018). Semin Cell Dev Biol. 2018 May;77:73-78. Epub 2017 Sep 24. PMID: 28941877 PMCID: PMC5862763

Locking the Elbow: Improved Antibody Fab Fragments as Chaperones for Structure Determination.

  Bailey LJ, Sheehy KM, Dominik PK, Liang WG, Rui H, Clark M, Jaskolowski M, Kim Y, Deneka D, Tang WJ, Kossiakoff AA. (2018). J Mol Biol. 2018 Feb 2;430(3):337-347. Epub 2017 Dec 19. PMID: 29273204 PMCID: PMC5800945

General Model for Retroviral Capsid Pattern Recognition by TRIM5 Proteins.

Wagner JM, Christensen DE, Bhattacharya A, Dawidziak DM, Roganowicz MD, Wan Y, Pumroy RA, Demeler B, Ivanov DN, Ganser-Pornillos BK, Sundquist WI, Pornillos O. (2018). J Virol. 92(4):e01563-17. Print 2018 Feb 15. PMID: 29187540 PMCID: PMC5790955

TRIM5α SPRY/coiled-coil interactions optimize avid retroviral capsid recognition.

  Roganowicz MD, Komurlu S, Mukherjee S, Plewka J, Alam SL, Skorupka KA, Wan Y, Dawidowski D, Cafiso DS, Ganser-Pornillos BK, Campbell EM, Pornillos O. (2018). PLoS Pathog. 2017 Oct 17;13(10):e1006686. eCollection 2017 Oct. PMID: 29040325 PMCID: PMC5667893

2017

The AAA ATPase Vps4 binds ESCRT-III substrates through a repeating array of dipeptide-binding pockets.

  Han H, Monroe N, Sundquist WI, Shen PS, Hill CP. (2017). Elife. 2017 Nov 22;6:e31324. PMID: 29165244 PMCID: PMC5716660

Multiscale Imaging of HIV-1 Transmission in Humanized Mice. 

  Kieffer, C, Ladinsky MS, Bjorkman, PJ. (2017). AIDS Res Hum Retroviruses. 2017 Nov;33(S1):S6-S7. PMID: 28882056 PMCID: PMC5685215

What’s in a name?

  Schaller MD, McDowell G, Porter A, Shippen D, Friedman KL, Gentry MS, Serio TR, Sundquist WI. (2017). Elife. 2017 Oct 24;6:e32437. PMID: 29063834 PMCID: PMC5655148

Structure and catalytic activation of the TRIM23 RING E3 ubiquitin ligase.

  Dawidziak DM, Sanchez JG, Wagner JM, Ganser-Pornillos BK, Pornillos O. (2017). Proteins. 2017 Oct;85(10):1957-1961. Epub 2017 Jul 24. PMID: 28681414 PMCID: PMC5638660

X-ray and EM structures of a natively glycosylated HIV-1 envelope trimer.

Gristick, HB, Wang, H, Bjorkman, PJ. (2017). Acta Crystallogr D Struct Biol. 2017 Oct 1;73(Pt 10):822-828. Epub 2017 Sep 29. PMID: 28994411 PMCID: PMC5633907

Loquacious-PD facilitates Drosophila Dicer-2 cleavage through interactions with the helicase domain and dsRNA.

  Trettin KD, Sinha NK, Eckert DM, Apple SE, Bass BL. (2017). PNAS. 114: e7939-48. PMID: 28874570 PMCID: PMC5617286

Long-term direct visualization of passively transferred fluorophore-conjugated antibodies.

  Schneider JR, Carias AM, Bastian AR, Cianci GC, Kiser PF, Veazey RS, Hope TJ. (2017). J Immunol Methods. 2017 Nov;450:66-72. Epub 2017 Aug 2. PMID: 28780040 PMCID: PMC5603196

A novel SH2 recognition mechanism recruits Spt6 to the doubly phosphorylated RNA polymerase II linker at sites of transcription.

Sdano, MA, Fulcher, JM, Palani, S, Chandrasekharan, MB, Parnell, TJ, Whitby, FG, Formosa, T, Hill, CP. (2017). Elife. 2017 Aug 16;6:e28723. PMID: 28826505 PMCID: PMC5599234

Asymmetric recognition of HIV-1 Envelope trimer by V1V2 loop-targeting antibodies.

  Wang, H, Gristick, HB, Scharf, L, West, AP, Jr, Galimidi, RP, Seaman, MS, Freund, NT, Nussenzweig, MC, Bjorkman, PJ. (2017). ELife 2017 May 26;6:e27389. PMID: 28548638 PMCID: PMC5472438  

Structural basis of protein translocation by the Vps4-Vta1 AAA ATPase.

  Monroe N, Han H, Shen PS, Sundquist WI, Hill CP. (2017). Elife. 2017 Apr 5;6:e24487. PMID: 28379137 PMCID: PMC5413351

LEM2 recruits CHMP7 for ESCRT-mediated nuclear envelope closure in fission yeast and human cells.

  Gu M, LaJoie D, Chen OS, von Appen A, Ladinsky MS, Redd MJ, Nikolova L, Bjorkman PJ, Sundquist WI, Ullman KS, Frost A. (2017). Proc Natl Acad Sci U S A. 2017 Mar 14;114(11):E2166-E2175. Epub 2017 Feb 27. PMID: 28242692 PMCID: PMC5358359

Longitudinal imaging of HIV-1 spread in humanized mice with parallel 3D immunofluorescence and electron tomography.

  Kieffer C, Ladinsky MS, Ninh A, Galimidi RP, Bjorkman PJ. (2017). Elife. 2017 Feb 15;6:e23282. PMID: 28198699 PMCID: PMC5338924

Pharmacokinetic and Chemical Synthesis Optimization of a Potent d-Peptide HIV Entry Inhibitor Suitable for Extended-Release Delivery.

  Redman JS, Francis JN, Marquardt R, Papac D, Mueller AL, Eckert DM, Welch BD, Kay MS. (2017) Mol Pharm. 2018 Mar 5;15(3):1169-1179. Epub 2018 Feb 22. PMID: 29436835. PMCID: PMC5893306

Structure of the fission yeast actomyosin ring during constriction.

  Swulius MT, Nguyen LT, Ladinsky MS, Mishra M, Jensen GJ. (2017). Proc Natl Acad Sci U S A. 2018 Feb 13;115(7):E1455-E1464. Epub 2018 Jan 18. PMID: 29348205 PMCID: PMC5816141

Distinguishing signal from autofluorescence in cryogenic correlated light and electron microscopy of mammalian cells.

  Carter SD, Mageswaran SK, Farino ZJ, Mamede JI, Oikonomou CM, Hope TJ, Freyberg Z, and Jensen GJ. (2017). J Struct Biol. 2018 Jan;201(1):15-25. Epub 2017 Oct 25. PMID: 29078993 PMCID: PMC5771259

A Survey of DDX21 Activity During Rev/RRE Complex Formation.

Hammond JA, Zhou L, Lamichhane R, Chu H-Y, Millar DP, Gerace L, Williamson JR. (2017). J Mol Biol. 2018 Feb 16;430(4):537-553. Epub 2017 Jul 10. PMID: 28705764 PMCID: PMC5762417

Immature HIV-1 lattice assembly dynamics are regulated by scaffolding from nucleic acid and the plasma membrane.

  Pak AJ, Grime JMA, Sengupta P, Chen AK, Durumeric AEP, Srivastava A, Yeager M, Briggs JAG, Lippincott-Schwartz J, Voth GA. (2017). Proc Natl Acad Sci U S A. 2017 Nov 21;114(47):E10056-E10065. Epub 2017 Nov 7. PMID: 29114055 PMCID: PMC5703280

Early cytoplasmic uncoating is associated with infectivity of HIV-1.

  Mamede JI, Cianci GC, Anderson MR, Hope TJ. (2017). Proc Natl Acad Sci U S A. 2017 Aug 22;114(34):E7169-E7178. doi: 10.1073/pnas.1706245114. Epub 2017 Aug 7. PMID: 28784755 PMCID: PMC5576815

HIV virions sense plasma membrane heterogeneity for cell entry.

  Yang S, Kreutzberger AJB, Kiessling V, Ganser-Pornillos BK, White JV, Tamm LK. (2017). Sci Adv. 2017 Jun 28;3(6):e1700338. eCollection 2017 Jun. PMID: 28782011 PMCID: PMC5489272

A DEAD-box protein acts through RNA to promote HIV-1 Rev-RRE assembly.

  Lamichhane R, Hammond JA, 3rd Pauszek RA, Anderson RM, Pedron I, van der Schans E, Williamson JR, Millar DP. (2017). Nucleic Acids Res. 2017 May 5;45(8):4632-4641. PMID: 28379444 PMCID: PMC5416872

Coexistence of potent HIV-1 broadly neutralizing antibodies and antibody-sensitive viruses in a viremic controller.

  Freund NT, Wang H, Scharf L, Noguiera L, Horwitz JA, Sievers SA, Sok D, Cai H, Golijanin J, Lorenzi JC, Halper-Stromber A, Toth I, Piechocka-Torcha A, Gristick HB, Sanders RW, Moore JP, Wang L-X, Seaman MS, Burton D, Gazumyan A, Walker BD, West AP, Bjorkman PJ, Nussenzweig MC. (2017). Science Trans Med. 2017 Jan 18;9(373):eaal2144. PMID: 28100831 PMCID: PMC5467220

A DEAD-Box Helicase Mediates an RNA Structural Transition in the HIV-1 Rev Response Element.

Hammond JA, Lamichhane, R, Millar DP, Williamson JR. (2017). J Mol Biol. 2017 Mar 10;429(5):697-714. Epub 2017 Jan 31. PMID: 28153748. PMCID: PMC5510989

Reverse-topology membrane scission by the ESCRT proteins.

154.  Schöeneberg J, Lee I, Iwasa JH, Hurley, JH. (2017). Nat Rev Mol Cell Biol. 2017 Jan;18(1):5-17. Epub 2016 Oct 5. PMID: 27703243 PMCID: PMC5198518

2016

Changes in HIV-1 Capsid Stability Induced by Common Cytotoxic-T-Lymphocyte-Driven Viral Sequence Mutations.

  Schommers P, Martrus G, Matschl U, Sirignano M, Lütgehetmann M, Richert L, Hope TJ, Fätkenheuer G, Altfeld M. (2016). J Virol. 2016 Jul 27;90(16):7579-7586. Print 2016 Aug 15. PMID: 27279617 PMCID: PMC4984629

Designed proteins induce the formation of nanocage-containing extracellular vesicles.

Votteler J, Ogohara C, Yi S, Hsia Y, Natterman U, Belnap DM, King NP, Sundquist WI. (2016). Nature. 540:292-5. Epub 2016 Nov 30. PMID: 27919066 PMCID: PMC5729044

Helical conformation in the CA-SP1 junction of the immature HIV-1 lattice determined from solid-state NMR of virus-like Particles.

  Bayro MJ, Ganser-Pornillos BK, Zadrozny KK, Yeager M, Tycko R. (2016). J Am Chem Soc. 2016 Sep 21;138(37):12029-32. Epub 2016 Sep 7. PMID: 27593947 PMCID: PMC5636003

Simultaneous measurement of emission color and 3D position of single molecules.

  Smith CS, Huisman M, Siemons M, Grünwald D, Stallinga S. (2016). Optics Express. 2016 Mar 7;24(5):4996-5013. PMID: 29092328 PMCID: PMC5499633

Cryo-EM structure of a CD4-bound open HIV-1 envelope trimer reveals structural rearrangements of the gp120 V1V2 loop.

  Wang H, Cohen AA, Galimidi RP, Gristick HB, Jensen GJ, Bjorkman PJ. (2016). Proc Natl Acad Sci U S A. 2016 Nov 15;113(46):E7151-E7158. Epub 2016 Oct 31. PMCID: PMC5135367

Heterogeneous structures formed by conserved RNA sequences within the HIV reverse transcription initiation site.

Coey A, Larsen K, Puglisi JD, Viani Puglisi E. (2016). RNA. 2016 Nov;22(11):1689-1698. Epub 2016 Sep 9. PMCID: PMC5066621

CRISPR-Cas9 nuclear dynamics and target recognition in living cells.

  Ma H, Tu LC, Naseri A, Huisman M, Zhang S, Grünwald D, Pederson T. (2016). Cell Biol. 2016 Aug 29;214(5):529-37. Epub 2016 Aug 22. PMCID: PMC5004447

Viruses exploit the tissue physiology of the host to spread in vivo.

  Sewald X, Motamedi N, Mothes W. (2016). Curr Opin Cell Biol. 2016 Aug;41:81-90. Epub 2016 May 3. PMCID: PMC4983526

Crystal structure of an HIV assembly and maturation switch.

  Wagner JM, Zadrozny K, Chrustowicz J, Purdy MD, Yeager M, Ganser-Pornillos BK, Pornillos O. (2016). Elife. 2016 Jul 14;5:e17063. PMCID: PMC4946879

Primate TRIM5 proteins form hexagonal nets on HIV-1 capsids.

  Li Y-L, Chandrasekaran V, Carter SD, Woodward CL, Christensen DE, Dryden KA, Pornillos O, Yeager M, Ganser-Pornillos BK, Jensen GJ, Sundquist, WI. (2016). Elife. 2016 Jun 2;5:e16269. PMCID: PMC4936896

Mechanism of B-box 2 domain-mediated higher-order assembly of the retroviral restriction factor TRIM5α.

  Wagner JM, Roganowicz MD, Skorupka K, Alam SL, Christensen DE, Doss G, Wan Y, Frank GA, Ganser-Pornillos BK, Sundquist WI, Pornillos O. (2016). Elife. 2016 Jun 2;5:e16309. PMCID: PMC4936894

KIF5B and Nup358 Cooperatively Mediate the Nuclear Import of HIV-1 during Infection.

Dharan A, Talley S, Tripathi A, Mamede JI, Majetschak M, Hope TJ, Campbell EM. (2016). PLoS Pathog. 2016 Jun 21;12(6):e1005700. eCollection 2016 Jun. PMCID: PMC4915687

Deciphering the Structure and Function of Nuclear Pores Using Single-Molecule Fluorescence Approaches.

  Musser SM, Grünwald D. (2016). J Mol Biol. 2016 May 22;428(10 Pt A):2091-119. Epub 2016 Mar 2. PMCID: PMC4909493

The Scientist as Illustrator.

  Iwasa JH. (2016). Trends Immunol. 2016 Apr;37(4):247-50. Epub 2016 Mar 9. PMCID: PMC4900463

Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II.

Sierra RG, Gati C, Laksmono H, Dao EH, Gul S, Fuller F, Kern J, Chatterjee R, Ibrahim M, Brewster AS, Young ID, Michels-Clark T, Aquila A, Liang M, Hunter MS, Koglin JE, Boutet S, Junco EA, Hayes B, Bogan MJ, Hampton CY, Puglisi EV, Sauter NK, Stan CA, Zouni A, Yano J, Yachandra VK, Soltis SM, Puglisi JD, DeMirci H. (2016). Nature Methods. 2016 Jan;13(1):59-62. Epub 2015 Nov 30. PMCID: PMC4890631

Regulatory evolution of innate immunity through co-option of endogenous retroviruses.

Chuong EB, Elde NC, Feschotte C. (2016). Science. 2016 Mar 4;351(6277):1083-7. PMCID: PMC4887275

Detection and Tracking of Dual-Labeled HIV Particles Using Wide-Field Live Cell Imaging to Follow Viral Core Integrity.

Mamede JI, Hope TJ. (2016). Methods Mol Biol. 2016;1354:49-59. PMID: 26714704 PMCID: PMC4876021

Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly.

  Grime JMA, Dama JF, Ganser-Pornillos BK, Woodward CL, Jensen GJ, Yeager M, Voth GA. (2016). Nature Comm. 2016 May 13;7:11568. PMID: 27174390 PMCID: PMC4869257

Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow.

  Ma H, Tu LC, Naseri A, Huiman M, Zhang S, Grünwald D, Pederson T. (2016). Nat Biotechnol. 2016 May;34(5):528-30. Epub 2016 Apr 18. PMID: 27088723 PMCID: PMC4864854

Meiotic Clade AAA ATPases: Protein Polymer Disassembly Machines.

  Monroe N, Hill CP. (2016). J Mol Biol. 2016 May 8;428(9 Pt B):1897-911. Epub 2015 Nov 10. PMID: PMID: 26555750 PMCID: PMC4860049

Th17 Cells Are Preferentially Infected Very Early after Vaginal Transmission of SIV in Macaques.

  Stieh DJ, Matias E, Xu H, Fought AJ, Blanchard JL, Marx PA, Veazey RS, Hope TJ. (2016). Cell Host Microbe. 2016 Apr 13;19(4):529-40. PMID: 27078070 PMCID: PMC4841252

TRIM5α Degradation via Autophagy Is Not Required for Retroviral Restriction

  Imam S, Talley S, Nelson RS, Dharan A, O'Connor C, Hope TJ, Campbell EM. (2016). J Virol. 2016 Jan 13;90(7):3400-10. PMID: 26764007 PMCID: PMC4794682.

2015

VIROLOGY. Visualizing trans-infection.

  Hope T. (2015). Science. 2015 Oct 30;350(6260):511-2. PMID: 26516268

New frontiers of biophysical methods: tools for structural biology and beyond.

  Millar DP, Trewhella, J. (2015). Curr Opin Struc Biol. 2014 Oct;28:viii-x. Epub 2014 Oct 4. PMID: 25292464.

Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping.

  Treweek, JB, Chan KY, Flytzanis NC, Yang B, Deverman BE, Greenbaum A, Lignell A, Xiao C, Cai L, Ladinsky MS, Bjorkman PJ, Fowlkes CC, Gradinaru V. (2015). Nat Protoc. 2015 Nov;10(11):1860-1896. Epub 2015 Oct 22. PMID: 26492141 PMCID: PMC4917295

Direct visualization of vaults within intact cells by electron cryo-tomography.

  Woodward CL, Mendonca LM, Jensen GJ. (2015).Cell Mol Life Sci. 2015 Sep;72(17):3401-9. Epub 2015 Apr 12. PMID: 25864047 PMCID: PMC4898762

Macromolecular machines and assemblies: Rise and fall at the molecular level.

  Forest, KT, Hill CP. (2015). Curr Opin Struct Biol. 2015 Apr;31:vii-viii. Epub 2015 May 29. PMID: 26027771 PMCID: PMC4878820

HIV-1 capsid: the multifaceted key player in HIV-1 infection.

  Campbell EM, Hope TJ. (2015). Nat Rev Microbiol. 2015 Aug;13(8):471-83. PMID: 26179359 PMCID: PMC4876022

CELL BIOLOGY. An ESCRT to seal the envelope.

  Sundquist WI, Ullman KS. (2015). Science. 2015 Jun 19;348(6241):1314-5. PMID: 26089496

A 4D view on mRNA.

  Smith CS, Tu LC, Grünwald D. (2015). Oncotarget. 2015 Oct 6;6(30):28515-6. PMID: 26387129 PMCID: PMC4745664

TRIM5α-Mediated Ubiquitin Chain Conjugation Is Required for Inhibition of HIV-1 Reverse Transcription and Capsid Destabilization.

  Campbell EM, Weingart J, Sette P, Opp S, Sastri J, O'Connor SK, Talley S, Diaz-Griffero F, Hirsch V, Bouamr F.  (2015). J Virol. 2015 Dec 16;90(4):1849-57. Print 2016 Feb 15. PMID: 26676782 PMCID: PMC4733990

Probability-based particle detection that enables threshold-free and robust in vivo single-molecule tracking.

  Smith CS, Stallinga S, Lidke KA, Rieger B, Grünwald D. (2015). Mol Biol Cell. 2015 Nov 5;26(22):4057-62. Epub 2015 Sep 30. PMID: 26424801 PMCID: PMC4710236

In vivo single-particle imaging of nuclear mRNA export in budding yeast demonstrates an essential role for Mex67p.

Smith CS, Lari A, Derrer CP, Ouwehand A, Rossouw A, Huisman M, Dange T, Hopman M, Joseph A, Zenklusen D, Weis K, Grünwald D, Montpetit B. (2015). J Cell Biol. 2015 Dec 21;211(6):1121-30. PMID: 26694837 PMCID: PMC4687877

Structure and membrane remodeling activity of ESCRT-III helical polymers.

  McCullough J, Clippinger AK, Talledge N, Skowyra ML, Saunders MG, Naismith TV, Colf LA, Afonine P, Arthur C, Sundquist WI, Hanson PI, Frost A. (2015). Science. 2015 Dec 18;350(6267):1548-51. Epub 2015 Dec 3. PMID: 26634441 PMCID: PMC4684769

Retroviruses use CD169-mediated trans-infection of permissive lymphocytes to establish infection.

  Sewald X, Ladinsky MS, Uchil PD, Beloor J, Pi R, Herrmann C, Motamedi N, Murooka TT, Brehm MA, Greiner DL, Shultz LD, Mempel TR, Bjorkman PJ, Kumar P, Mothes W. (2015). Science. 2015 Oct 30;350(6260):563-567. Epub 2015 Oct 1. PMID: 26429886 PMCID: PMC4651917

The Caltech Tomography Database and Automatic Processing Pipeline.

  Ding HJ, Oikonomou C, Jensen GJ. (2015). J Struct Biol. 2015 Oct 30;350(6260):563-567. Epub 2015 Oct 1. PMID: 26087141 PMCID: PMC4633326

FACT Disrupts Nucleosome Structure by Binding H2A-H2B with Conserved Peptide Motifs.

  Kemble DJ, McCullough LL, Whitby FG, Formosa T, Hill, CP. (2015). Molecular Cell. 2015 Oct 15;60(2):294-306. Epub 2015 Oct 8. PMID: 26455391 PMCID: PMC4620744

Broadly Neutralizing Antibody 8ANC195 Recognizes Closed and Open States of HIV-1 Env.

  Scharf L, Wang H, Gao H, Chen S, McDowall AW, Bjorkman PJ. (2015). Cell. 2015 Sep 10;162(6):1379-90. PMID: 26359989 PMCID: PMC4587768

Impact of Nucleoporin-Mediated Chromatin Localization and Nuclear Architecture on HIV Integration Site Selection.

  Wong RW, Mamede JI, Hope TJ. (2015). J Virol. 2015 Oct;89(19):9702-5. Epub 2015 Jul 1. PMID: 26136574 PMCID: PMC4577903

Toward a sustainable biomedical research enterprise: Finding consensus and implementing recommendations.

  Pickett CL, Corb BW, Matthews CR, Sundquist WI, Berg JM. (2015). Proc Natl Acad Sci U S A. 2015 Sep 1;112(35):10832-6. Epub 2015 Jul 20. PMID: 26195768 PMCID: PMC4568264

TRIM5α requires Ube2W to anchor Lys63-linked ubiquitin chains and restrict reverse transcription.

  Fletcher AJ, Christensen DE, Nelson C, Tan CP, Schaller T, Lehner PJ, Sundquist WI, Towers GJ. (2015). EMBO J. 2015 Aug 4;34(15):2078-95. Epub 2015 Jun 22. PMID: 26101372 PMCID: PMC4551353

RING Dimerization Links Higher-Order Assembly of TRIM5α to Synthesis of K63-Linked Polyubiquitin.

   Yudina Z, Roa A, Johnson R, Biris N, de Souza Aranha Vieira DA, Tsiperson V, Reszka N, Taylor AB, Hart PJ, Demeler B, Diaz-Griffero F, Ivanov DN. (2015). Cell Rep. 2015 Aug 4;12(5):788-97. Epub 2015 Jul 23. PMID: 26212332 PMCID: PMC4526822

Binding of Substrates to the Central Pore of the Vps4 ATPase Is Autoinhibited by the Microtubule Interacting and Trafficking (MIT) Domain and Activated by MIT Interacting Motifs (MIMs).

  Han H, Monroe N, Votteler J, Shakya B, Sundquist WI, Hill CP. (2015). J Biol Chem. 2015 May 22;290(21):13490-9. Epub 2015 Apr 1. PMID: 25833946 PMCID: PMC4505595

Determinants for degradation of SAMHD1, Mus81 and induction of G2 arrest in HIV-1 Vpr and SIVagm Vpr.

  DePaula-Silva AB, Cassiday PA, Chumley J, Bosque A, Monteiro-Filho CM, Mohan CS, Cone KR, Krogan N, Elde NC, Planelles V. (2015). Virology 2015 Mar;477:10-17. Epub 2015 Jan 22. PMID: 25618414 PMCID: PMC4455942

Nuclear accessibility of β-actin mRNA is measured by 3D single-molecule real-time tracking.

  Smith CSS, Preibisch S, Joseph A, Abrahamsson S, Rieger B, Myers E, Singer RHS, Grünwald D. (2015). J Cell Biol. 2015 May 25;209(4):609-19. PMID: 26008747 PMCID: PMC4442804

A multilaboratory comparison of calibration accuracy and the performance of external references in analytical ultracentrifugation.

  Zhao H, Eckert DM, Et. Al. (2015). Plos One. 2015 May 21;10(5):e0126420. eCollection 2015. PMID: 25942676 PMCID: PMC4440767

Overlapping Patterns of Rapid Evolution in the Nucleic Acid Sensors cGAS and OAS1 Suggest a Common Mechanism of Pathogen Antagonism and Escape.

  Hancks DC, Hartley MK, Hagan C, Clark NL, Elde NC. (2015). PLOS Genet. 2015 May 5;11(5):e1005203. eCollection 2015 May. PMID: 25942676 PMCID: PMC4420275

Design and characterization of ebolavirus GP prehairpin intermediate mimics as drug targets. 

  Clinton TR, Weinstock MT, Jacobsen MT, Szabo-Fresnais N, Pandya MJ, Whitby FG, Herbert AS, Prugar LI, McKinnon R, Hill CP, Welch BD, Dye JM, Eckert DM, Kay MS. (2015). Protein Sci.  2015 Apr;24(4):446-63. Epub 2014 Oct 31. PMID: 25287718 PMCID: PMC4380977

Fluorescent image analysis of HIV-1 and HIV-2 uncoating kinetics in the presence of old world monkey TRIM5α.

Takeda E, Kono K, Hulme AE, Hope TJ, Nakayama EE, Shioda T. (2015). PLoS One. 2015 Mar 24;10(3):e0121199. eCollection 2015. PMID: 25803716 PMCID: PMC4372348

Structural basis for the activation and inhibition of the UCH37 deubiquitylase. 

  VanderLinden RT, Hemmis CW, Schmitt B, Ndoja A, Whitby FG, Robinson H, Cohen RE, Yao T, Hill, CP. (2015). Mol Cell. 2015 Mar 5;57(5):901-911. Epub 2015 Feb 19. PMID: 25702872 PMCID: PMC4355076

Angiomotin functions in HIV-1 assembly and budding.

Mercenne G, Alam SL, Arii J, Lalonde MS, Sundquist WI. (2015). Elife. 2015 Jan 29;4:e03778. PMID: 25633977 PMCID: PMC4337731

Identification of capsid mutations that alter the rate of HIV-1 uncoating in infected cells.

  Hulme AE, Kelley Z, Okocha EA, Hope TJ. (2015). J Virol. 2015 Jan;89(1):643-51. Epub 2014 Oct 22. PMID: 25339776 PMCID: PMC4301138

Electron cryotomography studies of maturing HIV-1 particles reveal the assembly pathway of the viral core.

  Woodward CL, Cheng SN, Jensen GJ. (2015). J Virol. 2015 Jan 15;89(2):1267-77. Epub 2014 Nov 12. PMID: 25392219 PMCID: PMC4300640

2014

Function and dynamics of macromolecular complexes explored by integrative structural and computational biology.

  Purdy MD, Bennett BC, McIntire WE, Khan AK, Kasson PM, Yeager M. (2014). Curr Opin Struct Biol. 2014 Aug;27:138-48. Epub 2014 Sep 18. PMID: 25238653 PMCID: PMC6387792

Structural basis of HIV-1 capsid recognition by PF74 and CPSF6.

      Bhattacharya A, Alam, SL Fricke T, Zadrozny K, Sedzicki J, Taylor AB, Demeler B, Pornillos O, Ganser-Pornillos BK, Diaz-Griffero F, Ivanov DN, Yeager, M. (2014). Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):18625-30. Epub 2014 Dec 17. PMID: 25518861 PMCID: PMC4284599

Cytoplasmic HIV-1 RNA is mainly transported by diffusion in the presence or absence of Gag protein.

     Chen J, Grünwald D, Sardo L, Galli A, Plisov S, Nikolaitchik OA, Chen D, Lockett S, Larson DR, Pathak VK, Hu WS. (2014). Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):E5205-13. Epub 2014 Nov 17. PMID: 25404326 PMCID: PMC4260538

HIV-1 uncoating is facilitated by dynein and kinesin 1.

     Lukic Z, Dharan A, Fricke T, Diaz-Griffero F, Campbell EM. (2014). J Virol. 2014 Dec;88(23):13613-25. Epub 2014 Sep 17. PMID: 25231297 PMCID: PMC4248982

Vaginal challenge with an SIV-based dual reporter system reveals that infection can occur throughout the upper and lower female reproductive tract.

      Stieh DJ, Maric D, Kelley ZL, Anderson MR, Hattaway HZ, Beilfuss BA, Rothwangl KB, Veazey RS, Hope TJ. (2014). PLoS Pathog. 2014 Oct 9;10(10):e1004440. eCollection 2014 Oct. PMID: 25299616 PMCID: PMC4192600

MxB binds to the HIV-1 core and prevents the uncoating process of HIV-1.

      Fricke T, White TE, Schulte B, de Souza DA, Vieira A, Dharan A, Campbell EM, Brandariz-Nunez A, Diaz-Griffero F. (2014). Retrovirology. 2014 Aug 14;11:68. PMID: 25123063 PMCID: PMC4145229

Restriction of HIV-1 by rhesus TRIM5α is governed by alpha helices in the Linker2 region.

     Sastri J, Johnsen L, Smolin N, Imam S, Mukherjee S, Lukic Z, Brandariz-Nunez A, Robia SL, Diaz-Griffero F, Wiethoff C, Campbell EM. (2014). J Virol. 2014 Aug;88(16):8911-23. Epub 2014 May 28. PMID: 24872590 PMCID: PMC4136267

Recognition of the HIV capsid by the TRIM5α restriction factor is mediated by a subset of pre-existing conformations of the TRIM5α SPRY domain.

      Kovalskyy DB, Ivanov DN. (2014). Biochemistry. 2014 Mar 11;53(9):1466-76. Epub 2014 Feb 24. PMID: 24506064 PMCID: PMC4119003

The cyclosporin A washout assay to detect HIV-1 uncoating in infected cells.

      Hulme AE, Hope TJ. (2014). Methods Mol Biol. 2014;1087:37-46. PMID: 24158812 PMCID: PMC4084958

Multi-resolution correlative focused ion beam scanning electron microscopy: applications to cell biology.

     Narayan K, Danielson CM, Lagarec K, Lowekamp BC, Coffman P, Laquerre A, Phaneuf MW, Hope TJ, Subramaniam S. (2014). J Struct Biol. 2014 Mar;185(3):278-84. Epub 2013 Dec 1. PMID: 24300554 PMCID: PMC3943650

A phosphatidylinositol transfer protein integrates phosphoinositide signaling with lipid droplet metabolism to regulate a developmental program of nutrient stress-induced membrane biogenesis.

     Ren J, Pei-Chen LC, Pathak MC, Temple BR, Nile AH, Mousley CJ, Duncan MC, Eckert DM, Leiker TJ, Ivanova PT, Myers DS, Murphy RC, Brown HA, Verdaasdonk J, Bloom KS, Ortlund EA, Neiman AM, Bankaitis VA. (2014). Mol Biol Cell. 2014 Mar;25(5):712-27. Epub 2014 Jan 8. PMID: 24403601 PMCID: PMC3937096

The tripartite motif coiled-coil is an elongated antiparallel hairpin dimer.

    Sanchez JG, Okreglicka K, Chandrasekaran V, Welker JM, Sundquist WI, Pornillos, O. (2014). Proc Natl Acad Sci U S A. 2014 Feb 18;111(7):2494-9. Epub 2014 Feb 3. PMCID: PMC3932864

Electron tomography of HIV-1 infection in gut-associated lymphoid tissue.

    Ladinsky MS, Kieffer C, Olson G, Deruaz M, Vrbanac V, Tager AM, Kwon DS, Bjorkman PJ. (2014). PLoS Path. 2014 Jan 30;10(1):e1003899. eCollection 2014 Jan. PMCID: PMC3907528

The binding ability of the rhesus TRIM5α PRYSPRY domain to the capsid is necessary but not sufficient for HIV-1 restriction.

     Yang Y, Brandariz-Nuñez A, Fricke T, Ivanov DN, Sarnak Z, Diaz-Griffero F. (2014). Virology. 2014 Jan 5;448:217-28. Epub 2013 Oct 31. PMID: 24314652 PMCID: PMC3900861

2013

RNA purification by preparative polyacrylamide gel electrophoresis.

Petrov A, Wu T, Puglisi EV, Puglisi JD. (2013) Methods Enzymol.2013;530:315-30. PMID: 24034329

Macromolecular assemblies.

Rey FA, Sundquist WI. (2013). Curr Opin Struct Biol. 2013 Apr;23(2):224-8. Epub 2013 May 7. PMID:23663961

Rhesus monkey TRIM5α SPRY domain recognizes multiple epitopes that span several capsid monomers on the surface of the HIV-1 mature viral core.

      Biris N, Tomashevski A, Bhattacharya A, Diaz-Griffero F, Ivanov DN. (2013). J Mol Biol. 2013 Dec 13;425(24):5032-44. Epub 2013 Jul 23. PMID: 23886867 PMCID: PMC4116666

Lipid monolayer and sparse matrix screening for growing two-dimensional crystals for electron crystallography: methods and examples.

      Yeager M, Dryden KA, Ganser-Pornillos BK. (2013). Methods Mol. Bio. 2013;955:527-37. PMID: 23132079 PMCID: PMC4127334

Membrane fission reactions of the mammalian ESCRT pathway.

    McCullough J, Colf LA, Sundquist WI. (2013). Annu Rev Biochem. 2013;82:663-92. Epub 2013 Mar 18. PMID: 23527693 PMCID: PMC4047973

The oligomeric state of the active Vps4 AAA ATPase.

    Monroe N, Han H, Gonciarz MD, Eckert DM, Karren MA, Whitby FG, Sundquist WI, Hill CP. (2013). J Mol Biol. 2014 Feb 6;426(3):510-25. Epub 2013 Oct 23. PMID: 24161953 PMCID: PMC3919030

Contribution of oligomerization to the anti-HIV-1 properties of SAMHD1.

     Brandariz-Nuñez A, Valle-Casuso JC, White TE, Nguyen L, Bhattacharya A, Wang Z, Demeler B, Amie S, Knowlton C, Kim B, Ivanov DN, Diaz-Griffero F. (2013). Retrovirology. 2013 Nov 12;10:131. PMID: 24219908 PMCID: PMC3882887

Virus budding and the ESCRT pathway. 

    Votteler J, Sundquist WI. (2013). Cell Host Microbe. 2013 Sep 11;14(3):232-41. PMID: 24034610 PMCID: PMC3819203

Discovery of novel small-molecule HIV-1 replication inhibitors that stabilize capsid complexes.

    Lamorte L, Titolo S, Lemke CT, Goudreau N, Mercier JF, Wardrop E, Shah VB, von Schwedler UK, Langelier C, Banik SS, Aiken C, Sundquist WI, Mason SW. (2013). Antimicrob Agents Chemother. 2013 Oct;57(10):4622-31. Epub 2013 Jul 1. PMID: 23817385 PMCID: PMC3811413

Using antiubiquitin antibodies to probe the ubiquitination state within rhTRIM5α cytoplasmic bodies.

Danielson CM, Hope TJ. (2013). AIDS Res Hum Retroviruses. 2013 Oct;29(10):1373-85. Epub 2013 Jul 26. PMID: 23799296 PMCID: PMC3785812

The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards.

    Briegel A, Pilhofer M, Mastronarde D, Jensen GJ. (2013). J Struct Biol. 2013 Jul;183(1):95-8. Epub 2013 Apr 30. PMID: 23639902 PMCID: PMC3765063

Slower uncoating is associated with impaired replicative capability of simian-tropic HIV-1.

     Kono K, Takeda E, Tsutsui H, Kuroishi A, Hulme AE, Hope TJ, Nakayama EE, Shioda T. (2013). PloS One. 2013 Aug 13;8(8):e72531. eCollection 2013. PMID: 23967315 PMCID: PMC3742594

Electron cryotomography of ESCRT assemblies and dividing Sulfolobus cells suggests that spiraling filaments are involved in membrane scission.

  Dobro MJ, Samson RY, Yu Z, McCullough J, Ding HJ, Chong PL, Bell SD, Jensen GJ. (2013). Mol Biol Cell. 2013 Aug;24(15):2319-27. Epub 2013 Jun 12. PMID: 23761076 PMCID: PMC3727925

Interchangeable adaptors regulate mitochondrial dynamin assembly for membrane scission.

     Koirala S, Guo Q, Kalia R, Bui HT, Eckert DM, Frost A, Shaw JM. (2013). Proc Natl Acad Sci U S A. 2013 Apr 9;110(15):E1342-51. Epub 2013 Mar 25. PMCID: PMC3625255

Unclosed HIV-1 capsids suggest a curled sheet model of assembly.

     Yu Z, Dobro MJ, Woodward CL, Levandoski A, Danielson C, Sandrin V, Shi J, Aiken C, Zandi R, Hope TJ, Jensen GJ. (2013). J Mol Biol. 2013 Jan 9;425(1):112-23. Epub 2012 Oct 16. PMID: 23079241 PMCID: PMC3597093

Building a super elongation complex for HIV.

     Hill CP, Sundquist WI. (2013). Elife. 2013 Mar 8;2:e00577. PMID: 28340332 PMCID: PMC3592195

2012

Assemble, replicate, remodel and evade.

       Sundquist WI, Krug RM. (2012). Curr Opin Virol.  2012 Apr;2(2):111-4. Epub 2012 Mar 10. PMID: 22482706

Assembly and architecture of HIV.

      Ganser-Pornillos BK, Yeager M, Pornillos O. (2012). Adv Exp Med Biol. 2012;726:441-65. PMID: 22297526 PMCID: PMC6743068

Electron tomography of cells.

       Gan L, Jensen GJ. (2012). Quart Rev Biophys. 2012 Feb;45(1):27-56. Epub 2011 Nov 15. PMID: 22082691

ESCRT-III CHMP2A and CHMP3 form variable helical polymers in vitro and act synergistically during HIV-1 budding.

      Effanin G, Dordor A, Sandrin V, Martinelli N, Sundquist WI, Schoehn G, Weissenhorn W. (2012). Cell Microbiol. 2013 Feb;15(2):213-26. Epub 2012 Nov 6. PMCID: PMC3783020

Recruitment and dynamics of proteasome association with rhTRIM5α cytoplasmic complexes during HIV-1 infection.

     Danielson CM, Cianci GC, Hope TJ. (2012). Traffic. 2012 Sep;13(9):1206-17. Epub 2012 Jun 19. PMID: 22624877 PMCID: PMC3760259

Analysis of RNA folding and ribonucleoprotein assembly by single-molecule fluorescence spectroscopy.

     Pljevaljčić P, Robertson-Anderson R, Millar DP. (2012). Meth Mol Bio. 875:271-95. PMID: 22573447 PMCID: PMC3744346

Knockdown of MAP4 and DNAL1 produces a post-fusion and pre-nuclear translocation impairment in HIV-1 replication.

         Gallo D., Hope TJ. (2012). Virology. 2012;875:271-95. PMCID: PMC3732191

Unusual arginine formations in protein function and assembly: rings, strings, and stacks.

       Neves MA, Yeager M, Abagyan R. (2012). J Phys Chem B. 2012 Jun 14;116(23):7006-13. Epub 2012 Apr 19. PMID: 22497303 PMCID: PMC3613333

Interactions of the human LIP5 regulatory protein with endosomal sorting complexes required for transport.

Skalicky JJ, Arii J, Wenzel D, Stubblefield W-MB, Kztsuyama A, Uter NT, Bajorek M, Myszka DG, Sundquist WI. (2012). J Biol Chem. 2012 Dec 21;287(52):43910-26. Epub 2012 Oct 26. PMID: 23105106 PMCID: PMC3527974

Early stages of the HIV-1 capsid protein lattice formation.

      Grime JMA, Voth GA. (2012). Biophys J. 2012 Oct 17;103(8):1774-83. Epub 2012 Oct 16. PMID: 23083721 PMCID: PMC3475334

Distinct effects of two HIV-1 capsid assembly inhibitor families that bind the same site within the N-terminal domain of the viral CA protein.

        Lemke CT, Titolo S, von Schwedler U, Goudreau N, Mercier JF, Wardrop E, Faucher AM, Coulombe R, Banik SS, Fader L, Gagnon A, Kawai SH, Rancourt J, Tremblay M, Yoakim C, Simoneau B, Archambault J, Sundquist WI, Mason SW. (2012). J Virol. 2012 Jun;86(12):6643-55. Epub 2012 Apr 11. PMID: 22496222 PMCID: PMC3393593

HIV-1 assembly, budding, and maturation.

       Sundquist WI, Kräusslich H-G. (2012). Cold Spring Harb Perspect Med. 2012 Jul;2(7):a006924. PMID: 22762019 PMCID: PMC3385941

Host cell interactome of HIV-1 Rev includes RNA helicases involved in multiple facets of virus production.

   Naji S, Ambrus G, Cimermančič P, Reyes JR, Johnson J, Filbrandt R, Huber MD, Vesely P, Yates 3rd JR,Krogan NJ, Saphire AC, Gerace L. (2012). Mol Cell Proteom. 2012 Apr;11(4):M111.015313. Epub 2011 Dec 15. PMID: 22174317 PMCID: PMC3322577

DDX1 is an RNA-dependent ATPase involved in HIV-1 Rev function and virus replication.

        Edgcomb SP, Carmel AB, Naji S, Ambrus-Aikelin G, Reyes JR, Thompson J, Saphire AC, Gerace L, Williamson JR. (2012). J Mol Biol. 2012 Jan 6;415(1):61-74. Epub 2011 Oct 25. PMID: 22051512 PMCID: PMC3249508

2011

Global landscape of HIV-human protein complexes.

       Jager S, Cimermancic P, Gulbahce N, Johnson J, McGovern K, Clarke SC, Shales M, Mercenne G, Li K, Barry H, Jang GM, Akiva E, Pache L, Marlett J, Shoshannah LR, Stephens M, D’Orso I, Fernandes J, Fahey M, Mahon C, O’Donoghue AJ, Todorovic A, Morris JH, Maltby D, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez R, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ. (2011). Nature. 2011 Dec 21;481(7381):365-70. PMID: 22190034 PMCID: PMC3310911

Secondary structure of the HIV reverse transcription initiation complex by NMR.

        Puglisi, EV, Puglisi, JD (2011). J. Mol Biol. 2011 Jul 29;410(5):863-74. PMID: 21763492 PMCID: PMC3710119

Organization of the smallest eukaryotic spindle.

      Gan L, Ladinsky MS, Jensen GJ. (2011). Organization of the smallest eukaryotic spindle. Curr Bio. 2011 Sep 27;21(18):1578-83. Epub 2011 Sep 8. PMID: 21906950 PMCID: PMC3234289

Structure of the Bro1 domain protein BROX and functional analyses of the ALIX Bro1 domain in HIV-1 budding.

       Zhai Q, Landesman M, Robinson H, Sundquist WI, Hill CP. (2011). PLoS One. 2011;6(12):e27466. Epub 2011 Dec 5. PMID: 22162750 PMCID: PMC3230590

Design of in vitro symmetric complexes and analysis by hybrid methods reveal mechanisms of HIV capsid assembly.

Yeager, M. (2011). J Mol Biol.2011 Jul 22;410(4):534-52. PMID: 21763499 PMCID: PMC3166646

Activation of the retroviral budding factor ALIX.

        Zhai Q, Landesman MB, Chung H-Y, Dierkers A, Jeffries CM, Trewhella J, Hill CP, Sundquist WI. (2011). J Virol. 2011 Sep;85(17):9222-6. Epub 2011 Jun 29. PMID: 21715492 PMCID: PMC3165844

Single-molecule studies reveal that DEAD box protein DDX1 promotes oligomerization of HIV-1 Rev on the Rev response element.

       Robertson-Anderson R, Wang J, Edgcomb S, Carmel A, Williamson JR, Millar DP. (2011). J Mol Biol. 2011 Jul 29;410(5):959-71. PMID: 21763499 PMCID: PMC3140434

Enzymatic de novo pyrimidine nucleotide synthesis.

      Schultheisz HL, Szymczyna BR, Scott LG, Williamson JR. (2011). J Am Chem Soc. 2011 Jan 19;133(2):297-304. Epub 2010 Dec 17. PMID: 21166398 PMCID: PMC3134529

Trafficking of some old world primate TRIM5α proteins through the nucleus.

       Diaz-Griffero F, Gallo DE, Hope TJ, Sodroski J. (2011). Retrovirology. 2011 May 15;8:38. PMID: 21575157 PMCID: PMC3120760

Complementary assays reveal a relationship between HIV-1 uncoating and reverse transcription.

      Hulme A, Perez O, Hope TJ. (2011). Proc Natl Acad Sci U S A. 2011 Jun 14;108(24):9975-80. Epub 2011 May 31. PMID: 21628558 PMCID: PMC3116424

Alternative mechanism for bacteriophage adsorption to the motile bacterium Caulobacter crescentus.

        Guerrero-Ferreira R, Viollier P, Ely B, Poindexter J, Goergieva M, Jensen GJ, Wright E. (2011). Proc Natl Acad Sci U S A. 2011 Jun 14;108(24):9963-8. Epub 2011 May 25. PMID: 21613567 PMCID: PMC3116389

Long helical filaments are not seen encircling cells in electron cryotomograms of rod-shaped bacteria.

       Swulius MT, Chen S, Ding JH, Li Z, Briegel A, Pilhofer M, Tocheva EI, Lybarger SR, Johnson TL, Sandkvist M, Jensen GJ. (2011). Biochem Biophys Res Commun. 2011 Apr 22;407(4):650-5. Epub 2011 Mar 16. PMID: 21419100 PMCID: PMC3093302

Atomic-level modelling of the HIV capsid.

        Pornillos O, Ganser-Pornillos BK, Yeager M. (2011). Nature. 2011 Jan 20;469(7330):424-7. PMID: 21248851 PMCID: PMC3075868

Hexagonal assembly of a restricting TRIM5alpha protein.

        Ganser-Pornillos BK, Chandrasekaran V, Pornillos O, Sodroski JG, Sundquist WI, Yeager M. (2011). Proc Natl Acad Sci U S A. 2011 Jan 11;108(2):534-9. Epub 2010 Dec 27. PMID: 21187419 PMCID: PMC3021009

Identification and structural characterization of the ALIX-binding late domains of simian immunodeficiency virus SIVmac239 and SIVagmTan-1.

  Zhai Q, Landesman MB, Robinson H, Sundquist WI, Hill CP. (2011). J Virol. 2011 Jan;85(1):632-7. Epub 2010 Oct 20. PMID: 20962096 PMCID: PMC3014167

2010

Correlated light and electron cryo-microscopy.

       Briegel A, Chen S, Koster AJ, Plitzko JM, Schwartz CL, Jensen GJ. (2010). Meth Enzymol. 2010;481:317-41. PMID: 20887863

Disulfide bond stabilization of the hexameric capsomer of human immunodeficiency virus.

       Pornillos O, Ganser-Pornillos BK, Banumathi S, Hua Y, Yeager M. (2010). J Mol Biol. 2010 Sep 3;401(5):985-95. Epub 2010 Jun 26. PMID: 20600115 PMCID: PMC3050670

In vivo assembly of an archaeal virus studied with whole-cell electron cryotomography.

       Fu CY, Wang K, Gan L, Lanman J, Khayat R, Young MJ, Jensen GJ, Doerschuk PC, Johnson JE. (2010). Structure. 2010 Dec 8;18(12):1579-86. PMID: 21134637 PMCID: PMC3042139

Molecular architecture of a dynamin adaptor: implications for assembly of mitochondrial fission complexes.

        Koirala S, Bui HT, Schubert HL, Eckert DM, Hill CP, Kay MS, Shaw JM. (2010). J Cell Biol. 191:1127-39. PMID: 21149566 PMCID: PMC3002026

Multiscale computer simulation of the immature HIV-1 virion.

       Ayton GS, Voth GA. (2010).Biophys J. 2010 Dec 13;191(6):1127-39. PMID: 21044572 PMCID: PMC2966041

Structural and functional studies on the extracellular domain of BST2/tetherin in reduced and oxidized conformations.

        Schubert HL, Zhai Q, Sandrin V, Eckert DM, Garcia-Maya M, Saul L, Sundquist WI, Steiner RA, Hill CP. (2010). Proc Natl Acad Sci U S A. 2010 Oct 19;107(42):17951-6. Epub 2010 Sep 29. PMCID: PMC2964199

Design of a potent D-peptide HIV-1 entry inhibitor with a strong barrier to resistance.

        Welch BD, Francis JN, Redman JS, Paul S, Weinstock MT, Whitby FG, Eckert DM, Hill CP, Root MJ, Kay MS. (2010). J Virol. 2010 Nov;84(21):11235-44. Epub 2010 Aug 18. PMID: 20719956 PMCID: PMC2953169

Biosensor-based fragment screening using FastStep injections.

     Rich RL, Quinn JG, Morton T, Stepp JD, Myszka DG. (2010). Anal Biochem. 2010 Dec 15;407(2):270-7. Epub 2010 Aug 25. PMCID: PMC2949542

Calmodulin disrupts the structure of the HIV-1 MA protein.

        Chow JYH, Jeffries CM, Kwan AH, Guss JM, Trewhella J. (2010). J Mol Biol. 2010 Jul 23;400(4):702-14. Epub 2010 May 19. PMID: 20488189 PMCID: PMC2902600

Role of protein interactions in defining HIV-1 viral capsid shape and stability: a coarse-grained analysis.

        Krishna V, Ayton GS, Voth GA. (2010). Biophys J. 2010 Jan 6;98(1):18-26. PMID: 20085716 PMCID: PMC2800964

2009

"Spot and hop": internal referencing for surface plasmon resonance imaging using a three-dimensional microfluidic flow cell array.

       Eddings MA, Eckman JW, Arana CA, Connolly JE, Papalia GA, Gale BK, Myszka DG. (2009). Anal Biochem. 2009 Feb 15;385(2):309-13. doi: 10.1016/j.ab.2008.11.014. Epub 2008 Nov 20. PMID: 19059374 PMCID: PMC6691735

An improved cryogen for plunge freezing.

       Tivol WF, Briegel A, Jensen GJ. (2009). Microsc Microanal. 2008 Oct;14(5):375-9. PMID: 18793481 PMCID: PMC3058946

X-ray structures of the hexameric building block of the HIV capsid.

      Pornillos O, Ganser-Pornillos BK, Kelly BN, Hua Y, Whitby FG, Stout CD, Sundquist WI, Hill CP, Yeager M. (2009). Cell. 2009 Jun 26;137(7):1282-92. Epub 2009 Jun 11. PMID: 19523676 PMCID: PMC2840706

Fully automated, sequential tilt-series acquisition with Leginon.

      Suloway C, Shi J, Cheng A, Pulokas J, Carragher B, Potter CS, Zheng SQ, Agard DA, Jensen GJ. (2009). J Struct Biol. 2009 Jul;167(1):11-8. Epub 2009 Apr 8. PMID: 19361558 PMCID: PMC2724967

Structural basis for ESCRT-III protein autoinhibition.

       Bajorek M, Schubert HL, McCullough J, Langelier C, Eckert DM, Stubblefiel W-M B, Uter NT, Myszka DG, Hill CP, Sundquist WI. (2009). Nat Struct Mol Biol. 2009 Jul;16(7):754-62. Epub 2009 Jun 14. PMID: 19525971 PMCID: PMC2712734

Synergy of NMR, computation, and X-ray crystallography for structural biology.

       Szymczyna BR, Taurog RE, Young MJ, Snyder JC, Johnson JE, Williamson JR. (2009). Structure. 2009 Apr 15;17(4):499-507. PMID: 19368883 PMCID: PMC2705668

HIV-1 Rev protein assembles on viral RNA one molecule at a time.

     Pond SJ, Ridgeway WK, Robertson R, Wang J, Millar DP. (2009). Proc Natl Acad Sci U S A. 2009 Feb 3;106(5):1404-8. Epub 2009 Jan 21. PMID: 19164515 PMCID: PMC2635779

2008

Structural and functional studies of ALIX interactions with YPX(n)L late domains of HIV-1 and EIAV.

Zhai Q, Fisher RD, Chung H-Y, Myszka DG, Sundquist WI, Hill CP. (2008). Nature Struct Mol Biol. 2008 Jan;15(1):43-9. Epub 2007 Dec 9. PMID: 18066081

Continuous-flow microfluidic printing of proteins for array-based applications including surface plasmon resonance imaging.

      Natarajan S, Katsamba PS, Miles A, Eckman J, Papalia GA, Rich RL, Gale BK, Myszka DG. (2008). Anal Biochem. 2008 Feb 1;373(1):141-6. Epub 2007 Aug 19. PMID: 17868635

Radiation dose reduction and image enhancement in biological imaging through equally-sloped tomography.

      Lee E, Fahimian BP, Lancu CV, Suloway C, Murphy GE, Wright ER, Castano-Diez D, Jensen GJ, Miao J. (2008). J Struct Biol. 2008 Nov;164(2):221-7. Epub 2008 Aug 15. PMID: 18771735 PMCID: PMC3099251

The structural biology of HIV assembly.

       Ganser-Pornillos BK, Yeager M, Sundquist WI. (2008). Curr Opin Struct Biol. 2008 Apr;18(2):203-17. Epub 2008 Apr 9. PMID: 18406133 PMCID: PMC2819415

Biochemical and structural studies of yeast Vps4 oligomerization.

      Gonciarz MD, Whitby FG, Eckert DM, Kieffer C, Heroux A, Sundquist WI, Hill CP. (2008). J Mol Biol. 2008 Dec 26;384(4):878-95. Epub 2008 Oct 4. PMID: 18929572 PMCID: PMC2632936

Characterization of the steric defense of the HIV-1 gp41 N-trimer region.

        Eckert DM, Shi Y, Kim S, Welch BD, Kang E, Poff ES, Kay MS. (2008). Protein Sci. 2008 Dec;17(12):2091-100. Epub 2008 Sep 18. PMID: 18802030 PMCID: PMC2590922

Two distinct modes of ESCRT-III recognition are required for VPS4 functions in lysosomal protein targeting and HIV-1 budding.

       Kieffer C, Skalicky JJ, Morita E, De Dominico I, Ward DM, Kaplan J, Sundquist WI. (2008). Dev Cell. 2008 Jul;15(1):62-73. PMID: 18606141 PMCID: PMC2586299

Biochemical characterization of a recombinant TRIM5alpha protein that restricts human immunodeficiency virus type 1 replication.

       Langelier CR, Sandrin V, Eckert DM, Christensen DE, Chandrasekaran V, Alam SL, Aiken C, Olsen JC, Kar AK, Sodroski JG, Sundquist WI. (2008). J Virol. 2008 Dec;82(23):11682-94. Epub 2008 Sep 17. PMID: 18799573 PMCID: PMC2583683

ALIX-CHMP4 interactions in the human ESCRT pathway.

       McCullough J, Fisher RD, Whitby FG, Sundquist WI, Hill CP. (2008). Proc Natl Acad Sci U S A. 2008 Jun 3;105(22):7687-91. Epub 2008 May 29. PMID: 18511562 PMCID: PMC2409388

Cryo-EM structure of dodecameric Vps4p and its 2:1 complex with Vta1p.

      Yu Z, Gonciarz MD, Sundquist WI, Hill CP, Jensen GJ. (2008). J Mol Biol. 2008 Mar 21;377(2):364-77. Epub 2008 Jan 12. PMCID: PMC2279015

Peptide mimic of the HIV envelope gp120-gp41 interface.

       Kim S, Pang HB, Kay MS. (2008). J Mol Biol. 2008 Feb 22;376(3):786-97. Epub 2007 Dec 7. PMCID: PMC2265733

Probing the structural states of human immunodeficiency virus type 1 pr55gag by using monoclonal antibodies.

       Leblanc JJ, Perez O, Hope TJ. (2008). J. Virol. 2008 Mar;82(5):2570-4. Epub 2007 Dec 19. PMCID: PMC2258915

Protein structure and oligomerization are important for the formation of export-competent HIV-1 Rev-RRE complexes.

        Edgcomb SP, Aschrafi A, Kompfner E, Williamson JR, Gerace L, Hennig M. (2008). Protein Sci. 2008 Mar;17(3):420-30. doi: 10.1110/ps.073246608. Epub 2008 Jan 24. PMCID: PMC2248316

Visualization of a proteasome-independent intermediate during restriction of HIV-1 by rhesus TRIM5alpha.

        Campbell EM, Perez O, Anderson JL, Hope TJ. (2008). J Cell Biol. 2008 Feb 11;180(3):549-61. Epub 2008 Feb 4. PMCID: PMC2234241

2007

ESCRT-III recognition by VPS4 ATPases.

       Stuchell-Brereton MD, Skalicky JJ, Kieffer C, Karren MA, Ghaffarian S, Sundquist WI. (2007). Nature. 2007 Oct 11;449(7163):740-4. PMID: 17928862

Structure of full-length HIV-1 CA: a model for the mature capsid lattice.

       Ganser-Pornillos BK, Cheng A, Yeager M. (2007). Cell. 2007 Oct 5;131(1):70-9. PMID:17923088

How to assemble a capsid.

    Sundquist WI, Hill CP. (2007). Cell. 2007 Oct 5;131(1):17-9. PMID: 17923081

Molecular characterization of the Ran-binding zinc finger domain of Nup153.

        Higa MM, Alam SL, Sundquist WI, Ullman KS. (2007). J Biol Chem. 2007 Jun 8;282(23):17090-100. Epub 2007 Apr 10. PMID:17426026

Structural and biochemical studies of ALIX/AIP1 and its role in retrovirus budding.

        Fisher RD, Chung HY, Zhai Q, Robinson H, Sundquist WI, Hill CP. (2007). Cell. 2007 Mar 9;128(5):841-52. PMID: 17350572

An interferon-alpha-induced tethering mechanism inhibits HIV-1 and Ebola virus particle release but is counteracted by the HIV-1 Vpu protein.

     Neil SJ, Sandrin V, Sundquist WI, Bieniasz PD. (2007). Cell Host Microb. 2007 Sep 13;2(3):193-203. PMCID: PMC3793644

Structure of the antiviral assembly inhibitor CAP-1 complex with the HIV-1 CA protein.

       Kelly BN, Kyere S, Kinde I, Tang C, Howard BR, Robinson H, Sundquist WI, Summers MF, Hill CP. (2007). J Mol Biol. 2007 Oct 19;373(2):355-66. Epub 2007 Aug 15. PMID: 17826792 PMCID: PMC2066180

Potent D-peptide inhibitors of HIV-1 entry.

         Welch BD, VanDemark AP, Heroux A, Hill CP, Kay MS. (2007). Proc Natl Acad Sci U S A. 2007 Oct 23;104(43):16828-33. Epub 2007 Oct 17. PMCID: PMC2040420

Identification of human MVB12 proteins as ESCRT-I subunits that function in HIV budding.

         Morita E, Sandrin V, Alam SL, Eckert DM, Gygi SP, Sundquist WI. (2007). Cell Host Microb. 2007 Jul 12;2(1):41-53. PMCID: PMC2034311

Electron cryotomography of immature HIV-1 virions reveals the structure of the CA and SP1 Gag shells.

          Wright ER, Schooler JB, Ding HJ, Kieffer C, Fillmore C, Sundquist WI, Jensen GJ. (2007). EMBO J. 2007 Apr 18;26(8):2218-26. Epub 2007 Mar 29. PMCID: PMC1852790