The mission of the PCHPI is to understand HIV maturation and the early cellular events of HIV infection by characterizing HIV-host cell protein interactions/complexes at a high-resolution, molecular level. “Early cellular events” include those that occur after engagement of cell surface receptors and membrane fusion through to genome integration. Current projects are focused on CA and capsid interactions, proteins involved in trafficking and nuclear import, retroviral intasome structure, and analyses of the HIV-1 pre-integration complex.
Publications
Gres AT, Kirby KA, McFadden WM, Du H, Liu D, Xu C, Bryer AJ, Perilla JR, Shi J, Aiken C, Fu X, Zhang P, Francis AC, Melikyan GB, Sarafianos SG. (2023) Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization. Nat Commun. 14(1):5614. PMID: 37699872; PMC10497533.
Waheed AA, Zhu Y, Agostino E, Naing L, Hikichi Y, Soheilian F, Yoo SW, Song Y, Zhang P, Slusher BS, Haughey NJ, Freed EO. (2023) Neutral sphingomyelinase 2 is required for HIV-1 maturation. Proc Natl Acad Sci U S A. 120(28):e2219475120. PMID: 37406093; PMC10334776.
Bonnard D, Le Rouzic E, Singer MR, Yu Z, Le Strat F, Batisse C, Batisse J, Amadori C, Chasset S, Pye VE, Emiliani S, Ledoussal B, Ruff M, Moreau F, Cherepanov P, Benarous R. (2023) Biological and structural analyses of new potent allosteric inhibitors of HIV-1 integrase. Antimicrob Agents Chemother. 67(7):e0046223. PMID: 37310224; PMC10353390.
Kleinpeter AB, Zhu Y, Mallery DL, Ablan SD, Chen L, Hardenbrook N, Saiardi A, James LC, Zhang P, Freed EO. (2023) The effect of inositol hexakisphosphate on HIV-1 particle production and infectivity can be modulated by mutations that affect the stability of the immature Gag lattice. J Mol Biol. 168037.PMID: 37330292.
Sowd GA, Shi J, Fulmer A, Aiken C. (2023) HIV-1 capsid stability enables inositol phosphate-independent infection of target cells and promotes integration into genes. PLoS Pathog. 19(6):e1011423. PMID: 37267431; PMC10266667.
Bryer AJ, Rey JS, Perilla JR. (2023) Performance efficient macromolecular mechanics via sub-nanometer shape based coarse graining. Nat Commun. 14(1):2014. PMID: 37037809; PMC10086035.
Shen Q, Kumari S, Xu C, Jang S, Shi J, Burdick RC, Levintov L, Xiong Q, Wu C, Devarkar SC, Tian T, Tripler TN, Hu Y, Yuan S, Temple J, Feng Q, Lusk CP, Aiken C, Engelman AN, Perilla JR, Pathak VK, Lin C, Xiong Y. (2023) The capsid lattice engages a bipartite NUP153 motif to mediate nuclear entry of HIV-1 cores. Proc Natl Acad Sci U S A. 120(13):e2202815120. PMID: 36943880; PMC10068764.
Sarkar S, Zadrozny KK, Zadorozhnyi R, Russell RW, Quinn CM, Kleinpeter A, Ablan S, Meshkin H, Perilla JR, Freed EO, Ganser-Pornillos BK, Pornillos O, Gronenborn AM, Polenova T. (2023) Structural basis of HIV-1 maturation inhibitor binding and activity. Nat Commun. 14(1):1237. PMID: 36871077; PMC9985623.
Wu C, Xiong Y. (2023) Enrich and switch: IP6 and maturation of HIV-1 capsid. Nat Struct Mol Biol. 30(3):239-24. PMID: 36849641; PMC10033439.
Shen Q, Feng Q, Wu C, Xiong Q, Tian T, Yuan S, Shi J, Bedwell GJ, Yang R, Aiken C, Engelman AN, Lusk CP, Lin C, Xiong Y. (2023) Modeling HIV-1 nuclear entry with nucleoporin-gated DNA-origami channels. Nat Struct Mol Biol. 30(4):425-435. PMID: 36807645; PMC10121901.
Shen Q, Xiong Q, Zhou K, Feng Q, Liu L, Tian T, Wu C, Xiong Y, Melia TJ, Lusk CP, Lin C. (2023) Functionalized DNA-origami-protein nanopores generate large transmembrane channels with programmable size-selectivity. J Am Chem Soc. 145(2):1292-1300. PMID: 36577119; PMC9852090.
Luo W, Demidov V, Shen Q, Girão H, Chakraborty M, Maiorov A, Ataullakhanov FI, Lin C, Maiato H, Grishchuk EL. (2023) CLASP2 recognizes tubulins exposed at the microtubule plus-end in a nucleotide state-sensitive manner. Sci Adv. 9(1):eabq5404. PMID: 36598991; PMC9812398.
Singer MR, Dinh T, Levintov L, Annamalai AS, Rey JS, Briganti L, Cook NJ, Pye VE, Taylor IA, Kim K, Engelman AN, Kim B, Perilla JR, Kvaratskhelia M, Cherepanov P. (2023) The drug-induced interface that Drives HIV-1 integrase hypermultimerization and loss of function. mBio. 14(1):e0356022. PMID: 36744954; PMC9973045.
Porat-Dahlerbruch G, Polenova T. (2023) Simultaneous recoupling of chemical shift tensors of two nuclei by R-symmetry sequences. J Magn Reson. 348:107382. PMID: 36716616; PMC10023370.
Sheng Y, Morris K, Radecke J, Zhang P. (2022) Cryo-electron tomography remote data collection and subtomogram averaging. J Vis Exp. (185):10.3791/63923. PMID: 35913165; PMC10006545.
Zhang C, Guo C, Russell RW, Quinn CM, Li M, Williams JC, Gronenborn AM, Polenova T (2022). Magic-angle-spinning NMR structure of the kinesin-1 motor domain assembled with microtubules reveals the elusive neck linker orientation. Nat Commun. 13(1):6795. PMID: 36357375; PMC9649657.
Porat-Dahlerbruch G, Struppe J, Quinn CM, Gronenborn AM, Polenova T. (2022) 19F fast MAS (60-111 kHz) dipolar and scalar based correlation spectroscopy of organic molecules and pharmaceutical formulations. Solid State Nucl Magn Reson. 122:101831. PMID: 36182713; PMC10280467.
Francis AC, Cereseto A, Singh PK, Shi J, Poeschla E, Engelman AN, Aiken C, Melikyan GB. (2022) Localization and functions of native and eGFP-tagged capsid proteins in HIV-1 particles. PLoS Pathog. 18(8):e1010754. PMID: 35951676; PMC9426931.
Yoh SM, Mamede JI, Lau D, Ahn N, Sánchez-Aparicio MT, Temple J, Tuckwell A, Fuchs NV, Cianci GC, Riva L, Curry H, Yin X, Gambut S, Simons LM, Hultquist JF, König R, Xiong Y, García-Sastre A, Böcking T, Hope TJ, Chanda SK. (2022) Recognition of HIV-1 capsid by PQBP1 licenses an innate immune sensing of nascent HIV-1 DNA. Mol Cell. 82(15):2871-2884.e6. PMID: 35809572; PMC9552964.
Quinn CM, Zadorozhnyi R, Struppe J, Sergeyev IV, Gronenborn AM, Polenova T. (2021) Fast 19F magic-angle spinning nuclear magnetic resonance for the structural characterization of active pharmaceutical ingredients in blockbuster drugs. Anal Chem. 93(38):13029-13037. PMID: 34517697; PMC10280463.
Porat-Dahlerbruch G, Struppe J, Quinn CM, Gronenborn AM, Polenova T. (2022) Determination of accurate 19F chemical shift tensors with R-symmetry recoupling at high MAS frequencies (60-100 kHz). J Magn Reson. 340:107227. PMID: 35568013; PMC10280466.
Sarkar S, Runge B, Russell RW, Movellan KT, Calero D, Zeinalilathori S, Quinn CM, Lu M, Calero G, Gronenborn AM, Polenova T. (2022) Atomic-resolution structure of SARS-CoV-2 Nucleocapsid protein N-terminal domain. J Am Chem Soc. 144(23):10543-10555. PMID: 35638584; PMC9173677.
Xi Z, Ilina TV, Guerrero M, Fan L, Sluis-Cremer N, Wang YX, Ishima R. (2022) Relative domain orientation of the L289K HIV-1 reverse transcriptase monomer. Protein Sci. 31(5):e4307. PMID: 35481647; PMC8996465.
Olek M, Cowtan K, Webb D, Chaban Y, Zhang P (2022) IceBreaker: Software for high resolution single particle cryoEM with nonuniform ice. Structure 30(4):522-531.e4. PMID: 35150604; PMC9033277.
Ni T, Frosio T, Mendonça L, Sheng Y, Clare D, Himes BA, Zhang P. (2022) High-resolution in situ structure determination by cryo-electron tomography and subtomogram averaging using emClarity. Nat Protoc.17(2):421-444. PMID: 35022621; PMC9251519.
Gronenborn AM. (2022) Small, but powerful and attractive: 19F in biomolecular NMR. Structure. 30(1):6-14. doi: 10.1016/j.str.2021.09.009. PMID: 34995480; PMC8797020.
Bryer AJ, Reddy T, Lyman E, Perilla JR. (2022) Full scale structural, mechanical and dynamical properties of HIV-1 liposomes. PLoS Comput Biol. 18(1):e1009781. PMID: 35041642; PMC8797243.
Krebs AS, Mendonça LM, Zhang P. (2022) Structural analysis of retrovirus assembly and maturation. Viruses. 14(1):54. doi: 10.3390/v14010054. PMID: 35062258; PMC8778513.
Zadorozhnyi R, Sarkar S, Quinn CM, Zadrozny KK, Ganser-Pornillos BK, Pornillos O, Gronenborn AM, Polenova T. (2022) Determination of histidine protonation states in proteins by fast magic angle spinning NMR. Front Mol Biosci. 8:767040. PMID: 34957215; PMC8703106.
Maertens GN, Engelman AN, Cherepanov P. (2022) Structure and function of retroviral integrase. Nat Rev Microbiol. 20(1):20-34. PMID: 34244677; PMC8671357.
Ilina TV, Brosenitsch T, Sluis-Cremer N, Ishima R. (2021) Retroviral RNase H: Structure, mechanism, and inhibition. Enzymes. 50:227-247. PMID: 34861939; PMC8994160.
Ingram Z, Fischer DK, Ambrose Z. (2021) Disassembling the nature of capsid: Biochemical, genetic, and imaging approaches to assess HIV-1 capsid functions. Viruses. 13(11):2237. PMID: 34835043; PMC8618418.
Shen Q, Wu C, Freniere C, Tripler TN, Xiong Y. (2021) Nuclear Import of HIV-1. Viruses. 13(11):2242. PMID: 34835048; PMC8619967.
Byeon IL, Calero G, Wu Y, Byeon CH, Jung J, DeLucia M, Zhou X, Weiss S, Ahn J, Hao C, Skowronski J, Gronenborn AM. (2021) Structure of HIV-1 Vpr in complex with the human nucleotide excision repair protein hHR23A. Nat Commun. 12(1):6864. PMID: 34824204. PMC8617076.
Ni T, Zhu Y, Yang Z, Xu C, Chaban Y, Nesterova T, Ning J, Böcking T, Parker MW, Monnie C, Ahn J, Perilla JR, Zhang P. (2021) Structure of native HIV-1 cores and their interactions with IP6 and CypA. Sci Adv. 7(47):eabj5715. PMID: 34797722; PMC8604400.
Sowd GA, Shi J, Aiken C. (2021) HIV-1 CA inhibitors are antagonized by inositol phosphate stabilization of the viral capsid in cells. J Virol. 95(24):e0144521. PMID: 34613803. PMC8610598
Rey JS, Li W, Bryer AJ, Beatson H, Lantz C, Engelman AN, Perilla JR. (2021) Deep-learning in situ classification of HIV-1 virion morphology. Comput Struct Biotechnol J. 19:5688-5700. doi: 10.1016/j.csbj.2021.10.001. PMID: 34765089; PMC8554174.
Mendonça L, Howe A, Gilchrist JB, Sheng Y, Sun D, Knight ML, Zanetti-Domingues LC, Bateman B, Krebs AS, Chen L, Radecke J, Li VD, Ni T, Kounatidis I, Koronfel MA, Szynkiewicz M, Harkiolaki M, Martin-Fernandez ML, James W, Zhang P. (2021) Correlative multi-scale cryo-imaging unveils SARS-CoV-2 assembly and egress. Nat Commun. 12(1):4629. PMID: 34330917; PMC8324836.
Shen Q, Tian T, Xiong Q, Ellis Fisher PD, Xiong Y, Melia TJ, Lusk CP, Lin C. (2021) DNA-origami nanotrap for studying the selective barriers formed by phenylalanine-glycine-rich nucleoporins. J Am Chem Soc. 143(31):12294-12303. PMID: 34324340; PMC8363578.
Liang L, Ji Y, Zhao Z, Quinn CM, Han X, Bao X, Polenova T, Hou G. (2021) Accurate heteronuclear distance measurements at all magic-angle spinning frequencies in solid-state NMR spectroscopy. Chem Sci. 12(34):11554-11564. PMID: 34567504; PMC8409495.
Barski MS, Vanzo T, Zhao XZ, Smith SJ, Ballandras-Colas A, Cronin NB, Pye VE, Hughes SH, Burke TR Jr, Cherepanov P, Maertens GN. (2021) Structural basis for the inhibition of HTLV-1 integration inferred from cryo-EM deltaretroviral intasome structures. Nat Commun 12(1):4996. PMID: 34404793; PMC8370991.
Guo C, Fritz MP, Struppe J, Wegner S, Stringer J, Sergeyev IV, Quinn CM, Gronenborn AM, Polenova T. (2021) Fast 19F magic angle spinning NMR crystallography for structural characterization of fluorine-containing pharmaceutical compounds. Anal Chem. 2021 Jun 15;93(23):8210-8218. PMID: 34080855; PMC10280472.
Sergeyev IV, Quinn CM, Struppe J, Gronenborn A, Polenova T. (2021) Competing transfer pathways in direct and indirect dynamic nuclear polarization MAS NMR experiments on HIV-1 capsid assemblies: Implications for sensitivity and resolution. Magn Reson (Gott). 2(1):239-249. PMID: 34136885; PMC8203495
Perilla JR, Hadden-Perilla JA, Gronenborn AM, Polenova T. (2021) Integrative structural biology of HIV-1 capsid protein assemblies: Combining experiment and computation. Curr Opin Virol, 48:57-64. PMID: 33901736; PMC8187302.
Porat-Dahlerbruch G, Goldbourt A, Polenova T. Virus structures and dynamics by magic-angle spinning NMR. Annu Rev Virol. 2021 Sep 29;8(1):219-237. PMID: 34586870; PMC8973440.
Rosa A, Pye VE, Graham C, Muir L, Seow J, Ng KW, Cook NJ, Rees-Spear C, Parker E, Dos Santos MS, Rosadas C, Susana A, Rhys H, Nans A, Masino L, Roustan C, Christodoulou E, Ulferts R, Wrobel AG, Short CE, Fertleman M, Sanders RW, Heaney J, Spyer M, Kjær S, Riddell A, Malim MH, Beale R, MacRae JI, Taylor GP, Nastouli E, van Gils MJ, Rosenthal PB, Pizzato M, McClure MO, Tedder RS, Kassiotis G, McCoy LE, Doores KJ, Cherepanov P. (2021) SARS-CoV-2 can recruit a heme metabolite to evade antibody immunity. Sci Adv. 7(22):eabg7607. PMID: 33888467; PMC8163077.
Weiss SC, Vergara S, Lin G, and Calero G. (2021) Detection of microcrystals for cryoEM. Methods Mol Biol 2215:299-307. PMID: 33368010; PMC8188421.
Watanabe Y, Mendonça L, Allen E, Howe A, Lee M, Allen J, Chawla H, Pulido D, Donnellan F, Davies H, Ulaszewska,M, Belij-Rammerstorfer S, Morris S, Krebs A, Dejnirattisai W, Mongkolsapaya J, Supasa P, Screaton G, Green C, Lambe T, Zhang P, Gilbert S, Crispin M (2021) Native-like SARS-CoV-2 spike glycoprotein expressed by ChAdOx1 nCoV-19 vaccine. ACS Cent Sci 7(4):594-602. PMID: 34056089; PMC7836103.
Mendonça L, Sun D, Ning J, Liu J, Kotecha A, Olek M, Frosio T, Fu X, Himes BA, Kleinpeter AB, Freed EO, Zhou J, Aiken C, Zhang P (2021) CryoET structures of immature HIV Gag reveal a complete six-helix bundle. Commun Biol. 4(1):481. PMID: 33863979; PMC8052356.
Wei Y, Sluis-Cremer N (2021) Mutations in the HIV-1 3′-polypurine tract and integrase strand-transfer inhibitor resistance. Antimicrob Agents Chemother. 65(6):e02432-20. PMID: 33722887; PMC8316055.
Zhang P, Mendonça L (2021) Analysis of viruses in the cellular context by electron tomography, Encyclopedia of Virology (Fourth Edition) 1:242-247.
Zhong Z, Ning J, Boggs EA, Jang S, Wallace C, Telmer C, Bruchez MP, Ahn J, Engelman AN, Zhang P, Watkins SC, Ambrose Z. (2021) Cytoplasmic CPSF6 regulates HIV-1 capsid trafficking and infection in a Cyclophilin A-dependent manner. mBio. 12(2):e03142-20. PMID: 33758083; PMC8092277.
Engelman AN. (2021) HIV capsid and integration targeting. Viruses 13(1):E125. PMID: 33477441; PMC7830116.
Wilbourne M, Zhang P. (2021) Visualizing HIV-1 capsid and its interactions with antivirals and host factors. Viruses. 13(2):246. PMID: 33557422; PMC7914784.
Zhou X, Monnie C, DeLucia M, Ahn J.(2021) HIV-1 Vpr activates host CRL4-DCAF1 E3 ligase to degrade histone deacetylase SIRT7. Virol J. 18(1):48. PMID: 33648539; PMC7923639.
Sowd GA, Aiken C. (2021) Inositol phosphates promote HIV-1 assembly and maturation to facilitate viral spread in human CD4+ T cells. PLoS Pathog. 17(1):e1009190. PMID: 33476323; PMC7853515.
Ni T, Gerard S, Zhao G, Dent K, Ning J, Zhou J, Shi J, Anderson-Daniels J, Li W, Jang S, Engelman AN, Aiken C, Zhang P. (2020) Intrinsic curvature of the HIV-1 CA hexamer underlies capsid topology and interaction with cyclophilin A. Nat Struct Mol Biol 27(9):855-862. PMID: 32747784; PMC8064030
Ilina TV, Xi Z, Brosenitsch T, Sluis-Cremer N, Ishima R (2021) Large multidomain protein NMR: HIV-1 reverse transcriptase precursor in solution. Int J Mol Sci 21(24):9545. PMID: 33333923; PMC7765405.
Featherstone A, Aiken C. (2020) SERINC5 inhibits HIV-1 infectivity by altering the conformation of gp120 on HIV-1 particles. J Virol. 94(20):e00594-20. PMID: 32796070; PMC7527050.
Xu C, Fischer DK, Rankovic S, Li W, Dick RA, Runge B, Zadorozhnyi R, Ahn J, Aiken C, Polenova T, Engelman AN, Ambrose Z, Rousso I, Perilla JR. (2020) Permeability of the HIV-1 capsid to metabolites modulates viral DNA synthesis. PLoS Biol. 18(12):e3001015. PMID: 33332391; PMC7775124.
Temple J, Tripler TN, Shen Q, Xiong Y. (2020) A snapshot of HIV-1 capsid-host interactions. Curr Res Struct Biol. 2020;2:222-228. PMID: 34113849; PMC8189282.
Jennings J, Shi J, Varadarajan J, Jamieson PJ, Aiken C.(2020) The host cell metabolite inositol hexakisphosphate promotes efficient endogenous HIV-1 reverse transcription by stabilizing the viral capsid. mBio. 11(6):e02820-20. PMID: 33262260; PMC7733946.
Lu M, Russell RW, Bryer AJ, Quinn CM, Hou G, Zhang H, Schwieters CD, Perilla JR, Gronenborn AM, Polenova T. (2020) Atomic-resolution structure of HIV-1 capsid tubes by magic-angle spinning NMR. Nat Struct Mol Biol. 27(9):863-869. PMID: 32901160; PMC7490828.
Zhu Y, Sun D, Schertel A, Ning J, Fu X, Gwo PP, Watson AM, Zanetti-Domingues LC, Martin-Fernandez ML, Freyberg Z, Zhang P. (2020) Serial cryoFIB/SEM reveals cytoarchitectural disruptions in Leigh Syndrome patient cells. Structure. S0969-2126(20)30374-9. PMID: 33096015; PMC7802768.
Eschbach JE, Elliott JL, Li W, Zadrozny KK, Davis K, Mohammed SJ, Lawson DQ, Pornillos O, Engelman AN, Kutluay SB. (2020) Capsid lattice destabilization leads to premature loss of the viral genome and integrase enzyme during HIV-1 infection. J Virol 95(2):e00984-20. PMID: 33115869; PMC7944438.
Xu C, Katyal N, Nesterova T, Perilla JR. (2020) Molecular determinants of Ebola nucleocapsid stability from molecular dynamics simulations. J Chem Phys. 153(15):155102. PMID: 33092380; PMC7577750.
Sutton G, Sun D, Fu X, Kotecha A, Hecksel CW, Clare DK, Zhang P, Stuart DI, Boyce M. (2020) Assembly intermediates of orthoreovirus captured in the cell. Nat Commun. 11(1):4445. PMID: 32895380; PMC7477198.
Kraus J, Gupta R, Lu M, Gronenborn AM, Akke M, Polenova T (2020) Accurate backbone 13C and 15N chemical shift tensors in galectin-3 by MAS NMR and QM/MM: details of structure and environment matter. Chemphyschem. 21(13):1436-1443. PMID: 32363727; PMC8080305.
Ilina TV, Slack RL, Guerrero M, Ishima R (2020) Effect of lysyl-tRNA synthetase on the maturation of HIV-1 reverse transcriptase. ACS Omega 5(27):16619-16627. PMID: 32685828; PMC7364630.
Sun D, Varlakhanova NV, Tornabene BA, Ramachandran R, Zhang P, Ford MGJ. (2020) The cryo-EM structure of the SNX-BAR Mvp1 tetramer. Nat Commun 11(1):1506. PMID: 32198400; PMC7083883.
Chaudhuri E, Dash S, Balasubramaniam M, Padron A, Holland J, Sowd G, Villalta F, Engelman AN, Pandhare J, Dash C. (2020) The HIV-1 capsid-binding host factor CPSF6 is post-transcriptionally regulated by the cellular microRNA miR-125b. J Biol Chem. 295(15):5081-5094. PMID: 32152226; PMC7152771.
Cook NJ, Li W, Berta D, Badaoui M, Ballandras-Colas A, Nans A, Kotecha A, Rosta E, Engelman AN, Cherepanov P. (2020) Structural basis of second-generation HIV integrase inhibitor action and viral resistance. Science. 367(6479):806-810. PMID: 32001525; PMC7023979.
Cianfrocco MA, Kellogg EH. What could go wrong? A practical guide to single-particle cryo-EM: From biochemistry to atomic models. J Chem Inf Model. 2020 May 26;60(5):2458-2469. PMID: 32078321; PMC7253330.
Pye VE, Rosa A, Bertelli C, Struwe WB, Maslen SL, Corey R, Liko I, Hassall M, Mattiuzzo G, Ballandras-Colas A, Nans A, Takeuchi Y, Stansfeld PJ, Skehel JM, Robinson CV, Pizzato M, Cherepanov P. (2020) A bipartite structural organization defines the SERINC family of HIV-1 restriction factors. Nat Struct Mol Biol. 27(1):78-83. PMID: 31907454; PMC6956856.
Dick RA, Xu C, Morado DR, Kravchuk V, Ricana CL, Lyddon TD, Broad AM, Feathers JR, Johnson MC, Vogt VM, Perilla JR, Briggs JAG, Schur FKM. (2020) Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLoS Pathog. 16(1):e1008277. PMID: 31986188; PMC7004409.
Hassan A, Quinn CM, Struppe J, Sergeyev IV, Zhang C, Guo C, Runge B, Theint T, Dao HH, Jaroniec CP, Berbon M, Lends A, Habenstein B, Loquet A, Kuemmerle R, Perrone B, Gronenborn AM, Polenova T. (2019) Sensitivity boosts by the CPMAS CryoProbe for challenging biological assemblies. J Magn Reson. 311:106680. PMID: 31951864; PMC7060763.
Struppe J, Quinn CM, Sarkar S, Gronenborn AM, Polenova T. (2020) Ultrafast 1H MAS NMR crystallography for natural abundance pharmaceutical compounds. Mol Pharm. 17(2):674-682. PMID: 31891271; PMC7307729.
Loyola L, Achuthan V, Gilroy K, Borland G, Kilbey A, Mackay N, Bell M, Hay J, Aiyer S, Fingerman D, Villanueva RA, Cameron E, Kozak CA, Engelman AN, Neil J, Roth MJ. (2019) Disrupting MLV integrase:BET protein interaction biases integration into quiescent chromatin and delays but does not eliminate tumor activation in a MYC/Runx2 mouse model. PLoS Pathog. 15(12):e1008154. PMID: 31815961; PMC6974304.
Fu X, Ning J, Zhong Z, Ambrose Z, Watkins SC, Zhang P. (2019) AutoCLEM: An automated workflow for correlative live-cell fluorescence microscopy and cryo-electron tomography. Sci Rep. 9(1):19207. PMID: 31844138; PMC6915765.
Fritz M, Kraus J, Quinn CM, Yap GPA, Struppe J, Sergeyev IV, Gronenborn AM, Polenova T. (2019) Measurement of accurate interfluorine distances in crystalline organic solids: A high-spinning MAS NMR approach. J Phys Chem B. 123(50):10680-10690. PMID: 31682453; PMC7313266.
Carlon A, Gigli L, Ravera E, Parigi G, Gronenborn AM, Luchinat C. Assessing structural preferences of unstructured protein regions by NMR. Biophys J 117(10):1948-1953. PMID: 31676138; PMC7018990.
Bryer AJ, Hadden-Perilla JA, Stone JE, Perilla JR. (2019) High-performance analysis of biomolecular containers to measure small-molecule transport, transbilayer lipid diffusion, and protein cavities. J Chem Inf Model. 59(10):4328-4338. PMID: 31525965; PMC6817393.
Byeon IL, Jung J, Byeon CH, DeLucia M, Ahn J, Gronenborn AM. (2019) Complete 1H, 13C, 15N resonance assignments and secondary structure of the Vpr binding region of hHR23A (residues 223-363). Biomol NMR Assign. 14(1):13-17. PMID: 31463759; PMC7047585.
Lu M, Ishima R, Polenova T, Gronenborn AM. (2019) 19F NMR relaxation studies of fluorosubstituted tryptophans. J Biomol NMR. 73(8-9):401-409. PMID: 31435857; PMC6878660.
Slack RL, Ilina TV, Xi Z, Giacobbi NS, Kawai G, Parniak MA, Sarafianos SG, Sluis Cremer N, Ishima R. (2019) Conformational changes in HIV-1 reverse transcriptase that facilitate its maturation. Structure. 27(10):1581-1593.e3. PMID: 3147112; PMC6774901.
Huang PT, Summers BJ, Xu C, Perilla JR, Malikov V, Naghavi MH, Xiong Y. (2019) FEZ1 is recruited to a conserved cofactor site on capsid to promote HIV-1 trafficking. Cell Rep. 28(9):2373-2385.e7. PMID: 31422020; PMC6736649.
Summers BJ, Digianantonio KM, Smaga SS, Huang PT, Zhou K, Gerber EE, Wang W, Xiong Y. (2019) Modular HIV-1 capsid assemblies reveal diverse host-capsid recognition mechanisms. Cell Host Microbe 26(2):203-216.e6. PMID: 31415753; PMC6777739.
Anderson-Daniels J, Singh PK, Sowd GA, Li W, Engelman AN, Aiken C. (2019) Dominant negative MA-CA fusion protein is incorporated into HIV-1 cores and inhibits nuclear entry of viral preintegration complexes. J Virol. 93(21):e01118-19. PMID: 31413124; PMC6803256.
Zhang P. (2019) Advances in cryo-electron tomography and subtomogram averaging and classification. Curr Opin Struct Biol. 58:249-258. PMID: 31280905; PMC6863431.
Zhang DW, Luo RH, Xu L, Yang LM, Xu XS, Bedwell GJ, Engelman AN, Zheng YT, Chang S. (2019) A HTRF based competitive binding assay for screening specific inhibitors of HIV-1 capsid assembly targeting the C-Terminal domain of capsid. Antiviral Res. 169:104544. PMID: 31254557; PMC6901019.
Smaga SS, Xu C, Summers BJ, Digianantonio KM, Perilla JR, Xiong Y. (2019) MxB Restricts HIV-1 by Targeting the Tri-hexamer Interface of the Viral Capsid. Structure. 27(8):1234-1245.e5. PMID: 31155311; PMC7183857.
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Ji X, Wu Y, Yan J, Mehrens J, Yang H, Delucia M, Hao C, Gronenborn AM, Skowronski J, Ahn J, Xiong Y. (2013) Mechanism of allosteric activation of SAMHD1 by dGTP. Nat Struct Mol Biol 20(11):1304-9. PMID: 24141705; PMC3833828.
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Kshirsagar M, Carbonell J, Klein-Seetharaman J. Multitask learning for host-pathogen protein interactions. Bioinformatics 29(13):i217-i226. PMID: 23812987; PMC3694681.
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Yan J, Kaur S, DeLucia M, Hao C, Mehrens J, Wang C, Golczak M, Palczewski K, Gronenborn AM, Ahn J, and Skowronski J. (2013) Tetramerization of SAMHD1 is required for biological activity and inhibition of HIV infection. J Biol Chem 288(15):10406-17. PMID: 23426366; PMC3624423.
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Shah VB, Shi J, Hout DR, Oztop I, Krishnan L, Ahn J, Shotwell MS, Engelman A, Aiken C. (2012) The host proteins transportin SR2/TNPO3 and Cyclophilin A exert opposing effects on HIV-1 uncoating. J Virol. 87(1):422-32. PMC3536424 Free Text
Yang H, Ji X, Zhao G, Ning J, Zhao Q, Aiken C, Gronenborn AM, Zhang P, Xiong Y. (2012) Structural insight into HIV-1 capsid recognition by rhesus TRIM5α. Proc Natl Acad Sci USA. 109(45):18372-7. PMC3494900 Free Text
Hou G, Byeon IJ, Ahn J, Gronenborn AM, Polenova T. (2012) Recoupling of chemical shift anisotropy by R-symmetry sequences in magic angle spinning NMR spectroscopy. J Chem Phys. 137(13):134201. PMID: 23039592; PMC3477183 Free Text
Meng X, Zhao G, Yufenyuy E, Ke D, Ning J, Delucia M, Ahn J, Gronenborn AM, Aiken C, Zhang P. (2012) Protease cleavage leads to formation of mature trimer interface in HIV-1 capsid. PLoS Pathog. 8(8):e1002886. PMID: 22927821; PMC3426514.
Yeh JI, Levine AS, Du S, Chinte U, Ghodke H, Wang H, Shi H, Hsieh CL, Conway JF, Van Houten B, Rapić-Otrin V. (2012) Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair. Proc Natl Acad Sci U S A. 109(41):E2737-46. PMID: 22822215; PMC3478663.
Strunk KM, Wang K, Ke D, Gray JL, Zhang P. (2012) Thinning of large mammalian cells for cryo-TEM characterization by cryo-FIB milling. J Microsc. 247(3): 220. PMID: 22906009; PMC3748363.
Paramasivam S, Suiter CL, Hou G, Sun S, Palmer M, Hoch JC, Rovnyak D, Polenova T. (2012) Enhanced sensitivity by nonuniform sampling enables multidimensional MAS NMR spectroscopy of protein assemblies. J Phys Chem B. 116(25): 7416. PMID: 22667827; PMC3386641. Free Text
Wang K, Strunk K, Zhao G, Gray JL, Zhang P. (2012) 3D structure determination of native mammalian cells using cryo-FIB and cryo-electron tomography. J Struct Biol 180(2):318-26. PMID: 22796867; PMC3483467.
Yang R, Shi J, Byeon IL, Ahn J, Sheehan JH, Meiler J, Gronenborn AM, Aiken C. (2012) Second-site suppressors of HIV-1 capsid mutations: restoration of intracellular activities without correction of intrinsic capsid stability defects. Retrovirology 9(1): 30. PMID: 22515365; PMC3351742.
Byeon IL, Hou G, Han Y, Suiter CL, Ahn J, Jung J, Byeon CH, Gronenborn AM, Polenova TE. (2012) Motions on the millisecond timescale and multiple conformations of HIV-1 capsid protein: implications for structural polymorphism of CA assemblies. J Am Chem Soc, 134 (14) 6455-6466; PMID: 2242857; PMC3325613.
Pene-Dumitrescu T, Shu ST, Wales TE, Alvarado JJ, Shi H, Narute P, Moroco JA, Yeh JI, Engen JR, Smithgall TE. (2012) HIV-1 Nef interaction influences the ATP-binding site of the Src-family kinase, Hck. BMC Chem Biol, 12(1):1. PMID: 22420777; PMC3328272.
Ahn J, Hao C, Yan J, DeLucia M, Mehrens J, Wang C, Gronenborn AM, Skowronski J. (2012) HIV/SIV accessory virulence factor Vpx loads the host cell restriction factor SAMHD1 onto the E3 ubiquitin ligase complex CRL4DCAF1. J Biol Chem, 287:12550. PMID: 22362772; PMC3321004.
Krzysiak TC, Jung J, Thompson J, Baker D, Gronenborn AM. (2012) APOBEC2 is a monomer in solution: implications for APOBEC3G models. Biochemistry 51(9) 2008-17. PMID: 22339232; PMC3316327.
Ambrose Z, Lee K, Ndjomou J, Xu H, Oztop I, Matous J, Takemura T, Unutmaz D, Engelman A, Hughes SH, Kewalramani VN. (2012) Human immunodeficiency virus type 1 (HIV-1) capsid mutation N74D alters cyclophilin A dependence and impairs macrophage infection. J Virol. 86(8):4708-14. PMID: 22301145; PMC3318671.
Nouretdinov I, Gammerman A, Qi Y, Klein-Seetharaman J. (2012) Determining confidence of predicted interactions between HIV-1 and human proteins using conformal method. Pac Symp Biocomput 2012: 311-22. PMID: 22174286; PMC3249613.
Sun S, Han Y, Paramasivam S, Yan S, Siglin AE, Williams JC, Byeon IJ, Ahn J, Gronenborn AM, Polenova T. (2012) Solid-state NMR spectroscopy of protein complexes. Methods Mol Biol 831:303-31. PMID: 22167681; PMC4890720.
Jun S, Ke D, Debiec K, Zhao G, Meng X, Ambrose Z, Gibson GA, Watkins SC, and Zhang P. (2011) Direct visualization of HIV-1 with correlative live-cell microscopy and cryo-electron tomography. Structure 19 (11): 1573-1581. PMID: 22078557; PMC3217200.
Meng X, Zhao G, and Zhang P. (2011) Structure of HIV-1 capsid assemblies by cryo-electron microscopy and iterative helical real-space reconstruction. J Vis Exp (54):3041. PMID: 21860371; PMC3211131.
Zhao G, Ke D, Vu T, Ahn J, Shah VB, Yang R, Aiken C, Charlton LM, Gronenborn AM and Zhang P. (2011) Rhesus TRIM5α disrupts the HIV-1 capsid at the interhexamer interfaces. PLoS Path 7(3): e1002009. PMID: 21455494; PMC3063768.
Jung J, Byeon IJ, Ahn J, Gronenborn AM. (2011) Structure, dynamics, and Hck interaction of full-length HIV-1 Nef proteins. Proteins 79 (5): 1609-1622. PMID: 21365684; PMC3076547.
Du S, Betts L, Yang R, Shi H, Concel J, Ahn J, Aiken C, Zhang P, Yeh JI. (2011) Structure of the HIV-1 full-length capsid protein in a conformationally trapped unassembled state induced by small-molecule binding. J Mol Biol. 406, 371-386. PMID: 21146540; PMC3194004.
Hou G, Byeon IL, Ahn J, Concel J, Samoson A, Gronenborn AM, Polenova T. (2011) Spin diffusion driven by R-symmetry sequences: Applications to homonuclear correlation spectroscopy in MAS NMR of biological and organic solids. J Am Chem Soc 133, 3943-53. PMID: 21361320; PMC3148607.
Ahn J, Novince Z, Concel J, Byeon CH, Makhov AM, Byeon IJ, Zhang P, Gronenborn AM. (2011) The cullin-RING E3 ubiquitin ligase CRL4-DCAF1 complex dimerizes via a short helical region in DCAF1. Biochemistry. 50, 1359-1367. PMID: 21226479; PMC3072279.
Hou G, Byeon IL, Ahn J, Gronenborn AM, Polenova T. (2011) 1H-13C/1H-15N heteronuclear dipolar recoupling by R-symmetry sequences under fast magic angle spinning for dynamics analysis of biological and organic solids. J Am Chem Soc 133 (46), 18646-18655. PMID: 21995349; PMC3218250.
Zhao Z, Xia J, Tastan O, Singh I, Kshirsagar M, Carbonell J, Klein-Seetharaman J. (2011) Virus interactions with human signal transduction pathways. Int J Comput Biol Drug Des 4 (1): 83-105. PMID: 21330695; PMC3407688.
Alvarado JJ, Betts L, Moroco JA, Smithgall TE, and Yeh JI. (2010) Crystal structure of the Src-family kinase Hck SH3-SH2-linker regulatory region supports an SH3-dominant activation mechanism. J Biol Chem 285, 35455-35461. PMID: 2081066; PMC2975169.
Hou G, Paramasivam S, Byeon IL, Gronenborn AM, Polenova T. (2010) Determination of relative tensor orientations by γ-encoded chemical shift anisotropy/heteronuclear dipolar coupling 3D NMR spectroscopy in biological solids. Phys Chem Chem Phys 12, 14873-14883. PMID: 20936218; PMC3160241.
Ahn J, Vu T, Novince Z, Guerrero-Santoro J, Rapic-Otrin V, Gronenborn AM. (2010) HIV-1 Vpr loads uracil DNA glycosylase-2 onto DCAF1, a substrate recognition subunit of a cullin 4A-ring E3 ubiquitin ligase for proteasome-dependent degradation. J Biol Chem. 285, 37333-37341. PMID: 20870715; PMC2988339.
Dikeakos JD, Atkins KM, Thomas L, Emert-Sedlak L, Byeon, IL, Jung J, Ahn J, Wortmann WD, Kukull B, Saito M, Koizumi H, Williamson DM, Hiyoshi M, Barklis E, Takiguchi M, Suzu S, Gronenborn AM, Smithgall TE and Thomas G. (2010) Small molecule inhibition of HIV-1-induced MHC-I downregulation identifies a temporally regulated switch in Nef action. Mol Biol Cell, 21, 3279-92. PMID: 20702582; PMC2947465.
Ahn J, Byeon IJ, Dharmasena S, Huber K, Concel J, Gronenborn AM, Sluis-Cremer N. (2010) The RNA binding protein HuR does not interact directly with HIV-1 reverse transcriptase and does not affect reverse transcription in vitro. Retrovirology 7:40. PMID: 20459669; PMC2873509.
Han Y, Ahn J, Concel J, Byeon IL, Gronenborn AM, Yang J, Polenova T. (2010) Solid-State NMR studies of HIV-1 capsid protein assemblies. J Am Chem Soc, 132,1976-1987. PMID: 20092249; PMC2829833.
Jung J, Byeon IJ, Ahn J, Concel J, Gronenborn AM. (2010) 1H, 15N and 13C assignments of the dimeric C-terminal domain of HIV-1 capsid protein. Biomol NMR Assign 4:21-23. PMID: 19921549; PMC3448961.
Venkatachari, N.J., Walker, L.A., Tastan, O., Le, T., Dempsey, T.M., Li, Y., Yanamala, N., Srinivasan, A., Klein-Seetharaman, J., Montelaro, R.C., and Ayyavoo, V. (2010) Human immunodeficiency virus type 1 Vpr: oligomerization is an essential feature for its incorporation into virus particles. Virol J. 7, 119. PMID: 20529298; PMC2894018.
Qi Y, Tastan O, Carbonell JG, Klein-Seetharaman J, Weston J (2010) Semi-supervised multi-task learning for predicting interactions between HIV-1 and human proteins. Bioinformatics 26 (18): i645-i652. PMID: 20823334; PMC2935441.
Byeon IJ, Meng X, Jung J, Zhao G, Yang R, Ahn J, Shi J, Concel J, Aiken C, Zhang P, Gronenborn AM. (2009) Structural convergence between Cryo-EM and NMR reveals intersubunit interactions critical for HIV-1 capsid function. Cell 139:780-790. PMID: 19914170; PMC2782912. Also see commentary in Viruses.
Iwatani Y, Chan DS, Liu L, Yoshii H, Shibata J, Yamamoto N, Levin JG, Gronenborn AM, Sugiura W. (2009) HIV-1 Vif-mediated ubiquitination/degradation of APOBEC3G involves four critical lysine residues in its C-terminal domain. Proc Natl Acad Sci USA 106:19539-19544. PMID: 19887642; PMC2772817.
Wang J, Zuo X, Yu P, Byeon IJ, Jung J, Wang X, Dyba M, Seifert S, Schwieters CD, Qin J, Gronenborn AM, Wang YX. (2009) Determination of multicomponent protein structures in solution using global orientation and shape restraints. J Am Chem Soc 131:10507-10515. PMID: 19722627; PMC2873192.
Tastan O, Qi Y, Carbonell JG, Klein-Seetharaman J. (2009) Prediction of interactions between HIV-1 and human proteins by information integration. Pac Symp Biocomput 2009:516-27. PMID: 19209727; PMC3263379.
Balakrishnan S, Tastan O, Carbonell J, Klein-Seetharaman J. (2009) Alternative paths in HIV-1 targeted human signal transduction pathways. BMC Genomics 10 Suppl 3:S30. PMID: 19958495; PMC2788384.