Projects

The mission of the Pittsburgh Center for HIV Protein Interactions (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 (intracellular trafficking, uncoating, restriction, reverse transcription, nuclear import, etc). Current projects are focused on CA and capsid interactions, the structure of Vpr and its interactions with host DNA repair machinery, reverse transcriptase interactions, the biology and structure of CPSF6 and TNPO3, retroviral intasome structure, and biochemical and proteomic analyses of the HIV-1 pre-integration complex. Further we have two technology development programs, one to develop nanocrystal screening specifically for MicroElectron Diffraction and the other to develop ultra-fast MAS NMR methods for structure determination of native particles.

Publications

*Sowd GA, Shi J, Aiken C. HIV-1 CA inhibitors are antagonized by inositol phosphate stabilization of the viral capsid in cells. J Virol. 2021 Oct 6:JVI0144521. doi: 10.1128/JVI.01445-21. Epub ahead of print. PMID: 34613803.
*Maertens GN, Engelman AN, Cherepanov P. Structure and function of retroviral integrase. Nat Rev Microbiol. 2021 Jul 9;. doi: 10.1038/s41579-021-00586-9. [Epub ahead of print] Review. PubMed PMID: 34244677; NIHMSID:NIHMS1747709.
*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.
*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.
*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, 2021, 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. doi: 10.1128/mBio.03142-20. 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
*Assembly intermediates of orthoreovirus captured in the cell. 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
*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. 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. 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. 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. doi: 10.1021/acs.jcim.9b01178. Epub 2020 Mar 9. 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. 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. 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. 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.
*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. 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. 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. 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. 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 Free Text 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. Free Text PMC7183857
*Siddiqui MA, Saito A, Halambage UD, Ferhadian D, Fischer DK, Francis AC, Melikyan GB, Ambrose Z, Aiken C, Yamashita M. (2019) A novel phenotype links HIV-1 capsid stability to cGAS-mediated DNA sensing. J Virol. 93(16). pii: e00706-19. PMC6675898 Free Text
*Gupta R, Zhang H, Lu M, Hou G, Caporini M, Rosay M, Maas W, Struppe J, Ahn J, Byeon IL, Oschkinat H, Jaudzems K, Barbet-Massin E, Emsley L, Pintacuda G, Lesage A, Gronenborn AM, Polenova T. (2019) Dynamic nuclear polarization magic angle spinning NMR combined with MD simulations permits detection of order and disorder in viral assemblies. J Phys Chem B. 123(24):5048-5058.  PMC6767624
*Brigham BS, Kitzrow JP, Reyes JC, Musier-Forsyth K, Munro JB. (2019) Intrinsic conformational dynamics of the HIV-1 genomic RNA 5'UTR. Proc Natl Acad Sci U S A. 116(21):10372-10381. PMC6534999 Free Text
*Yan J, Shun MC, Zhang Y, Hao C, Skowronski J. (2019) HIV-1 Vpr counteracts HLTF-mediated restriction of HIV-1 infection in T cells. Proc Natl Acad Sci U S A. 116(19):9568-9577. PMC6511057 Free Text
*Barnes CO, Wu Y, Song J, Lin G, Baxter EL, Brewster AS, Nagarajan V, Holmes A, Soltis SM, Sauter NK, Ahn J, Cohen AE, Calero G. (2019) The crystal structure of dGTPase reveals the molecular basis of dGTP selectivity. Proc Natl Acad Sci U S A. 116(19):9333-9339. PMC6511015 Free Text
*Peng W, Shi J, Márquez CL, Lau D, Walsh J, Faysal KMR, Byeon CH, Byeon IL, Aiken C, Böcking T. (2019) Functional analysis of the secondary HIV-1 capsid binding site in the host protein cyclophilin A. Retrovirology 16(1):10. PMC6449974 Free Text
*Jang S, Cook NJ, Pye VE, Bedwell GJ, Dudek AM, Singh PK, Cherepanov P, Engelman AN. (2019) Differential role for phosphorylation in alternative polyadenylation function versus nuclear import of SR-like protein CPSF6. Nucleic Acids Res. 47(9):4663-4683. PMC6511849 Free Text
*Lu M, Wang M, Sergeyev IV, Quinn CM, Struppe J, Rosay M, Maas W, Gronenborn AM, Polenova T. (2019) (19)F Dynamic nuclear polarization at fast magic angle spinning for NMR of HIV-1 capsid protein assemblies. J Am Chem Soc. 141(14):5681-5691. PMC6521953 Free Text
*Russell RW, Fritz MP, Kraus J, Quinn CM, Polenova T, Gronenborn AM. (2019) Accuracy and precision of protein structures determined by magic angle spinning NMR spectroscopy: for some 'with a little help from a friend'. J Biomol NMR. 2019 Jul;73(6-7):333-346. PMID: 30847635; PMC6693955.
*Fischer DK, Saito A, Kline C, Cohen R, Watkins SC, Yamashita M, Ambrose Z. (2019) CA mutation N57A has distinct strain-specific HIV-1 capsid uncoating and infectivity phenotypes. J Virol. 93(9). pii: e00214-19. PMC6475785 Free Text
*Balasubramaniam M, Zhou J, Addai A, Martinez P, Pandhare J, Aiken C, Dash C. (2019) PF74 inhibits HIV-1 integration by altering the composition of the preintegration complex. J Virol. 93(6) pii: e01741-18. PMC6401427 Free Text
*Fast magic angle spinning ¹⁹F NMR of HIV-1 capsid protein assemblies. (2018) Wang M, Lu M, Fritz M, Quinn C, Byeon IJ, Byeon CH, Struppe J, Maas W, Gronenborn A, Polenova T. Angew Chem Int Ed Engl. 57(50):16375-16379. PMC6279522 Free Text
*Dynamic regulation of HIV-1 capsid interaction with the restriction factor TRIM5α identified by magic-angle spinning NMR and molecular dynamics simulations. (2018) Quinn CM, Wang M, Fritz MP, Runge B, Ahn J, Xu C, Perilla JR, Gronenborn AM, Polenova T. Proc Natl Acad Sci U S A. 115(45):11519-11524. PMC6233135 Free Text
*HIV-1 Vpr reprograms CLR4(DCAF1) E3 ubiquitin ligase to antagonize Exonuclease 1-mediated restriction of HIV-1 infection. (2018) Yan J, Shun MC, Hao C, Zhang Y, Qian J, Hrecka K, DeLucia M, Monnie C, Ahn J, Skowronski J. MBio. 2018 Oct 23;9(5). pii: e01732-18. doi: 10.1128/mBio.01732-18. PMC6199497.  Free Text
*Fast Magic Angle Spinning ¹⁹F NMR of HIV-1 Capsid Protein Assemblies. (2018) Wang M, Lu M, Fritz M, Quinn C, Byeon IJ, Byeon CH, Struppe J, Maas W, Gronenborn A, Polenova T.  Angew Chem Int Ed Engl. 57(50):16375-16379.  PMC6279522 Free Text
*Structures of the fungal dynamin-related protein Vps1 reveal a unique, open helical architecture. (2018) Varlakhanova NV, Alvarez FJD, Brady TM, Tornabene BA, Hosford CJ, Chappie JS, Zhang P, Ford MGJ. J Cell Biol 217(10):3608-3624. PMC6168280 Free Text
*All-atom virus simulations. (2018) Hadden JA and Perilla JR. Curr Opin Virol. 31:82-91. PMC6456034 Free Text
*Inositol phosphates are assembly co-factors for HIV-1. (2018) Dick RA, Zadrozny KK, Xu C, Schur FKM, Lyddon TD, Ricana CL, Wagner JM, Perilla JR, Ganser-Pornillos BK, Johnson MC, Pornillos O, Vogt VM. Nature 560(7719):509-512. PMC6242333 Free Text
*Critical Role of the Human T-Cell Leukemia Virus Type 1 Capsid N-Terminal Domain for Gag-Gag Interactions and Virus Particle Assembly. (2018) Martin JL, Mendonça LM, Marusinec R, Zuczek J, Angert I, Blower RJ, Mueller JD, Perilla JR, Zhang W, Mansky LM. J Virol. 2018 Jun 29;92(14). pii: e00333-18. PMC6026748 Free Text
*Binding thermodynamics of metal ions to HIV-1 ribonuclease H domain. (2019) Oda M, Xi Z, Inaba S, Slack RL, Ishima R. J Therm Anal Calorim. 2019 Mar;135(5):2647-2653. PMC6402781 Free Text
*19F Magic angle spinning NMR spectroscopy and density functional theory calculations of fluorosubstituted tryptophans: Integrating experiment and theory for accurate determination of chemical shift tensors. (2018) Lu M, Sarkar S, Wang M, Kraus J, Fritz M, Quinn CM, Bai S, Holmes ST, Dybowski C, Yap GPA, Struppe J, Sergeyev IV, Maas W, Gronenborn AM, Polenova, T. J Phys Chem B 122(23):6148-6155. PMC6203958 Free Text
*Truncated CPSF6 forms higher order complexes that bind and disrupt HIV-1 capsid. (2018) Ning J, Zhong Z, Fischer DK, Harris G, Watkins SC, Ambrose Z, Zhang P. J Virol. 2018 Apr 11. pii: JVI.00368-18. doi: 10.1128/JVI.00368-18.  PMC6002704  Free Text
*emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging. (2018) Himes B, Zhang P. Nat Methods. 15(11):955-961. PMC6281437  Free Text
*Backbone amide 15N chemical shift tensors report on hydrogen bonding interactions in proteins: A magic angle spinning NMR study. (2018) Paramasivam S, Gronenborn AM, Polenova T. (2018) Solid State Nucl Magn Reson. 92:1-6.  PMC6261280 Free Text
*Determination of accurate backbone chemical shift tensors in microcrystalline proteins by integrating MAS NMR and QM/MM. (2018) Fritz M, Quinn CM, Wang M, Hou G, Lu X, Koharudin LMI, Struppe J, Case DA, Polenova T, Gronenborn AM. Phys Chem Chem Phys. 20(14):9543-9553. PMC5892194 Free Text
*Chemical shifts of the carbohydrate binding domain of Galectin-3 from magic angle spinning NMR and hybrid quantum mechanics/molecular mechanics calculations. (2018) Kraus J, Gupta R, Yehl J, Lu M, Case DA, Gronenborn AM, Akke M, Polenova T. J Phys Chem B. 122(11):2931-2939. PMC5892201 Free Text
*Quenching protein dynamics interferes with HIV capsid maturation. (2017) Wang M, Quinn CM, Perilla JR, Zhang H, Shirra R Jr, Hou G, Byeon IJ, Suiter CL, Ablan S, Urano E, Nitz TJ, Aiken C, Freed EO, Zhang P, Schulten K, Gronenborn AM, Polenova T. Nat Commun. 8(1):1779. PMC5701193 Free Text
*The HIV-1 p66 homodimeric RT exhibits different conformations in the binding-competent and -incompetent NNRTI site. (2017) Sharaf NG, Xi Z, Ishima R, Gronenborn AM.  Proteins 85(12):2191-2197. PMC5751703 Free Text 
*HIV-1 Vpr protein directly loads helicase-like transcription factor (HLTF) onto the CRL4-DCAF1 E3 ubiquitin ligase. (2017) Zhou X, DeLucia M, Hao C, Hrecka K, Monnie C, Skowronski J, Ahn J. J Biol Chem 292(51):21117-21127. PMC5743084 Free Text
*Capsid-dependent host factors in HIV-1 infection. (2017) Yamashita M, Engelman AN. Trends Microbiol. 25(9):741-755. PMC5562514 Free Text
*CryoEM structure of MxB reveals a novel oligomerization interface critical for HIV restriction. (2017) Alvarez FJD, He S, Perilla JR, Jang S, Schulten K, Engelman AN, Scheres SHW, Zhang P. Sci Adv. 3(9):e1701264. PMC5600524 Free Text
*Interferon-inducible CD169/Siglec1 attenuates anti-HIV-1 effects of IFN-α. (2017) Akiyama H, Ramirez NP, Gibson G, Kline C, Watkins S, Ambrose Z, Gummuluru S.  J Virol. 91(21). pii: e00972-17. PMC5640826 Free Text
*Expanding the horizons for structural analysis of fully protonated protein assemblies by NMR spectroscopy at MAS frequencies above 100 kHz. (2017) Struppe J, Quinn CM, Lu M, Wang M, Hou G, Lu X, Kraus J, Andreas LB, Stanek J, Lalli D, Lesage A, Pintacuda G, Maas W, Gronenborn AM, Polenova T. (2017) Solid State Nucl Magn Reson. pii: S0926-2040(17)30048-6. PMC5824719 Free Text
*Structural basis for spumavirus GAG tethering to chromatin. (2017) Lesbats P, Serrao E, Maskell DP, Pye VE, O'Reilly N, Lindemann D, Engelman AN, Cherepanov P. Proc Natl Acad Sci U S A. 114(21):5509-5514. PMC5448199 Free Text
*CryoEM structure refinement by integrating NMR chemical shifts with molecular dynamics simulations. (2017) Perilla JR, Zhao G, Lu M, Ning J, Hou G, Byeon IL, Gronenborn AM, Polenova T, Zhang P. J Phys Chem B. 121(15):3853-3863.  PMC5459578 Free Text
*Inhibition of HIV-1 maturation via small molecule targeting of the amino-terminal domain in the viral capsid protein. (2017) Wang W, Zhou J, Halambage UD, Jurado KA, Jamin AV, Wang Y, Engelman AN, Aiken C. J Virol. 91(9). pii: e02155-16. PMC5391466 Free Text
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*A supramolecular assembly mediates lentiviral DNA integration. Ballandras-Colas A, Maskell DP, Serrao E, Locke J, Swuec P, Jónsson SR, Kotecha A, Cook NJ, Pye VE, Taylor IA, Andrésdóttir V, Engelman AN, Costa A, Cherepanov P. Science. 2017 Jan 6;355(6320):93-95. PMC5321526 Free Text
*Toward closing the gap: Quantum mechanical calculations and experimentally measured chemical shifts of a microcrystalline lectin. Fritz M, Quinn CM, Wang M, Hou G, Lu X, Koharudin LM, Polenova T, Gronenborn AM. J Phys Chem B.121(15):3574-3585  PMC5465307 Free Text
*A supramolecular assembly mediates lentiviral DNA integration. Ballandras-Colas A, Maskell DP, Serrao E, Locke J, Swuec P, Jónsson SR, Kotecha A, Cook NJ, Pye VE, Taylor IA, Andrésdóttir V, Engelman AN, Costa A, Cherepanov P. Science. 2017 Jan 6;355(6320):93-95. PMC5321526 Free Text
*In vitro protease cleavage and computer simulations reveal the HIV-1 capsid maturation pathway. (2016) Ning J, Erdemci-Tandogan G, Yufenyuy EL, Wagner J, Himes BA, Zhao G, Aiken C, Zandi R, Zhang P. Nat Commun. 7:13689. PMC5159922 Free Text
*NMR structure of the HIV-1 reverse transcriptase thumb subdomain. (2016) Sharaf NG, Brereton AE, Byeon IL, Andrew Karplus P, Gronenborn AM. J Biomol NMR. 66(4):273-280.  PMC5218889 Free Text
*HIV-1 capsid function is regulated by dynamics: Quantitative atomic-resolution insights by integrating magic-angle-spinning NMR, QM/MM, and MD. (2016) Zhang H, Hou G, Lu M, Ahn J, Byeon IL, Langmead CJ, Perilla JR, Hung I, Gor'kov PL, Gan Z, Brey WW, Case DA, Schulten K, Gronenborn AM, Polenova T. J Am Chem Soc. 138(42):14066-14075. PMC5380593 Free Text
*The DDB1-DCAF1-Vpr-UNG2 crystal structure reveals how HIV-1 Vpr steers human UNG2 toward destruction. (2016) Wu Y, Zhou X, Barnes CO, DeLucia M, Cohen AE, Gronenborn AM, Ahn J, Calero G. Nat Struct Mol Biol. 23,  933–940  PMC5385928 Free Text
*SLX4/SLX1 independent downregulation of MUS81/EME1 by HIV-1 Vpr. (2016) Zhou X, DeLucia M, Ahn J. J Biol Chem 291(33):16936-47. PMC5016100 Free Text
*Time-resolved imaging of single HIV-1 uncoating in vitro and in living cells. (2016) Francis AC, Marin M, Shi J, Aiken C, Melikyan GB. PLoS Pathog 12(6):e1005709. PMC4913920 Free Text
*HIV-1 and HIV-2 exhibit divergent interactions with HLTF and UNG2 DNA repair proteins. (2016) Hrecka K, Hao C, Shun MC, Kaur S, Swanson SK, Florens L, Washburn MP, Skowronski J. Proc Natl Acad Sci U S A 113(27):E3921-30. PMC4941427 Free Text
*Establishment and reversal of HIV-1 latency in naïve and central memory CD4+ T cells in vitro. (2016) Zerbato JM, Serrao E, Lenzi G, Kim B, Ambrose Z, Watkins SC, Engelman AN, Sluis-Cremer N. J Virol. 90(18):8059-73. PMC5008097 Free Text
*Conformational plasticity of the NNRTI-binding pocket in HIV-1 reverse transcriptase: A fluorine nuclear magnetic resonance study. (2016) Sharaf NG, Ishima R, Gronenborn AM. Biochemistry. 2016 Jul 19;55(28):3864-73. PMC4955860 Free Text
*Nuclear magnetic resonance structure of the APOBEC3B catalytic domain: Structural basis for substrate binding and DNA deaminase activity. (2016) Byeon IL, Byeon CH, Wu T, Mitra M, Singer D, Levin JG, Gronenborn AM. Biochemistry 55(21):2944-59.  PMC4943463 Free Text
*Transmission electron microscopy for the evaluation and optimization of crystal growth. Stevenson HP, Lin G, Barnes CO, Sutkeviciute I, Krzysiak T, Weiss SC, Reynolds S, Wu Y, Nagarajan V, Makhov AM, Lawrence R, Lamm E, Clark L, Gardella TJ, Hogue BG, Ogata CM, Ahn J, Gronenborn AM, Conway JF, Vilardaga JP, Cohen AE, Calero G. (2016) Acta Crystallogr D Struct Biol. 72(Pt 5):603-15. PMC4854312   Free Text
*Click labeling of unnatural sugars metabolically incorporated into viral envelope glycoproteins enables visualization of single particle fusion. Oum YH, Desai TM, Marin M, Melikyan GB.  (2016) J Virol Methods 233:62-71. PMC5161462 Free Text
*Roles of capsid-interacting host factors in multimodal inhibition of HIV-1 by PF74.  Saito A, Ferhadian D, Sowd GA, Serrao E, Shi J, Halambage UD, Teng S, Soto J, Siddiqui MA, Engelman AN, Aiken C, Yamashita M. (2016) J Virol 90(12):5808-23. PMC4886767 Free Text
*Molecular architecture of the retroviral capsid. Perilla JR, Gronenborn AM. (2016) Trends Biochem Sci 41(5):410-20. PMC4879823 Free Text
*The Cleavage and Polyadenylation Specific Factor 6 (CPSF6) subunit of the capsid-recruited pre-messenger RNA Cleavage Factor I (CFIm) complex mediates HIV-1 integration into genes.  Rasheedi S, Shun MC, Serrao E, Sowd GA, Qian J, Hao C, Dasgupta T, Engelman AN, Skowronski J. (2016) J Biol Chem 291(22):11809-19. PMC4882448 Free Text
*Analysis of the mechanical properties of wild type and hyperstable mutants of the HIV-1 capsid. Ramalho R, Rankovic S, Zhou J, Aiken C, Rousso I. (2016) Retrovirology 13(1):17.  PMC4793510 Free Text
*Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site. Liu C, Perilla JR, Ning J, Lu M, Hou G, Ramalho R, Himes BA, Zhao G, Bedwell GJ, Byeon IJ, Ahn J, Gronenborn AM, Prevelige PE, Rousso I, Aiken C, Polenova T, Schulten K, Zhang P. (2016) Nat Commun 7:10714. PMC4785225 Free Text
*Cryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function. Ballandras-Colas A, Brown M, Cook NJ, Dewdney TG, Demeler B, Cherepanov P, Lyumkis D, Engelman AN. Nature 2016; 530:358-61. PMC4908968 Free Text
*Dynamic nuclear polarization enhanced MAS NMR for structural analysis of HIV-1 protein assemblies. Gupta R, Lu M, Hou G, Caporini MA, Rosay M, Maas WE, Struppe JO, Suiter CL, Ahn J, Byeon IL, Franks WT, Orwick-Rydmark M, Bertarello A, Oschkinat H, Lesage A, Pintacuda G, Gronenborn AM, Polenova TE. (2016) J Phys Chem B 120(2):329-39. PMC4890707 Free Text
*Dynamic allostery governs cyclophilin A-HIV capsid interplay. Lu M, Hou G, Zhang H, Suiter CL, Ahn J, Byeon IL, Perilla JR, Langmead CJ, Hung I, Gor'kov PL, Gan Z, Brey W, Aiken C, Zhang P, Schulten K, Gronenborn AM, Polenova T. (2015) Proc Natl Acad Sci U S A. 112(47):14617-22. PMC4664340  Free Text
*Fluorescent protein-tagged Vpr dissociates from HIV-1 core after viral fusion and rapidly enters the cell nucleus. Desai TM, Marin M, Sood C, Shi J, Nawaz F, Aiken C, Melikyan GB. (2015) Retrovirology 12(1):88. PMC4625717 Free Text
*Analysis of local molecular motions of aromatic sidechains in proteins by 2D and 3D fast MAS NMR spectroscopy and quantum mechanical calculations. Paluch P, Pawlak T, Jeziorna A, Trébosc J, Hou G, Vega AJ, Amoureux JP, Dracinsky M, Polenova T, Potrzebowski MJ. (2015) Phys Chem Chem Phys 17(43):28789-801. PMC4890705 Free Text
*RF inhomogeneity and how it controls CPMAS. Gupta R, Hou G, Polenova T, Vega AJ. (2015) Solid State Nuclear Magnetic Resonance. 72:17-26.  PMC4674349. Free Text
*Temporal transcriptional response to latency reversing agents identifies specific factors regulating HIV-1 viral transcriptional switch. Venkatachari NJ, Zerbato JM, Jain S, Mancini AE, Chattopadhyay A, Sluis-Cremer N, Bar-Joseph Z, Ayyavoo V. (2015) Retrovirology  12(1):85. PMC459464 Free Text
*Sensitivity of nonuniform sampling NMR. Palmer MR, Suiter CL, Henry GE, Rovnyak J, Hoch JC, Polenova T, Rovnyak D. (2015) J Physical Chem B 119(22):6502-15. PMC4857715 Free Text
*Combined zero-quantum and spin-diffusion mixing for efficient homonuclear correlation spectroscopy under fast MAS: broadband recoupling and detection of long-range correlations. Lu X, Guo C, Hou G, Polenova T. (2015) J Biomol NMR 61(1):7-20. PMC4485404 Free Text
*Structural integrity of the ribonuclease H domain in HIV-1 reverse transcriptase. Slack RL, Spiriti J, Ahn J, Parniak MA, Zuckerman DM, Ishima R. (2015) Proteins 83(8):1526-38. PMC4509971 Free Text
*Structural basis for retroviral integration into nucleosomes. Maskell DP, Renault L, Serrao E, Lesbats P, Matadeen R, Hare S, Lindemann D, Engelman AN, Costa A, Cherepanov P.  (2015) Nature 523(7560):366-9.  PMC4530500 Free Text
*Structural basis of clade-specific engagement of SAMHD1 restriction factors by lentiviral Vpx virulence factors. Wu Y, Koharudin LM, Mehrens J, DeLucia M, Byeon CH, Byeon IJ, Calero G, Ahn J, Gronenborn AM. (2015) J Biol Chem 290(29):17935-45. PMC4505041 Free Text
*Cyclin A2 - CDK regulates SAMHD1 phosphohydrolase domain. Yan J, Hao C, DeLucia M, Swanson S, Florens L, Washburn MP, Ahn J, Skowronski J. (2015) J Biol Chem 290(21):13279-92.  PMC4505580  Free Text
*MAS NMR of HIV-1 protein assemblies. Suiter CL, Quinn CM, Lu M, Hou G, Zhang H, Polenova T. (2015) J Magn Reson. 253:10-22. PMC4432874 Free Text
*Magic angle spinning NMR of viruses. Quinn CM, Lu M, Suiter CL, Hou G, Zhang H, Polenova T. (2015) Prog Nucl Magn Reson Spectrosc 86-87C: 21-40. PMC4413014 Free Text
*Sequence and structural determinants of human APOBEC3H deaminase and anti-HIV-1 activities. Mitra M, Singer D, Mano Y, Hritz J, Nam G, Gorelick RJ, Byeon IL, Gronenborn AM, Iwatani Y, Levin JG. (2015) Retrovirology 12:3. PMC4323217. Free Text
*Correlative fluorescence and electron microscopy. (2014) Schirra RT Jr, Zhang P. Curr Protoc Cytom 70:12. PMC4211606. Free Text

*Structural insight into HIV-1 restriction by MxB. Fribourgh JL, Nguyen HC, Matreyek KA, Alvarez FJ, Summers BJ, Dewdney TG, Aiken C, Zhang P, Engelman A, Xiong Y. (2014) Cell Host Microbe 16(5):627-38. PMC4252739 Free Text

*Structural basis of allosteric activation of Sterile Alpha Motif and Histidine-Aspartate Domain containing protein 1 (SAMHD1) by nucleoside triphosphates. (2014) Koharudin LM, Wu Y, DeLucia M, Mehrens J, Gronenborn AM, Ahn J. (2014) J Biol Chem 289(47):32617-27. PMC4239615 Free Text

*Accurate measurement of heteronuclear dipolar couplings by phase-alternating R-symmetry (PARS) sequences in magic angle spinning NMR spectroscopy. Hou G, Lu X, Vega AJ, Polenova T. (2014) J Chem Phys 141(10):104202. PMC4162908 Free Text

*Interaction with the SH3-SH2 region of the Src-family kinase Hck structures the HIV-1 Nef dimer for kinase activation and effector recruitment. Alvarado JJ, Tarafdar S, Yeh JI, Smithgall TE. (2014) J Biol Chem 289(41):28539-53. PMC4192505 Free Text

*Solid-state NMR structural and dynamics studies of HIV-1 protein assemblies. Hou G, Han Y, Suiter C, Zhang H, Polenova T, Gan Z, Brey WW, Hung I, Gor’kov P.  (2014) MagLab Reports 21 (1) 41-42. Free Text

*Solid-state NMR structural and dynamics studies of HIV-1 protein assemblies. Hou, G., Han, Y., Suiter, C., Zhang, H., Polenova, T., Gan, Z., Brey, W., Hung, I., Gor’kov, P. (2013) MagLab Reports 20 (2) 50-51.

 *The p66 immature precursor of HIV-1 reverse transcriptase. Sharaf NG, Poliner E, Slack RL, Christen MT, Byeon IJ, Parniak MA, Gronenborn AM, Ishima R. (2014) Proteins 82(10):2343-52. Free Text

*HIV-1 uncoating: connection to nuclear entry and regulation by host proteins. Ambrose Z, Aiken C. (2014) Virology 454-455:371-9. PMC3988234 Free Text

*A probe to monitor performance of ¹⁵N longitudinal relaxation experiments for proteins in solution. Ishima R. (2014) J Biomol NMR 58(2):113-22. PMC3951101 Free Text

*Magic angle spinning NMR studies of protein assemblies: recent advances in methodology and applications. Hou G, Suiter CL, Yan S, Zhang H, Polenova T. (2013) Annual Reports on NMR Spectroscopy, 80, pp. 293-357.

*A magic-angle spinning NMR method for the site-specific measurement of proton chemical-shift anisotropy in biological and organic solids. Hou G, Gupta R, Polenova T, Vega AJ. (2014) Israel Journal of Chemistry 54 (1-2), pp. 171-193. PMC4255364 Free Text

*Sensitivity gains, linearity, and spectral reproducibility in nonuniformly sampled multidimensional MAS NMR spectra of high dynamic range. Suiter CL, Paramasivam S, Hou G, Sun S, Rice D, Hoch JC, Rovnyak D, Polenova T. (2014) J Biomol NMR 59(2):57-73. PMC4142058 Free Text

*Structural basis for nuclear import of splicing factors by human Transportin 3. Maertens GN, Cook NJ, Wang W, Hare S, Gupta SS, Oztop I, Lee K, Pye VE, Cosnefroy O, Snijders AP, Kewalramani VN, Fassati A, Engelman A, Cherepanov P. (2014) Proc Natl Acad Sci USA 111(7):2728-33. PMC3932936 Free text

*In Vivo Functions of CPSF6 for HIV-1 as Revealed by HIV-1 Capsid Evolution in HLA-B27-Positive Subjects. Henning MS, Dubose BN, Burse MJ, Aiken C, Yamashita M. (2014) PLoS Pathogens 10(1):e1003868. PMC3887095 Free text

*Mechanisms of allosteric activation and inhibition of the deoxyribonucleoside triphosphate triphosphohydrolase from Enterococcus faecalis. Vorontsov II, Wu Y, Delucia M, Minasov G, Mehrens J, Shuvalova L, Anderson WF, Ahn J. (2014) J Biol Chem 289(5):2815-24.  PMC3908413 Free Text Cover Image and Paper of the Week

*Binding of HIV-1 Vpr protein to the human homolog of the yeast DNA repair protein RAD23 (hHR23A) requires its xeroderma pigmentosum complementation group C binding (XPCB) domain as well as the ubiquitin-associated 2 (UBA2) domain. Jung J, Byeon IJ, Delucia M, Koharudin LM, Ahn J, Gronenborn AM. (2014) J Biol Chem 289(5):2577-88.  PMC3908392 Free Text

*Magic angle spinning NMR reveals sequence-dependent structural plasticity, dynamics, and the spacer peptide 1 conformation in HIV-1 capsid protein assemblies. Han Y, Hou G, Suiter CL, Ahn J, Byeon IJ, Lipton AS, Burton SD, Hung I, Gor'kov PL, Gan Z, Brey WW, Rice D, Gronenborn AM, Polenova TE. (2013) J Am Chem Soc 135(47):17793-803. PMC3928671 Free Text

*Structural determinants of human APOBEC3A enzymatic and nucleic acid binding properties. Mitra M, Hercík K, Byeon IJ, Ahn J, Hill S, Hinchee-Rodriguez K, Singer D, Byeon CH, Charlton LM, Nam G, Heidecker G, Gronenborn AM, Levin JG. (2013) Nucleic Acids Res 42(2):1095-110. PMC3902935 Free Text

*Viral and cellular requirements for the nuclear entry of retroviral preintegration nucleoprotein complexes. Matreyek KA, Engelman A. (2013) Viruses 5(10):2483-511.  PMC3814599 Free Text

*Mechanism of allosteric activation of SAMHD1 by dGTP. Ji X, Wu Y, Yan J, Mehrens J, Yang H, Delucia M, Hao C, Gronenborn AM, Skowronski J, Ahn J, Xiong Y. (2013) Nat Struct Mol Biol 20(11):1304-9. PMC3833828 Free Text

*Evolutionary toggling of Vpx/Vpr specificity results in divergent recognition of the restriction factor SAMHD1. Fregoso OI, Ahn J, Wang C, Mehrens J, Skowronski J, Emerman M. (2013) PLoS Pathog 9(7):e1003496. PMC3715410 Free Text

*HIV-2 and SIVmac accessory virulence factor Vpx down-regulates SAMHD1 enzyme catalysis prior to proteasome-dependent degradation. DeLucia M, Mehrens J, Wu Y, Ahn J.  (2013) J Biol Chem 288(26):19116-26. PMC3696684 Free Text

*Correlative cryo-electron tomography and optical microscopy of cells.  Zhang P. Curr Opin Struct Biol 23(5):763-70. PMC3812453. Free Text

*Evidence for biphasic uncoating during HIV-1 infection from a novel imaging assay. Xu H, Franks T, Gibson G, Huber K, Rahm N, Strambio De Castillia C, Luban J, Aiken C, Watkins S, Sluis-Cremer N, Ambrose Z. (2013) Retrovirology 10(1):70. PMC3716918 Free Text

*Multitask learning for host-pathogen protein interactions. Kshirsagar M, Carbonell J, Klein-Seetharaman J. Bioinformatics 29(13):i217-i226. PMC3694681. Free Text

*NMR structure of human restriction factor APOBEC3A reveals substrate binding and enzyme specificity. Byeon I-JL, Ahn J, Mitra M, Byeon C-H, Hercík K, Hritz J, Charlton LM, Levin JG, Gronenborn AM. (2013) Nature Commun 4:1890. PMC3674325 Free Text

*Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Zhao G, Perilla JR, Yufenyuy EL, Meng X, Chen B, Ning J, Ahn J, Gronenborn AM, Schulten K, Aiken C, Zhang P. (2013) Nature 497(7451):643-6. PMC3729984 Free Text

*Broadband homonuclear correlation spectroscopy driven by combined R2n(v) sequences under fast magic angle spinning for NMR structural analysis of organic and biological solids. Hou G, Yan S, Trébosc J, Amoureux J-P, Polenova T. (2013) J Magn Reson 232:18-30. PMC3703537 Free Text

*Correlative microscopy for 3D structural analysis of dynamic interactions.  Jun S, Zhao G, Ning J, Gibson GA, Watkins SC, Zhang P (2013) J Vis Exp (76), e50386, doi:10.3791/50386. PMC3728906. Free Text

*Tubular crystals and helical arrays: structural determination of HIV-1 capsid assemblies using Iterative Helical Real-Space Reconstruction. Zhang P, Meng X,and Zhao G. (2013) Methods Mol Biol 955:381-99. Free Text

 *Tetramerization of SAMHD1 is required for biological activity and inhibition of HIV infection. Yan J,  Kaur S,  DeLucia M,  Hao C,  Mehrens J,  Wang C,  Golczak M,  Palczewski K,  Gronenborn AM,  Ahn J, and Skowronski J. (2013) J Biol Chem 288(15):10406-17. PMC3624423 Free Text

 *Probing structure and dynamics of protein assemblies by magic angle spinning NMR spectroscopy. Yan S, Suiter CL, Hou G, Zhang H, Polenova T.  (2013) Acc Chem Res 46(9):2047-58. PMC3748245 Free Text

 *Multidimensional magic angle spinning NMR spectroscopy for site-resolved measurement of proton chemical shift anisotropy in biological solids. Hou G, Paramasivam S, Yan S, Polenova T, Vega AJ. (2013) J Am Chem Soc. 135(4):1358-68. PMC3586542 Free Text

 *The host proteins transportin SR2/TNPO3 and Cyclophilin A exert opposing effects on HIV-1 uncoating. Shah VB, Shi J, Hout DR, Oztop I, Krishnan L, Ahn J, Shotwell MS, Engelman A, Aiken C. (2012) J Virol. 87(1):422-32. PMC3536424 Free Text

 *Structural insight into HIV-1 capsid recognition by rhesus TRIM5α. Yang H, Ji X, Zhao G, Ning J, Zhao Q, Aiken C, Gronenborn AM, Zhang P, Xiong Y. (2012) Proc Natl Acad Sci USA. 109(45):18372-7. PMC3494900 Free Text

 *Recoupling of chemical shift anisotropy by R-symmetry sequences in magic angle spinning NMR spectroscopy. Hou G, Byeon IJ, Ahn J, Gronenborn AM, Polenova T. (2012) J Chem Phys. 137(13):134201. PMC3477183 Free Text

 *Protease cleavage leads to formation of mature trimer interface in HIV-1 capsid. Meng X, Zhao G, Yufenyuy E, Ke D, Ning J, Delucia M, Ahn J, Gronenborn AM, Aiken C, Zhang P. (2012) PLoS Pathog. 2012 Aug;8(8):e1002886. PMC3426514 Free Text

 *Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair. Yeh JI, Levine AS, Du S, Chinte U, Ghodke H, Wang H, Shi H, Hsieh CL, Conway JF, Van Houten B, Rapić-Otrin V. Proc Natl Acad Sci U S A. 2012 Oct 9;109(41):E2737-46. PMC3478663 Free Text

*Thinning of large mammalian cells for cryo-TEM characterization by cryo-FIB milling. Strunk KM, Wang K, Ke D, Gray JL, Zhang P. (2012) J Microsc. 247(3): 220. PMC3748363 Free Text

*Enhanced sensitivity by nonuniform sampling enables multidimensional MAS NMR spectroscopy of protein assemblies. Paramasivam S, Suiter CL, Hou G, Sun S, Palmer M, Hoch JC, Rovnyak D, Polenova T. (2012) J Phys Chem B. 116(25): 7416. PMC3386641 Free Text

*3D structure determination of native mammalian cells using cryo-FIB and cryo-electron tomography. Wang K, Strunk K, Zhao G, Gray JL, Zhang P. (2012) J Struct Biol 180(2):318-26. PMC3483467 Free Text

*Second-site suppressors of HIV-1 capsid mutations: restoration of intracellular activities without correction of intrinsic capsid stability defects. Yang R, Shi J, Byeon IL, Ahn J, Sheehan JH, Meiler J, Gronenborn AM, Aiken C. (2012) Retrovirology 9(1): 30.  PMC3351742 Free Text

*Motions on the millisecond timescale and multiple conformations of HIV-1 capsid protein: implications for structural polymorphism of CA assemblies. Byeon IL, Hou G, Han Y, Suiter CL, Ahn J, Jung J, Byeon CH, Gronenborn AM, Polenova TE. (2012) J Am Chem Soc, 134 (14) 6455-6466. PMC3325613 Free Text

*HIV-1 Nef interaction influences the ATP-binding site of the Src-family kinase, Hck. Pene-Dumitrescu T, Shu ST, Wales TE, Alvarado JJ, Shi H, Narute P, Moroco JA, Yeh JI, Engen JR, Smithgall TE. (2012) BMC Chem Biol, 12(1):1. PMC3328272 Free Text

*HIV/SIV accessory virulence factor Vpx loads the host cell restriction factor SAMHD1 onto the E3 ubiquitin ligase complex CRL4DCAF1. Ahn J, Hao C, Yan J, DeLucia M, Mehrens J, Wang C, Gronenborn AM, Skowronski J. (2012) J Biol Chem, 287:12550.  PMC3321004 Free Text

*APOBEC2 is a monomer in solution: implications for APOBEC3G models. Krzysiak TC, Jung J, Thompson J, Baker D, Gronenborn AM. (2012) Biochemistry 51(9) 2008-17. PMC3316327 Free Text

*Human immunodeficiency virus type 1 (HIV-1) capsid mutation N74D alters cyclophilin A dependence and impairs macrophage infection. Ambrose Z, Lee K, Ndjomou J, Xu H, Oztop I, Matous J, Takemura T, Unutmaz D, Engelman A, Hughes SH, Kewalramani VN. (2012) J Virol, 86(8):4708-14. PMC3318671 Free Text

*CryoEM analysis of capsid assembly and structural changes upon interactions with a host restriction factor, TRIM5α. Zhao G and Zhang P. (2014) Methods Mol Biol. 1087:13-28.PMC4506781 Free Text

*Determining confidence of predicted interactions between HIV-1 and human proteins using conformal method. Nouretdinov I, Gammerman A, Qi Y, Klein-Seetharaman J. (2012) Pac Symp Biocomput 2012: 311-22. PMC3249613 Free Text

*Solid-state NMR spectroscopy of protein complexes. Sun S, Han Y, Paramasivam S, Yan S, Siglin AE, Williams JC, Byeon IJ, Ahn J, Gronenborn AM, Polenova T. (2012) Methods Mol Biol 831:303-31. PubMed

*Direct visualization of HIV-1 with correlative live-cell microscopy and cryo-electron tomography. Jun S, Ke D, Debiec K, Zhao G, Meng X, Ambrose Z, Gibson GA, Watkins SC, and Zhang P. (2011) Structure 19 (11): 1573-1581. PMC3217200 Free Text

*Structure of HIV-1 capsid assemblies by cryo-electron microscopy and iterative helical real-space reconstruction. Meng X, Zhao G, and Zhang P. (2011) J Vis Exp (54) PMC3211131 Free Text

*Rhesus TRIM5α disrupts the HIV-1 capsid at the interhexamer interfaces. Zhao G, Ke D, Vu T, Ahn J, Shah VB, Yang R, Aiken C, Charlton LM, Gronenborn AM and Zhang P. (2011) PLoS Path 7(3): e1002009. PMC3063768 Free Text

*Structure, dynamics, and Hck interaction of full-length HIV-1 Nef proteins. Jung J, Byeon IJ, Ahn J, Gronenborn AM. (2011) Proteins 79 (5): 1609-1622. PMC3076547 Free Text

*Structure of the HIV-1 full-length capsid protein in a conformationally trapped unassembled state induced by small-molecule binding. Du S, Betts L, Yang R, Shi H, Concel J, Ahn J, Aiken C, Zhang P, Yeh JI. (2011) J Mol Biol. 406, 371-386. PMC3194004 Free Text

*Spin diffusion driven by R-symmetry sequences: Applications to homonuclear correlation spectroscopy in MAS NMR of biological and organic solids. Hou G, Byeon IL, Ahn J, Concel J, Samoson A, Gronenborn AM, Polenova T. (2011) J Am Chem Soc 133, 3943-53. PMC3148607 Free Text

*The cullin-RING E3 ubiquitin ligase CRL4-DCAF1 complex dimerizes via a short helical region in DCAF1. Ahn J, Novince Z, Concel J, Byeon CH, Makhov AM, Byeon IJ, Zhang P, Gronenborn AM. (2011) Biochemistry. 50, 1359-1367. PMC3072279 Free Text

*1H-13C/1H-15N heteronuclear dipolar recoupling by R-symmetry sequences under fast magic angle spinning for dynamics analysis of biological and organic solids. Hou G, Byeon IL, Ahn J, Gronenborn AM, Polenova T. (2011) J Am Chem Soc 133 (46), 18646-18655. PMC3218250 Free Text

*Virus interactions with human signal transduction pathways. Zhao Z, Xia J, Tastan O, Singh I, Kshirsagar M, Carbonell J, Klein-Seetharaman J. (2011) Int J Comput Biol Drug Des 4 (1): 83-105. PMC3407688 Free Text

*Crystal structure of the Src-family kinase Hck SH3-SH2-linker regulatory region supports an SH3-dominant activation mechanism. Alvarado JJ, Betts L, Moroco JA, Smithgall TE, and Yeh JI. (2010) J Biol Chem 285, 35455-35461. PMC2975169 Free Text

*Determination of relative tensor orientations by γ-encoded chemical shift anisotropy/heteronuclear dipolar coupling 3D NMR spectroscopy in biological solids. Hou G, Paramasivam S, Byeon IL, Gronenborn AM, Polenova T. (2010) Phys Chem Chem Phys 12, 14873-14883. PMC3160241 Free Text

*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. Ahn J, Vu T, Novince Z, Guerrero-Santoro J, Rapic-Otrin V, Gronenborn AM. (2010) J Biol Chem. 285, 37333-37341. PMC2988339 Free Text

*Small molecule inhibition of HIV-1-induced MHC-I downregulation identifies a temporally regulated switch in Nef action. 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) Mol Biol Cell, 21, 3279-92. PMC2947465 Free Text

*The RNA binding protein HuR does not interact directly with HIV-1 reverse transcriptase and does not affect reverse transcription in vitro. Ahn J, Byeon IJ, Dharmasena S, Huber K, Concel J, Gronenborn AM, Sluis-Cremer N. (2010) Retrovirology 7:40. PMC2873509  Free Text

*Solid-State NMR studies of HIV-1 capsid protein assemblies. Han Y, Ahn J, Concel J, Byeon IL, Gronenborn AM, Yang J, Polenova T. (2010) J Am Chem Soc, 132,1976-1987. PMC2829833 Free Text

*1H, 15N and 13C assignments of the dimeric C-terminal domain of HIV-1 capsid protein. Jung J, Byeon IJ, Ahn J, Concel J, Gronenborn AM. (2010) Biomol NMR Assign 4:21-23. PMC3448961 Free Text

*Human immunodeficiency virus type 1 Vpr: oligomerization is an essential feature for its incorporation into virus particles. 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) Virol J 7, 119. PMC2894018 Free Text

*Semi-supervised multi-task learning for predicting interactions between HIV-1 and human proteins. Qi Y, Tastan O, Carbonell JG, Klein-Seetharaman J, Weston J (2010) Bioinformatics 26 (18): i645-i652. PMC2935441 Free Text

*Structural convergence between Cryo-EM and NMR reveals intersubunit interactions critical for HIV-1 capsid function. Byeon IJ, Meng X, Jung J, Zhao G, Yang R, Ahn J, Shi J, Concel J, Aiken C, Zhang P, Gronenborn AM. (2009) Cell 139:780-790. PMC2782912  Free Text Also see commentary in Viruses.

*HIV-1 Vif-mediated ubiquitination/degradation of APOBEC3G involves four critical lysine residues in its C-terminal domain. Iwatani Y, Chan DS, Liu L, Yoshii H, Shibata J, Yamamoto N, Levin JG, Gronenborn AM, Sugiura W. (2009) Proc Natl Acad Sci USA 106:19539-19544. PMC2772817 Free Text

*Determination of multicomponent protein structures in solution using global orientation and shape restraints. 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) J Am Chem Soc 131:10507-10515. PMC2873192 Free Text

*Prediction of interactions between HIV-1 and human proteins by information integration. Tastan O, Qi Y, Carbonell JG, Klein-Seetharaman J. (2009) Pac Symp Biocomput 2009:516-27. PMC3263379 Free Text

*Alternative paths in HIV-1 targeted human signal transduction pathways. Balakrishnan S, Tastan O, Carbonell J, Klein-Seetharaman J. (2009) BMC Genomics 10 Suppl 3:S30. PMC2788384 Free Text

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