Publications

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Recent publications from the HARC Center
 
2017
 
Adolph MB, Ara A, Feng Y, Wittkopp CJ, Emerman M, Fraser JS, Chelico L. Cytidine deaminase efficiency of the lentiviral viral restriction factor APOBEC3C correlates with dimerization. Nucleic Acids Res. 2017 Feb 1 PMC5389708
 
Boehm D, Jeng M, Camus G, Gramatica A, Schwarzer R, Johnson JR, Hull PA, Montano M, Sakane N, Pagans S, Godin R, Deeks SG, Krogan NJ, Greene WC, Ott M. SMYD2-Mediated Histone Methylation Contributes to HIV-1 Latency.
 
Du D, Roguev A, Gordon DE, Chen M, Chen SH, Shales M, Shen JP, Ideker T, Mali P, Qi LS, Krogan NJ. Genetic interaction mapping in mammalian cells using CRISPR interference. Nat Methods. 2017 Jun;14(6):577-580.
 

Faust TB, Yang L, Jang GM, Johnson JR, Yang S, Krogan N, Frankel A. PJA2 ubiquitinates the HIV-1 Tat protein with low site specificity to activate viral transcription. Sci Rep. 2017 Mar 27;7:45394. PMC5366948

Lobingier BT, Hüttenhain R, Eichel K, Miller KB, Ting AY, von Zastrow M, Krogan NJ. An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells. Cell. 2017 Apr 6;169(2):350-360
 
Meyer NO, O'Donoghue AJ, Schulze-Gahmen U, Ravalin M, Moss SM, Winter MB, Knudsen GM, Craik, CS Multiplex substrate profiling by mass spectrometry for kinases reveals quantitative substrate motifs. Anal Chem. 2017 Apr 18;89(8):4550-4558
 

Nakamura RL, Burlingame MA, Yang S, Crosby DC, Talbot DJ, Chui K, Frankel AD, Renslo AR. Identification and optimization of thienopyridine carboxamides as inhibitors of HIV regulatory complexes. Antimicrob Agents Chemother. 2017 Apr 17. pii: AAC.02366-16.

Peterlin BM, Liu P, Wang X, Cary D, Shao W, Leoz M, Hong T, Pan T, Fujinaga K. Hili inhibits HIV replication in activated T cells. J Virol. 2017 May 12;91(11). pii: e00237-17 PMC5432865

Qi S, Li Z, Schulze-Gahmen U, Stjepanovic, G, Zhou Q. and Hurley, JH Structural basis for ELL2 and AFF4 activation of HIV-1 proviral transcription. Nat Commun. 2017 Jan 30;8:14076. doi: 10.1038/ncomms14076. PMC5290273
 

Rauch BJ, Silvis MR, Hultquist JF, Waters CS, McGregor MJ, Krogan NJ, Bondy-Denomy J. Inhibition of CRISPR-Cas9 with Bacteriophage Proteins. Cell. 2017 Jan 12;168(1-2):150-158. PMC523596

Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, Lewis NE, Chang AN, Kreisberg JF, Krogan N, Qi L, Ideker T, Mali P. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nat Methods. 2017 Mar 20. doi: 10.1038/nmeth.4225. PMC5449203

Zheng SQ, Palovcak E, Armache JP, Verba KA, Cheng Y, Agard DA. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat Methods. 2017 Apr;14(4):331-332.

2016

Ball, K.A, Jeffrey R. Johnson, Mary K. Lewinski, John Guatelli, Erik Verschueren, Nevan J. Krogan, Matthew P. Jacobson, Non-Degradative Ubiquitination of Protein Kinases PLoS Comput Biol. 2016 Jun 2;12(6):e1004898. PMC4890936

Besnard E, Hakre S, Kampmann M, Lim HW, Hosmane NN, Martin A, Bassik MC, Verschueren E, Battivelli E, Chan J, Svensson JP, Gramatica A, Conrad RJ, Ott M, Greene WC, Krogan NJ, Siliciano RF, Weissman JS, Verdin E. The mTOR Complex Controls HIV Latency. Cell Host Microbe. 2016; 20: 785-97. PMCID in Process.

Carlson LA, Bai Y, Keane SC, Doudna JA, Hurley JH. Reconstitution of selective HIV-1 RNA packaging in vitro by membrane-bound Gag assemblies. Elife. 2016; 5. PMC4946900.

Cary DC, Peterlin BM. Targeting the latent reservoir to achieve functional HIV cure. F1000Res. 2016; 5. PMC4882755.
 
Cary DC, Fujinaga K, Peterlin BM. Molecular mechanisms of HIV latency. J Clin Invest. 2016 Feb;126(2):448-54. doi: 10.1172/JCI80565. Epub 2016 Jan 5. PubMed PMID: 26731470; PubMed Central PMC4731164
 

Faust TB, Yang L, Jang GM, Johnson JR, Yang S, Krogan N, Frankel A. PJA2 ubiquitinates the HIV-1 Tat protein with low site specificity to activate viral transcription. Sci Rep. 2017 Mar 27;7:45394. PMC5366948

Fernandes JD, Faust TB, Strauli NJ, Smith C, Crosby DC, Nakamura RL, Hernandez RD, Frankel AD. Functional segregation of overlapping genes in HIV. Cell. 2016; 167: 1762-73. PMC Journal - In Process.
 
Fernandes JD, Booth DS, Frankel AD. A structurally plastic ribonucleoprotein complex mediates post-transcriptional gene regulation in HIV-1. Wiley Interdiscip Rev RNA. 2016 Mar 1.  7: 470-86. PMC5026123.
 

Frauenfeld J, Loving R, Armache JP, Sonnen AF, Guettou F, Moberg P, Zhu L, Jegerschold C, Flayhan A, Briggs JA, Garoff H, Low C, Cheng Y, Nordlund P. A saposin-lipoprotein nanoparticle system for membrane proteins. Nat Methods. 2016; 13: 345-51. PMC4894539.

Gable JE, Lee GM, Acker TM, Hulce KR, Gonzalez ER, Schweigler P, Melkko S, Farady CJ, Craik CS. Fragment-Based Protein-Protein Interaction Antagonists of a Viral Dimeric Protease. ChemMedChem. 2016 Apr 19;11(8):862-9. doi: 10.1002/cmdc.201500526. Epub 2016 Jan 28. PubMed PMID: 26822284; PubMed Central PMCID: PMC4838516.

Galilee M, Britan-Rosich E, Griner SL, Uysal S, Baumgartel V, Lamb DC, Kossiakoff AA, Kotler M, Stroud RM, Marx A, Alian A. The Preserved HTH-Docking Cleft of HIV-1 Integrase Is Functionally Critical. Structure. 2016; 24: 1936-46. PMC5093063.

Gao Y, Cao E, Julius D, Cheng Y. TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action. Nature. 2016; 534: 347-51. PMC4911334.

Hultquist JF, Schumann K, Woo JM, Manganaro L, McGregor MJ, Doudna J, Simon V, Krogan NJ, Marson A. A Cas9 Ribonucleoprotein Platform for Functional Genetic Studies of HIV-Host Interactions in Primary Human T Cells. Cell Rep. 2016; 17: 1438-52. PMC5123761

Park RJ, Wang T, Koundakjian D, Hultquist JF, Lamothe-Molina P, Monel B, Schumann K, Yu H, Krupzcak KM, Garcia-Beltrain W, Piechocka-Trocha A, Krogan N, Marson A, Sabatini DM, Lander ES, Hacohen N, Walker BD. A genome-wide CRISPR screen reveals a restricted set of HIV host dependency factors. Nature Genetics. 2016; Dec. 19, 2016, doi: 10.1038/ng.3741. PMC Journal - In Process.

Schulze-Gahmen U, Echeverria I, Stjepanovic G, Bai Y, Lu H, Schneidman-Duhovny D, Doudna JA, Zhou Q, Sali A, Hurley JH. Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex. Elife. 2016; 5: e15910. PMC5072841

Wu S, Armache JP, Cheng Y. Single-particle cryo-EM data acquisition by using direct electron detection camera. Microscopy (Oxf). 2016 Feb;65(1):35-41. doi: 10.1093/jmicro/dfv355. Epub 2015 Nov 6. PubMed PMID: 26546989; PubMed Central PMCID: PMC4749049.

Finer-Moore J, Czudnochowski N, O'Connell JD 3rd, Wang AL, Stroud RM. Crystal Structure of the Human tRNA m(1)A58 Methyltransferase-tRNA3(Lys) Complex: Refolding of Substrate tRNA Allows Access to the Methylation Target. J Mol Biol. 2015 Dec 4;427(24):3862-76. doi: 10.1016/j.jmb.2015.10.005. Epub 2015 Oct 22. PubMed PMID: 26470919.

Jones SK Jr, Clarke SC, Craik CS, Bennett RJ. Evolutionary Selection on Barrier Activity: Bar1 Is an Aspartyl Protease with Novel Substrate Specificity. MBio. 2015 Nov 24;6(6):e01604-15. doi: 10.1128/mBio.01604-15. PubMed PMID: 26604258; PubMed Central PMCID: PMC4669382.
 

Dunyak BM, Nakamura RL, Frankel AD, Gestwicki JE. Selective Targeting of Cells via Bispecific Molecules That Exploit Coexpression of Two Intracellular Proteins. ACS Chem Biol. 2015 Nov 20;10(11):2441-7. doi: 10.1021/acschembio.5b00426. Epub 2015 Sep 2. PubMed PMID: 26322864.

 
Pak V, Eifler TT, Jäger S, Krogan NJ, Fujinaga K, Peterlin BM. CDK11 in TREX/THOC Regulates HIV mRNA 3' End Processing. Cell Host Microbe. 2015 Nov 11;18(5):560-70. doi: 10.1016/j.chom.2015.10.012. PubMed PMID: 26567509; PubMed Central PMCID: PMC4648707.
 

Li X, Zheng S, Agard DA, Cheng Y. Asynchronous data acquisition and on-the-fly analysis of dose fractionated cryoEM images by UCSFImage. J Struct Biol. 2015 Nov;192(2):174-8. doi: 10.1016/j.jsb.2015.09.003. Epub 2015 Sep 11. PubMed PMID: 26370395; PubMed Central PMCID: PMC4633327.

Chiu PL, Li X, Li Z, Beckett B, Brilot AF, Grigorieff N, Agard DA, Cheng Y, Walz T. Evaluation of super-resolution performance of the K2 electron-counting camera using 2D crystals of aquaporin-0. J Struct Biol. 2015 Nov;192(2):163-73. doi: 10.1016/j.jsb.2015.08.015. Epub 2015 Aug 28. PubMed PMID: 26318383; PubMed Central PMCID: PMC4633381.

Jayaraman B, Mavor D, Gross JD, Frankel AD. Thermodynamics of Rev-RNA Interactions in HIV-1 Rev-RRE Assembly. Biochemistry. 2015 Oct 27;54(42):6545-54. doi: 10.1021/acs.biochem.5b00876. Epub 2015 Oct 13. PubMed PMID: 2642268

Shen QT, Ren X, Zhang R, Lee IH, Hurley JH. HIV-1 Nef hijacks clathrin coats by stabilizing AP-1:Arf1 polygons. Science. 2015 Oct 23;350(6259):aac5137. doi: 10.1126/science.aac5137. PubMed PMID: 26494761; PubMed Central PMCID: PMC4638387.

Barad BA, Echols N, Wang RY, Cheng Y, DiMaio F, Adams PD, Fraser JS. EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy. Nat Methods. 2015 Oct;12(10):943-6. doi: 10.1038/nmeth.3541. Epub 2015 Aug 17. PubMed PMID: 26280328; PubMed Central PMCID: PMC4589481.

Shah PS, Wojcechowskyj JA, Eckhardt M, Krogan NJ. Comparative mapping of host-pathogen protein-protein interactions. Curr Opin Microbiol. 2015 Oct;27:62-8. doi: 10.1016/j.mib.2015.07.008. Epub 2015 Aug 10. Review. PubMed PMID: 26275922; PubMed Central PMCID: PMC4659747.

Mirrashidi KM, Elwell CA, Verschueren E, Johnson JR, Frando A, Von Dollen J, Rosenberg O, Gulbahce N, Jang G, Johnson T, Jäger S, Gopalakrishnan AM, Sherry J, Dunn JD, Olive A, Penn B, Shales M, Cox JS, Starnbach MN, Derre I, Valdivia R, Krogan NJ, Engel J. Global Mapping of the Inc-Human Interactome Reveals that Retromer Restricts Chlamydia Infection. Cell Host Microbe. 2015 Jul 8;18(1):109-21. doi: 10.1016/j.chom.2015.06.004. Epub 2015 Jun 25. PubMed PMID: 26118995; PubMed Central PMCID: PMC4540348.

Schumann K, Lin S, Boyer E, Simeonov DR, Subramaniam M, Gate RE, Haliburton GE, Ye CJ, Bluestone JA, Doudna JA, Marson A. Generation of knock-in primary human T cells using Cas9 ribonucleoproteins. Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):10437-42. doi: 10.1073/pnas.1512503112. Epub 2015 Jul 27. PubMed PMID: 26216948; PubMed Central PMCID: PMC4547290.

O'Donoghue AJ, Knudsen GM, Beekman C, Perry JA, Johnson AD, DeRisi JL, Craik CS, Bennett RJ. Destructin-1 is a collagen-degrading endopeptidase secreted by Pseudogymnoascus destructans, the causative agent of white-nose syndrome. Proc Natl Acad Sci U S A. 2015 Jun 16;112(24):7478-83. doi: 10.1073/pnas.1507082112. Epub 2015 May 5. Erratum in: Proc Natl Acad Sci U S A. 2015 Jun 16;112(24):E3152. PubMed PMID: 25944934; PubMed Central PMCID: PMC4475985.
 
Kane JR, Stanley DJ, Hultquist JF, Johnson JR, Mietrach N, Binning JM, Jónsson SR, Barelier S, Newton BW, Johnson TL, Franks-Skiba KE, Li M, Brown WL, Gunnarsson HI, Adalbjornsdóttir A, Fraser JS, Harris RS, Andrésdóttir V, Gross JD, Krogan NJ. Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity. Cell Rep. 2015 May 26;11(8):1236-50. doi: 10.1016/j.celrep.2015.04.038. Epub 2015 May 14. PubMed PMID: 25981045; PubMed Central PMCID: PMC4613747.
 

Kane JR, Stanley DJ, Hultquist JF, Johnson JR, Mietrach N, Binning JM, Jónsson SR, Barelier S, Newton BW, Johnson TL, Franks-Skiba KE, Li M, Brown WL, Gunnarsson HI, Adalbjornsdóttir A, Fraser JS, Harris RS, Andrésdóttir V, Gross JD, Krogan NJ. Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity. Cell Rep. 2015 May 26;11(8):1236-50. doi: 10.1016/j.celrep.2015.04.038. Epub 2015 May 14. PubMed PMID: 25981045.

Cheng Y. Single-Particle Cryo-EM at Crystallographic Resolution. Cell. 2015 Apr 23;161(3):450-457. doi: 10.1016/j.cell.2015.03.049. Review. PubMed PMID: 25910205; PubMed Central PMCID: PMC4409662.

Zhao M, Wu S, Zhou Q, Vivona S, Cipriano DJ, Cheng Y, Brunger AT. Mechanistic insights into the recycling machine of the SNARE complex. Nature. 2015 Feb 5;518(7537):61-7. doi: 10.1038/nature14148. Epub 2015 Jan 12. PubMed PMID: 25581794; PubMed Central PMCID: PMC4320033.
 
Ramage HR, Kumar GR, Verschueren E, Johnson JR, Von Dollen J, Johnson T, Newton B, Shah P, Horner J, Krogan NJ, Ott M. A combined proteomics/genomics approach links hepatitis C virus infection with nonsense-mediated mRNA decay. Mol Cell. 2015 Jan 22;57(2):329-40. doi: 10.1016/j.molcel.2014.12.028. PubMed PMID: 25616068; PubMed Central PMCID: PMC4305532.
 
Davis ZH, Verschueren E, Jang GM, Kleffman K, Johnson JR, Park J, Von Dollen J, Maher MC, Johnson T, Newton W, Jäger S, Shales M, Horner J, Hernandez RD, Krogan NJ, Glaunsinger BA. Global mapping of herpesvirus-host protein complexes reveals a transcription strategy for late genes. Mol Cell. 2015 Jan 22;57(2):349-60. doi: 10.1016/j.molcel.2014.11.026. Epub 2014 Dec 24. PubMed PMID: 25544563; PubMed Central PMCID: PMC4305015.
 
Fujinaga K, Luo Z, Schaufele F, Peterlin BM. Visualization of positive transcription elongation factor b (P-TEFb) activation in living cells. J Biol Chem. 2015 Jan 16;290(3):1829-36. doi: 10.1074/jbc.M114.605816. Epub 2014 Dec 9. PubMed PMID: 25492871; PubMed Central PMCID: PMC4340424.
 
Kim J, Wu S, Tomasiak TM, Mergel C, Winter MB, Stiller SB, Robles-Colmanares Y, Stroud RM, Tampé R, Craik CS, Cheng Y. Subnanometre-resolution electron cryomicroscopy structure of a heterodimeric ABC exporter. Nature. 2015 Jan 15;517(7534):396-400. doi: 10.1038/nature13872. Epub 2014 Nov 2. PubMed PMID: 25363761; PubMed Central PMCID: PMC4372080.
 
Eifler TT, Shao W, Bartholomeeusen K, Fujinaga K, Jäger S, Johnson JR, Luo Z, Krogan NJ, Peterlin BM. Cyclin-dependent kinase 12 increases 3' end processing of growth factor-induced c-FOS transcripts. Mol Cell Biol. 2015 Jan;35(2):468-78. doi: 10.1128/MCB.01157-14. Epub 2014 Nov 10. PubMed PMID: 25384976; PubMed Central PMCID: PMC4272423.
 
Jayaraman B, Crosby DC, Homer C, Ribeiro I, Mavor D, Frankel AD. RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev-Rev response element complex. Elife. 2014 Dec 8;3:e04120. doi: 10.7554/eLife.04120. PubMed PMID: 25486594; PubMed Central PMCID: PMC4360532.
 
Booth DS, Cheng Y, Frankel AD. The export receptor Crm1 forms a dimer to promote nuclear export of HIV RNA. Elife. 2014 Dec 8;3:e04121. doi: 10.7554/eLife.04121. PubMed PMID: 25486595; PubMed Central PMCID: PMC4360530.
 
Morris JH, Knudsen GM, Verschueren E, Johnson JR, Cimermancic P, Greninger AL, Pico AR. Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. Nat Protoc. 2014 Nov;9(11):2539-54. doi: 10.1038/nprot.2014.164. Epub 2014 Oct 2. PubMed PMID: 25275790; PubMed Central PMCID: PMC4332878.
 
Mahon C, Krogan NJ, Craik CS, Pick E. Cullin E3 ligases and their rewiring by viral factors. Biomolecules. 2014 Oct 13;4(4):897-930. doi: 10.3390/biom4040897. Review. PubMed PMID: 25314029; PubMed Central PMCID: PMC4279162.
 
Holton JM, Classen S, Frankel KA, Tainer JA. The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures. FEBS J. 2014 Sep;281(18):4046-60. doi: 10.1111/febs.12922. Epub 2014 Sep 17. PubMed PMID: 25040949; PubMed Central PMCID: PMC4282448.
 
Bai Y, Tambe A, Zhou K, Doudna JA. RNA-guided assembly of Rev-RRE nuclear export complexes. Elife. 2014 Aug 27;3:e03656. doi: 10.7554/eLife.03656. PubMed PMID: 25163983; PubMed Central PMCID: PMC4142337.
 
Pandeló José D, Bartholomeeusen K, da Cunha RD, Abreu CM, Glinski J, da Costa TB, Bacchi Rabay AF, Pianowski Filho LF, Dudycz LW, Ranga U, Peterlin BM, Pianowski LF, Tanuri A, Aguiar RS. Reactivation of latent HIV-1 by new semi-synthetic ingenol esters. Virology. 2014 Aug;462-463:328-39. doi: 10.1016/j.virol.2014.05.033. Epub 2014 Jul 9. PubMed PMID: 25014309; PubMed Central PMCID: PMC4383768.
 
Fujinaga K, Luo Z, Peterlin BM. Genetic analysis of the structure and function of 7SK small nuclear ribonucleoprotein (snRNP) in cells. J Biol Chem. 2014 Jul 25;289(30):21181-90. PubMed PMID: 24917669; PubMed Central PMCID: PMC4110320.
 
Gable JE, Lee GM, Jaishankar P, Hearn BR, Waddling CA, Renslo AR, Craik CS. Broad-spectrum allosteric inhibition of herpesvirus proteases. Biochemistry. 2014 Jul 22;53(28):4648-60. doi: 10.1021/bi5003234. Epub 2014 Jul 11. PubMed PMID: 24977643; PubMed Central PMCID: PMC4108181.
 
Hu S, Sharma SC, Scouras AD, Soudackov AV, Carr CA, Hammes-Schiffer S, Alber T, Klinman JP. Extremely elevated room-temperature kinetic isotope effects quantify the critical role of barrier width in enzymatic C-H activation. J Am Chem Soc. 2014 Jun 11;136(23):8157-60. doi: 10.1021/ja502726s. Epub 2014 Jun 2. PubMed PMID: 24884374; PubMed Central PMCID: PMC4188422.