Publications

Recent publications from the HARC Center

2020 - 2021

Billesbølle CB, Azumaya CM, Kretsch RC, Powers AS, Gonen S, Schneider S, Arvedson T, Dror RO, Cheng Y, Manglik A. Structure of hepcidin-bound ferroportin reveals iron homeostatic mechanisms. Nature. 2020 Oct;586(7831):807-811. doi: 10.1038/s41586-020-2668-z. Epub 2020 Aug 19. PMID: 32814342; PMCID: PMC7906036.

Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Correa Marrero M, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, Batra J, Richards AL, Stevenson E, Gordon DE, Rojc A, Obernier K, Fabius JM, Soucheray M, Miorin L, Moreno E, Koh C, Tran QD, Hardy A, Robinot R, Vallet T, Nilsson-Payant BE, Hernandez-Armenta C, Dunham A, Weigang S, Knerr J, Modak M, Quintero D, Zhou Y, Dugourd A, Valdeolivas A, Patil T, Li Q, Hüttenhain R, Cakir M, Muralidharan M, Kim M, Jang G, Tutuncuoglu B, Hiatt J, Guo JZ, Xu J, Bouhaddou S, Mathy CJP, Gaulton A, Manners EJ, Félix E, Shi Y, Goff M, Lim JK, McBride T, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, De Wit E, Leach AR, Kortemme T, Shoichet B, Ott M, Saez-Rodriguez J, tenOever BR, Mullins RD, Fischer ER, Kochs G, Grosse R, García-Sastre A, Vignuzzi M, Johnson JR, Shokat KM, Swaney DL, Beltrao P, Krogan NJ. The Global Phosphorylation Landscape of SARS-CoV-2 Infection. Cell. 2020 Jun 28;. doi: 10.1016/j.cell.2020.06.034. [Epub ahead of print] PubMed PMID: 32645325; PubMed Central PMCID: PMC7321036.

Braberg H, Echeverria I, Bohn S, Cimermancic P, Shiver A, Alexander R, Xu J, Shales M, Dronamraju R, Jiang S, Dwivedi G, Bogdanoff D, Chaung KK, Hüttenhain R, Wang S, Mavor D, Pellarin R, Schneidman D, Bader JS, Fraser JS, Morris J, Haber JE, Strahl BD, Gross CA, Dai J, Boeke JD, Sali A, Krogan NJ. Genetic interaction mapping informs integrative structure determination of protein complexes. Science. 2020 Dec 11;370(6522):eaaz4910. doi: 10.1126/science.aaz4910. PMID: 33303586; PMCID: PMC7946025.

Cakir M, Obernier K, Forget A, Krogan NJ. Target Discovery for Host-Directed Antiviral Therapies: Application of Proteomics Approaches. mSystems. 2021 Oct 26;6(5):e0038821. doi: 10.1128/mSystems.00388-21. Epub 2021 Sep 14. PMID: 34519533; PMCID: PMC8547474.

Cary DC, Peterlin BM. Proteasomal Inhibition Potentiates Latent HIV Reactivation. AIDS Res Hum Retroviruses. 2020 Oct;36(10):800-807. doi: 10.1089/AID.2020.0040. Epub 2020 Aug 27. PMID: 32683901; PMCID: PMC7549009.

Castro-Gonzalez S, Chen Y, Benjamin J, Shi Y, Serra-Moreno R. Residues T48 and A49 in HIV-1 NL4-3 Nef are responsible for the counteraction of autophagy initiation, which prevents the ubiquitin-dependent degradation of Gag through autophagosomes. Retrovirology. 2021 Oct 28;18(1):33. doi: 10.1186/s12977-021-00576-y. PMID: 34711257; PMCID: PMC8555152.

Castro-Gonzalez S, Simpson S, Shi Y, Chen Y, Benjamin J, Serra-Moreno R. HIV Nef-mediated Ubiquitination of BCL2: Implications in Autophagy and Apoptosis. Front Immunol. 2021 May 6;12:682624. doi: 10.3389/fimmu.2021.682624. PMID: 34025682; PMCID: PMC8134690.

Chesarino NM, Emerman M. Polymorphisms in Human APOBEC3H Differentially Regulate Ubiquitination and Antiviral Activity. Viruses. 2020 Mar 30;12(4). doi: 10.3390/v12040378. PubMed PMID: 32235597; PubMed Central PMCID: PMC7232234.

Dvořáková H, Leontovyč R, Macháček T, O'Donoghue AJ, Šedo O, Zdráhal Z, Craik CS, Caffrey CR, Horák P, Mikeš L. Isoforms of Cathepsin B1 in Neurotropic Schistosomula of Trichobilharzia regenti Differ in Substrate Preferences and a Highly Expressed Catalytically Inactive Paralog Binds Cystatin. Front Cell Infect Microbiol. 2020;10:66. doi: 10.3389/fcimb.2020.00066. eCollection 2020. PubMed PMID: 32175287; PubMed Central PMCID: PMC7054455.

Eckhardt M, Hultquist JF, Kaake RM, Hüttenhain R, Krogan NJ. A systems approach to infectious disease. Nat Rev Genet. 2020 Jun;21(6):339-354. doi: 10.1038/s41576-020-0212-5. Epub 2020 Feb 14. Review. PubMed PMID: 32060427.

Fabius JM, Krogan NJ. Creating collaboration by breaking down scientific barriers. Cell. 2021 Apr 29;184(9):2271-2275. doi: 10.1016/j.cell.2021.02.022. Epub 2021 Mar 24. PMID: 33765441.

Flower TG, Buffalo CZ, Hooy RM, Allaire M, Ren X, Hurley JH. Structure of SARS-CoV-2 ORF8, a rapidly evolving coronavirus protein implicated in immune evasion. bioRxiv [Preprint]. 2020 Aug 27:2020.08.27.270637. doi: 10.1101/2020.08.27.270637. PMID: 32869027; PMCID: PMC7457612.

Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, Titus EW, Cakir M, Soucheray M, McGregor M, Cakir Z, Jang G, O'Meara MJ, Tummino TA, Zhang Z, Foussard H, Rojc A, Zhou Y, Kuchenov D, Hüttenhain R, Xu J, Eckhardt M, Swaney DL, Fabius JM, Ummadi M, Tutuncuoglu B, Rathore U, Modak M, Haas P, Haas KM, Naing ZZC, Pulido EH, Shi Y, Barrio-Hernandez I, Memon D, Petsalaki E, Dunham A, Marrero MC, Burke D, Koh C, Vallet T, Silvas JA, Azumaya CM, Billesbølle C, Brilot AF, Campbell MG, Diallo A, Dickinson MS, Diwanji D, Herrera N, Hoppe N, Kratochvil HT, Liu Y, Merz GE, Moritz M, Nguyen HC, Nowotny C, Puchades C, Rizo AN, Schulze-Gahmen U, Smith AM, Sun M, Young ID, Zhao J, Asarnow D, Biel J, Bowen A, Braxton JR, Chen J, Chio CM, Chio US, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam VL, Li F, Li J, Li YL, Li Y, Liu X, Lo M, Lopez KE, Melo AA, Moss FR 3rd, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech TH Jr, Safari M, Sangwan S, Schaefer K, Thomas PV, Thwin AC, Trenker R, Tse E, Tsui TKM, Wang F, Whitis N, Yu Z, Zhang K, Zhang Y, Zhou F, Saltzberg D, Hodder AJ, Shun-Shion AS, Williams DM, White KM, Rosales R, Kehrer T, Miorin L, Moreno E, Patel AH, Rihn S, Khalid MM, Vallejo-Gracia A, Fozouni P, Simoneau CR, Roth TL, Wu D, Karim MA, Ghoussaini M, Dunham I, Berardi F, Weigang S, Chazal M, Park J, Logue J, McGrath M, Weston S, Haupt R, Hastie CJ, Elliott M, Brown F, Burness KA, Reid E, Dorward M, Johnson C, Wilkinson SG, Geyer A, Giesel DM, Baillie C, Raggett S, Leech H, Toth R, Goodman N, Keough KC, Lind AL, Klesh RJ, Hemphill KR, Carlson-Stevermer J, Oki J, Holden K, Maures T, Pollard KS, Sali A, Agard DA, Cheng Y, Fraser JS, Frost A, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Alessi DR, Davies P, Frieman MB, Ideker T, Abate C, Jouvenet N, Kochs G, Shoichet B, Ott M, Palmarini M, Shokat KM, García-Sastre A, Rassen JA, Grosse R, Rosenberg OS, Verba KA, Basler CF, Vignuzzi M, Peden AA, Beltrao P, Krogan NJ. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020 Oct 15;. doi: 10.1126/science.abe9403. [Epub ahead of print] PubMed PMID: 33060197.

Hiatt J, Cavero DA, McGregor MJ, Zheng W, Budzik JM, Roth TL, Haas KM, Wu D, Rathore U, Meyer-Franke A, Bouzidi MS, Shifrut E, Lee Y, Kumar VE, Dang EV, Gordon DE, Wojcechowskyj JA, Hultquist JF, Fontaine KA, Pillai SK, Cox JS, Ernst JD, Krogan NJ, Marson A. Efficient generation of isogenic primary human myeloid cells using CRISPR-Cas9 ribonucleoproteins. Cell Rep. 2021 May 11;35(6):109105. doi: 10.1016/j.celrep.2021.109105. PubMed PMID: 33979618; NIHMSID:NIHMS1709014.

Kaake RM, Echeverria I, Kim SJ, Von Dollen J, Chesarino NM, Feng Y, Yu C, Ta H, Chelico L, Huang L, Gross J, Sali A, Krogan NJ. Characterization of an A3G-VifHIV-1-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host-Pathogen Complexes. Mol Cell Proteomics. 2021 Aug 11;20:100132. doi: 10.1016/j.mcpro.2021.100132. Epub ahead of print. PMID: 34389466; PMCID: PMC8459920.

Kazuki, K., Ahmad, S., Zhu, Z., Young, J.M., Mu, X., Park, S., Malik, H.S., Hur, S. Structural analysis of RIG-I-like receptors reveals ancient rules of engagement between diverse RNA helicases and TRIM ubiquitin ligases. Mol Cell. 2021 Feb 4;81(3):599-613.e8. PMID: 33373584.

Krchlíková V, Fábryová H, Hron T, Young JM, Koslová A, Hejnar J, Strebel K, Elleder D. Antiviral Activity and Adaptive Evolution of Avian Tetherins. J Virol. 2020 Jun 1;94(12). doi: 10.1128/JVI.00416-20. Print 2020 Jun 1. PubMed PMID: 32238588; PubMed Central PMCID: PMC7307100.

Kwon Y, Kaake RM, Echeverria I, Suarez M, Karimian Shamsabadi M, Stoneham C, Ramirez PW, Kress J, Singh R, Sali A, Krogan N, Guatelli J, Jia X. Structural basis of CD4 downregulation by HIV-1 Nef. Nat Struct Mol Biol. 2020 Sep;27(9):822-828. doi: 10.1038/s41594-020-0463-z. Epub 2020 Jul 27. PMID: 32719457; PMCID: PMC7483821.

Langer S, Yin X, Diaz A, Portillo AJ, Gordon DE, Rogers UH, Marlett JM, Krogan NJ, Young JAT, Pache L, Chanda SK. The E3 Ubiquitin-Protein Ligase Cullin 3 Regulates HIV-1 Transcription. Cells. 2020 Sep 1;9(9). doi: 10.3390/cells9092010. PubMed PMID: 32882949.

Lohse MB, Brenes LR, Ziv N, Winter MB, Craik CS, Johnson AD. An Opaque Cell-Specific Expression Program of Secreted Proteases and Transporters Allows Cell-Type Cooperation in Candida albicans. Genetics. 2020 Aug 24;. doi: 10.1534/genetics.120.303613. [Epub ahead of print] PubMed PMID: 32839241.

Lohse MB, Gulati M, Craik CS, Johnson AD, Nobile CJ. Combination of Antifungal Drugs and Protease Inhibitors Prevent Candida albicans Biofilm Formation and Disrupt Mature Biofilms. Front Microbiol. 2020;11:1027. doi: 10.3389/fmicb.2020.01027. eCollection 2020. PubMed PMID: 32523574; PubMed Central PMCID: PMC7261846.

McDonnell MM, Karvonen SC, Gaba A, Flath B, Chelico L, Emerman M. Highly-potent, synthetic APOBEC3s restrict HIV-1 through deamination-independent mechanisms. PLoS Pathog. 2021 Jun 25;17(6):e1009523. doi: 10.1371/journal.ppat.1009523. PMID: 34170969; PMCID: PMC8266076.

Miller-Vedam LE, Bräuning B, Popova KD, Schirle Oakdale NT, Bonnar JL, Prabu JR, Boydston EA, Sevillano N, Shurtleff MJ, Stroud RM, Craik CS, Schulman BA, Frost A, Weissman JS. Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients. Elife. 2020 Nov 25;9:e62611. doi: 10.7554/eLife.62611. Epub ahead of print. PMID: 33236988.

Painter MM, Zimmerman GE, Merlino MS, Robertson AW, Terry VH, Ren X, McLeod MR, Gomez-Rodriguez L, Garcia KA, Leonard JA, Leopold KE, Neevel AJ, Lubow J, Olson E, Piechocka-Trocha A, Collins DR, Tripathi A, Raghavan M, Walker BD, Hurley JH, Sherman DH, Collins KL. Concanamycin A counteracts HIV-1 Nef to enhance immune clearance of infected primary cells by cytotoxic T lymphocytes. Proc Natl Acad Sci U S A. 2020 Sep 22;117(38):23835-23846. doi: 10.1073/pnas.2008615117. Epub 2020 Sep 8. PMID: 32900948; PMCID: PMC7519347.

Palovcak E, Asarnow D, Campbell MG, Yu Z, Cheng Y. Enhancing the signal-to-noise ratio and generating contrast for cryo-EM images with convolutional neural networks. IUCrJ. 2020 Oct 24;7(Pt 6):1142-1150. doi: 10.1107/S2052252520013184. PMID: 33209325; PMCID: PMC7642784.

Richards AL, Eckhardt M, Krogan NJ. Mass spectrometry-based protein-protein interaction networks for the study of human diseases. Mol Syst Biol. 2021 Jan;17(1):e8792. doi: 10.15252/msb.20188792. PMID: 33434350; PMCID: PMC7803364.

Roth TL, Li PJ, Blaeschke F, Nies JF, Apathy R, Mowery C, Yu R, Nguyen MLT, Lee Y, Truong A, Hiatt J, Wu D, Nguyen DN, Goodman D, Bluestone JA, Ye CJ, Roybal K, Shifrut E, Marson A. Pooled Knockin Targeting for Genome Engineering of Cellular Immunotherapies. Cell. 2020 Apr 30;181(3):728-744.e21. doi: 10.1016/j.cell.2020.03.039. Epub 2020 Apr 16. PubMed PMID: 32302591; PubMed Central PMCID: PMC7219528.

Rutishauser RL, Deguit CDT, Hiatt J, Blaeschke F, Roth TL, Wang L, Raymond KA, Starke CE, Mudd JC, Chen W, Smullin C, Matus-Nicodemos R, Hoh R, Krone M, Hecht FM, Pilcher CD, Martin JN, Koup RA, Douek DC, Brenchley JM, Sékaly RP, Pillai SK, Marson A, Deeks SG, McCune JM, Hunt PW. TCF-1 regulates HIV-specific CD8+ T cell expansion capacity. JCI Insight. 2021 Feb 8;6(3):e136648. doi: 10.1172/jci.insight.136648. PMID: 33351785; PMCID: PMC7934879.

Sevillano N, Green EM, Votteler J, Kim DY, Ren X, Yang B, Liu X, Lourenço AL, Hurley JH, Farr-Jones S, Gross JD, Cheng Y, Craik CS. Identification of recombinant Fabs for structural and functional characterization of HIV-host factor complexes. PLoS One. 2021 May 13;16(5):e0250318. doi: 10.1371/journal.pone.0250318. PMID: 33983947; PMCID: PMC8118348.

Tenthorey, J.L., Young, C., Sodeinde, A., Emerman M., and Malik, H.S. Mutational resilience of antiviral restriction favors primate TRIM5α in host-virus evolutionary arms races. Elife. 2020 Sep 15;9:e59988. doi: 10.7554/eLife.59988. PMCID: PMC7492085

Tutuncuoglu B, Cakir M, Batra J, Bouhaddou M, Eckhardt M, Gordon DE, Krogan NJ. The Landscape of Human Cancer Proteins Targeted by SARS-CoV-2. Cancer Discov. 2020 Jul;10(7):916-921. doi: 10.1158/2159-8290.CD-20-0559. Epub 2020 May 22. PubMed PMID: 32444466; PubMed Central PMCID: PMC7357668.

Wang F, Liu Y, Yu Z, Li S, Feng S, Cheng Y, Agard DA. General and robust covalently linked graphene oxide affinity grids for high-resolution cryo-EM. Proc Natl Acad Sci U S A. 2020 Sep 29;117(39):24269-24273. doi: 10.1073/pnas.2009707117. Epub 2020 Sep 10. PMID: 32913054; PMCID: PMC7533693.

Wang R, Simoneau CR, Kulsuptrakul J, Bouhaddou M, Travisano K, Hayashi JM, Carlson-Stevermer J, Oki J, Holden K, Krogan NJ, Ott M, Puschnik AS. Functional genomic screens identify human host factors for SARS-CoV-2 and common cold coronaviruses. bioRxiv [Preprint]. 2020 Sep 24:2020.09.24.312298. doi: 10.1101/2020.09.24.312298. PMID: 32995787; PMCID: PMC7523113.

2019-2020

Ali I, Ruiz DG, Ni Z, Johnson JR, Zhang H, Li PC, Khalid MM, Conrad RJ, Guo X, Min J, Greenblatt J, Jacobson M, Krogan NJ, Ott M.Crosstalk between RNA Pol II C-Terminal Domain Acetylation and Phosphorylation via RPRD Proteins.Mol Cell. 2019 Jun 20;74(6):1164-1174.e4. doi: 10.1016/j.molcel.2019.04.008. Epub 2019 May 1. PubMed PMID: 31054975; PubMed Central PMCID: PMC6588463.

Ball KA, Chan LM, Stanley DJ, Tierney E, Thapa S, Ta HM, Burton L, Binning JM, Jacobson MP, Gross JD.Conformational Dynamics of the HIV-Vif Protein Complex.Biophys J. 2019 Apr 23;116(8):1432-1445. doi: 10.1016/j.bpj.2019.03.014. Epub 2019 Mar 23. PubMed PMID: 30961890; PubMed Central PMCID: PMC6486493.

Binning JM, Chesarino NM, Emerman M, Gross JD.Structural Basis for a Species-Specific Determinant of an SIV Vif Protein toward Hominid APOBEC3G Antagonism.Cell Host Microbe. 2019 Dec 11;26(6):739-747.e4. doi: 10.1016/j.chom.2019.10.014. PubMed PMID: 31830442; PubMed Central PMCID: PMC6913891.

Bruning JM, Wang Y, Oltrabella F, Tian B, Kholodar SA, Liu H, Bhattacharya P, Guo S, Holton JM, Fletterick RJ, Jacobson MP, England PM. Covalent Modification and Regulation of the Nuclear Receptor Nurr1 by a Dopamine Metabolite. Cell Chem Biol. 2019 May 16;26(5):674-685.e6. doi: 10.1016/j.chembiol.2019.02.002. Epub 2019 Mar 7. PubMed PMID: 30853418; PubMed Central PMCID: PMC7185887.

Budzik JM, Swaney DL, Jimenez-Morales D, Johnson JR, Garelis NE, Repasy T, Roberts AW, Popov LM, Parry TJ, Pratt D, Ideker T, Krogan NJ, Cox JS.Dynamic post-translational modification profiling of M. tuberculosis-infected primary macrophages.Elife. 2020 Jan 17;9. doi: 10.7554/eLife.51461. [Epub ahead of print] PubMed PMID: 31951200. 

Buffalo CZ, Stürzel CM, Heusinger E, Kmiec D, Kirchhoff F, Hurley JH, Ren X.Structural Basis for Tetherin Antagonism as a Barrier to Zoonotic Lentiviral Transmission.Cell Host Microbe. 2019 Sep 11;26(3):359-368.e8. doi: 10.1016/j.chom.2019.08.002. Epub 2019 Aug 22. PubMed PMID: 31447307; PubMed Central PMCID: PMC6742535.

Buffalo CZ, Iwamoto Y, Hurley JH, Ren X.How HIV Nef Proteins Hijack Membrane Traffic To Promote Infection.J Virol. 2019 Dec 15;93(24). doi: 10.1128/JVI.01322-19. Print 2019 Dec 15. Review. PubMed PMID: 31578291; PubMed Central PMCID: PMC6880166.

Calderon D, Nguyen MLT, Mezger A, Kathiria A, Müller F, Nguyen V, Lescano N, Wu B, Trombetta J, Ribado JV, Knowles DA, Gao Z, Blaeschke F, Parent AV, Burt TD, Anderson MS, Criswell LA, Greenleaf WJ, Marson A, Pritchard JK.Landscape of stimulation-responsive chromatin across diverse human immune cells.Nat Genet. 2019 Oct;51(10):1494-1505. doi: 10.1038/s41588-019-0505-9. Epub 2019 Sep 30. PubMed PMID: 31570894; PubMed Central PMCID: PMC6858557

Cary DC, Rheinberger M, Rojc A, Peterlin BM.HIV Transcription Is Independent of Mediator Kinases.AIDS Res Hum Retroviruses. 2019 Aug;35(8):710-717. doi: 10.1089/AID.2019.0039. Epub 2019 May 29. PubMed PMID: 31044597; PubMed Central PMCID: PMC6688115.

Colón-Thillet R, Hsieh E, Graf L, McLaughlin RN Jr, Young JM, Kochs G, Emerman M, Malik HS. Combinatorial mutagenesis of rapidly evolving residues yields super-restrictor antiviral proteins. PLoS Biol. 2019 Oct;17(10):e3000181. doi: 10.1371/journal.pbio.3000181. eCollection 2019 Oct. PubMed PMID: 31574080; PubMed Central PMCID: PMC6772013.

Diep J, Ooi YS, Wilkinson AW, Peters CE, Foy E, Johnson JR, Zengel J, Ding S, Weng KF, Laufman O, Jang G, Xu J, Young T, Verschueren E, Kobluk KJ, Elias JE, Sarnow P, Greenberg HB, Hüttenhain R, Nagamine CM, Andino R, Krogan NJ, Gozani O, Carette JE.Enterovirus pathogenesis requires the host methyltransferase SETD3.Nat Microbiol. 2019 Dec;4(12):2523-2537. doi: 10.1038/s41564-019-0551-1. Epub 2019 Sep 16. PubMed PMID: 31527793; PubMed Central PMCID: PMC6879830.

Eckhardt M, Hultquist JF, Kaake RM, Hüttenhain R, Krogan NJ. A systems approach to infectious disease. Nat Rev Genet. 2020 Feb 14;. doi: 10.1038/s41576-020-0212-5. [Epub ahead of print] Review. PubMed PMID: 32060427.

Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Huettenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 Apr 30;. doi: 10.1038/s41586-020-2286-9. [Epub ahead of print] PubMed PMID: 32353859.

Gordon DE, Watson A, Roguev A, Zheng S, Jang GM, Kane J, Xu J, Guo JZ, Stevenson E, Swaney DL, Franks-Skiba K, Verschueren E, Shales M, Crosby DC, Frankel AD, Marson A, Marazzi I, Cagney G, Krogan NJ. A Quantitative Genetic Interaction Map of HIV Infection. Mol Cell. 2020 Apr 16;78(2):197-209.e7. doi: 10.1016/j.molcel.2020.02.004. Epub 2020 Feb 20. PubMed PMID: 32084337.

Holton JM.Challenge data set for macromolecular multi-microcrystallography.Acta Crystallogr D Struct Biol. 2019 Feb 1;75(Pt 2):113-122. doi: 10.1107/S2059798319001426. Epub 2019 Feb 6. PubMed PMID: 30821701; PubMed Central PMCID: PMC6400260.

Hüttenhain R, Xu J, Burton LA, Gordon DE, Hultquist JF, Johnson JR, Satkamp L, Hiatt J, Rhee DY, Baek K, Crosby DC, Frankel AD, Marson A, Harper JW, Alpi AF, Schulman BA, Gross JD, Krogan NJ. ARIH2 Is a Vif-Dependent Regulator of CUL5-Mediated APOBEC3G Degradation in HIV Infection. Cell Host Microbe. 2019 Jul 10;26(1):86-99.e7. doi: 10.1016/j.chom.2019.05.008. Epub 2019 Jun 25. PubMed PMID: 31253590; PubMed Central PMCID: PMC7153695.

Leenay RT, Aghazadeh A, Hiatt J, Tse D, Roth TL, Apathy R, Shifrut E, Hultquist JF, Krogan N, Wu Z, Cirolia G, Canaj H, Leonetti MD, Marson A, May AP, Zou J. Large dataset enables prediction of repair after CRISPR-Cas9 editing in primary T cells. Nat Biotechnol. 2019 Sep;37(9):1034-1037. doi: 10.1038/s41587-019-0203-2. Epub 2019 Jul 29. PubMed PMID: 31359007; NIHMSID:NIHMS1577182.

Li M, Johnson JR, Truong B, Kim G, Weinbren N, Dittmar M, Shah PS, Von Dollen J, Newton BW, Jang GM, Krogan NJ, Cherry S, Ramage H.Identification of antiviral roles for the exon-junction complex and nonsense-mediated decay in flaviviral infection.Nat Microbiol. 2019 Jun;4(6):985-995. doi: 10.1038/s41564-019-0375-z. Epub 2019 Mar 4. PubMed PMID: 30833725; PubMed Central PMCID: PMC6533143.

McDonnell MM, Crawford KHD, Dingens AS, Bloom JD, Emerman M. APOBEC3C Tandem Domain Proteins Create Super Restriction Factors against HIV-1. mBio. 2020 Apr 28;11(2). doi: 10.1128/mBio.00737-20. PubMed PMID: 32345636.

Morris KL, Jones JR, Halebian M, Wu S, Baker M, Armache JP, Avila Ibarra A, Sessions RB, Cameron AD, Cheng Y, Smith CJ. Cryo-EM of multiple cage architectures reveals a universal mode of clathrin self-assembly. Nat Struct Mol Biol. 2019 Oct;26(10):890-898. doi: 10.1038/s41594-019-0292-0. Epub 2019 Oct 3. PubMed PMID: 31582853; PubMed Central PMCID: PMC7100586.

Nguyen DN, Roth TL, Li PJ, Chen PA, Apathy R, Mamedov MR, Vo LT, Tobin VR, Goodman D, Shifrut E, Bluestone JA, Puck JM, Szoka FC, Marson A.Polymer-stabilized Cas9 nanoparticles and modified repair templates increase genome editing efficiency.Nat Biotechnol. 2020 Jan;38(1):44-49. doi: 10.1038/s41587-019-0325-6. Epub 2019 Dec 9. PubMed PMID: 31819258; PubMed Central PMCID: PMC6954310.

Ravalin M, Theofilas P, Basu K, Opoku-Nsiah KA, Assimon VA, Medina-Cleghorn D, Chen YF, Bohn MF, Arkin M, Grinberg LT, Craik CS, Gestwicki JE. Specificity for latent C termini links the E3 ubiquitin ligase CHIP to caspases. Nat Chem Biol. 2019 Aug;15(8):786-794. doi: 10.1038/s41589-019-0322-6. Epub 2019 Jul 18. PubMed PMID: 31320752; PubMed Central PMCID: PMC6693490.

Sauter NK, Kern J, Yano J, Holton JM. Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction. Acta Crystallogr D Struct Biol. 2020 Feb 1;76(Pt 2):176-192. doi: 10.1107/S2059798320000418. Epub 2020 Feb 4. PubMed PMID: 32038048; PubMed Central PMCID: PMC7008510. 
 

Selyutina A, Persaud M, Simons LM, Bulnes-Ramos A, Buffone C, Martinez-Lopez A, Scoca V, Di Nunzio F, Hiatt J, Marson A, Krogan NJ, Hultquist JF, Diaz-Griffero F. Cyclophilin A Prevents HIV-1 Restriction in Lymphocytes by Blocking Human TRIM5α Binding to the Viral Core. Cell Rep. 2020 Mar 17;30(11):3766-3777.e6. doi: 10.1016/j.celrep.2020.02.100. PubMed PMID: 32187548.

Wang F, Yu Z, Betegon M, Campbell MG, Aksel T, Zhao J, Li S, Douglas SM, Cheng Y, Agard DA. Amino and PEG-amino graphene oxide grids enrich and protect samples for high-resolution single particle cryo-electron microscopy. J Struct Biol. 2020 Feb 1;209(2):107437. doi: 10.1016/j.jsb.2019.107437. Epub 2019 Dec 19. PubMed PMID: 31866389; NIHMSID:NIHMS1548553.

 

2018-2019

Basu K, Green EM, Cheng Y, Craik CS. Why recombinant antibodies - benefits and applications. Curr Opin Biotechnol. 2019 Mar 5;60:153-158. doi: 10.1016/j.copbio.2019.01.012. [Epub ahead of print] Review. PubMed PMID: 30849700; NIHMSID:NIHMS1523214.
 
Batra J, Hultquist JF, Liu D, Shtanko O, Von Dollen J, Satkamp L, Jang GM, Luthra P, Schwarz TM, Small GI, Arnett E, Anantpadma M, Reyes A, Leung DW, Kaake R, Haas P, Schmidt CB, Schlesinger LS, LaCount DJ, Davey RA, Amarasinghe GK, Basler CF, Krogan NJ. Protein Interaction Mapping Identifies RBBP6 as a Negative Regulator of Ebola Virus Replication. Cell. 2018 Dec 13;175(7):1917-1930.e13. doi: 10.1016/j.cell.2018.08.044. PubMed PMID: 30550789; PubMed Central PMCID: PMC6366944.  
 
Binning JM, Smith AM, Hultquist JF, Craik CS, Caretta Cartozo N, Campbell MG, Burton L, La Greca F, McGregor MJ, Ta HM, Bartholomeeusen K, Peterlin BM, Krogan NJ, Sevillano N, Cheng Y, Gross JD. Fab-based inhibitors reveal ubiquitin independent functions for HIV Vif neutralization of APOBEC3 restriction factors. PLoS Pathog. 2018 Jan 5;14(1):e1006830. doi: 10.1371/journal.ppat.1006830. eCollection 2018 Jan. PubMed PMID: 29304101; PubMed Central PMCID: PMC5773222.
 
Chen SH, Jang GM, Hüttenhain R, Gordon DE, Du D, Newton BW, Johnson JR, Hiatt J, Hultquist JF, Johnson TL, Liu YL, Burton LA, Ye J, Reichermeier KM, Stroud RM, Marson A, Debnath J, Gross JD, Krogan NJ. CRL4AMBRA1 targets Elongin C for ubiquitination and degradation to modulate CRL5 signaling. EMBO J. 2018 Sep 14;37(18). pii: e97508. doi: 10.15252/embj.201797508. Epub 2018 Aug 30. PubMed PMID: 30166453; PubMed Central PMCID: PMC6138441.
 
Cheng Y. Membrane protein structural biology in the era of single particle cryo-EM. Curr Opin Struct Biol. 2018 Oct;52:58-63. doi: 10.1016/j.sbi.2018.08.008. Epub 2018 Sep 13. Review. PubMed PMID: 30219656; PubMed Central PMCID: PMC6296881.
 
Cheng Y. Single-particle cryo-EM-How did it get here and where will it go. Science. 2018 Aug 31;361(6405):876-880. doi: 10.1126/science.aat4346. Review. PubMed PMID: 30166484; PubMed Central PMCID: PMC6460916.
 
Dai Y, Wynn JE, Peralta AN, Sherpa C, Jayaraman B, Li H, Verma A, Frankel AD, Le Grice SF, Santos WL. Discovery of a Branched Peptide That Recognizes the Rev Response Element (RRE) RNA and Blocks HIV-1 Replication. J Med Chem. 2018 Nov 8;61(21):9611-9620. doi: 10.1021/acs.jmedchem.8b01076. Epub 2018 Oct 18. PubMed PMID: 30289719; PubMed Central PMCID: PMC6557124.
 
Eckhardt M, Zhang W, Gross AM, Von Dollen J, Johnson JR, Franks-Skiba KE, Swaney DL, Johnson TL, Jang GM, Shah PS, Brand TM, Archambault J, Kreisberg JF, Grandis JR, Ideker T, Krogan NJ. Multiple Routes to Oncogenesis are Promoted by the Human Papillomavirus-Host Protein Network. Cancer Discov. 2018 Sep 12. pii: CD-17-1018. doi: 10.1158/2159-8290.CD-17-1018. [Epub ahead of print] PubMed PMID: 30209081.
 
Faust TB, Li Y, Bacon CW, Jang GM, Weiss A, Jayaraman B, Newton BW, Krogan NJ, D'Orso I, Frankel AD. The HIV-1 Tat protein recruits a ubiquitin ligase to reorganize the 7SK snRNP for transcriptional activation. Elife. 2018 May 30;7. pii: e31879. doi: 10.7554/eLife.31879. PubMed PMID: 29845934; PubMed Central PMCID: PMC5999396.
 
Ferdin J, Goričar K, Dolžan V, Plemenitaš A, Martin JN, Peterlin BM, Deeks SG, Lenassi M. Viral protein Nef is detected in plasma of half of HIV-infected adults with undetectable plasma HIV RNA. PLoS One. 2018 Jan 24;13(1):e0191613. doi: 10.1371/journal.pone.0191613. eCollection 2018. PubMed PMID: 29364927; PubMed Central PMCID: PMC5783402.
 
Hultquist JF, Hiatt J, Schumann K, McGregor MJ, Roth TL, Haas P, Doudna JA, Marson A, Krogan NJ. CRISPR-Cas9 genome engineering of primary CD4+ T cells for the interrogation of HIV-host factor interactions. Nat Protoc. 2019 Jan;14(1):1-27. doi: 10.1038/s41596-018-0069-7. PubMed PMID: 30559373.
 
Hurley JH, Johannes L. Retro Styles for Vesicle Coats. Biochemistry. 2019 Feb 12;58(6):433-434. doi: 10.1021/acs.biochem.8b01271. Epub 2019 Jan 17. PubMed PMID: 30653311; PubMed Central PMCID: PMC6372322.
 
Jayaraman B, Fernandes JD, Yang S, Smith C, Frankel AD. Highly Mutable Linker Regions Regulate HIV-1 Rev Function and Stability. Sci Rep. 2019 Mar 26;9(1):5139. doi: 10.1038/s41598-019-41582-7. PubMed PMID: 30914719; PubMed Central PMCID: PMC6435700.
 
Leoz M, Kukanja P, Luo Z, Huang F, Cary DC, Peterlin BM, Fujinaga K. HEXIM1-Tat chimera inhibits HIV-1 replication. PLoS Pathog. 2018 Nov;14(11):e1007402. doi: 10.1371/journal.ppat.1007402. eCollection 2018 Nov. PubMed PMID: 30395647; PubMed Central PMCID: PMC6245832.
 
Masand R, Paulo E, Wu D, Wang Y, Swaney DL, Jimenez-Morales D, Krogan NJ, Wang B. Proteome Imbalance of Mitochondrial Electron Transport Chain in Brown Adipocytes Leads to Metabolic Benefits. Cell Metab. 2018 Mar 6;27(3):616-629.e4. doi: 10.1016/j.cmet.2018.01.018. PubMed PMID: 29514069; PubMed Central PMCID: PMC6020063
 
Morris KL, Buffalo CZ, Stürzel CM, Heusinger E, Kirchhoff F, Ren X, Hurley JH. HIV-1 Nefs Are Cargo-Sensitive AP-1 Trimerization Switches in Tetherin Downregulation. Cell. 2018 Jul 26;174(3):659-671.e14. doi: 10.1016/j.cell.2018.07.004. PubMed PMID: 30053425.
 
Nayak A, Kim DY, Trnka MJ, Kerr CH, Lidsky PV, Stanley DJ, Rivera BM, Li KH, Burlingame AL, Jan E, Frydman J, Gross JD, Andino R. A Viral Protein Restricts Drosophila RNAi Immunity by Regulating Argonaute Activity and Stability. Cell Host Microbe. 2018 Oct 10;24(4):542-557.e9. doi: 10.1016/j.chom.2018.09.006. PubMed PMID: 30308158; PubMed Central PMCID: PMC6450077.
 
Palovcak E, Wang F, Zheng SQ, Yu Z, Li S, Betegon M, Bulkley D, Agard DA, Cheng Y. A simple and robust procedure for preparing graphene-oxide cryo-EM grids. J Struct Biol. 2018 Jul 11. pii: S1047-8477(18)30165-5. doi: 10.1016/j.jsb.2018.07.007. [Epub ahead of print] PubMed PMID: 30017701.
 
Paulo E, Wu D, Wang Y, Zhang Y, Wu Y, Swaney DL, Soucheray M, Jimenez-Morales D, Chawla A, Krogan NJ, Wang B. Sympathetic inputs regulate adaptive thermogenesis in brown adipose tissue through cAMP-Salt inducible kinase axis. Sci Rep. 2018 Jul 20;8(1):11001. doi: 10.1038/s41598-018-29333-6. PubMed PMID: 30030465; PubMed Central PMCID: PMC6054673.
 
Roth TL, Puig-Saus C, Yu R, Shifrut E, Carnevale J, Li PJ, Hiatt J, Saco J, Krystofinski P, Li H, Tobin V, Nguyen DN, Lee MR, Putnam AL, Ferris AL, Chen JW, Schickel JN, Pellerin L, Carmody D, Alkorta-Aranburu G, Del Gaudio D, Matsumoto H, Morell M, Mao Y, Cho M, Quadros RM, Gurumurthy CB, Smith B, Haugwitz M, Hughes SH, Weissman JS, Schumann K, Esensten JH, May AP, Ashworth A, Kupfer GM, Greeley SAW, Bacchetta R, Meffre E, Roncarolo MG, Romberg N, Herold KC, Ribas A, Leonetti MD, Marson A. Reprogramming human T cell function and specificity with non-viral genome targeting. Nature. 2018 Jul;559(7714):405-409. doi: 10.1038/s41586-018-0326-5. Epub 2018 Jul 11. PubMed PMID: 29995861.
 

Schulze-Gahmen U, Hurley JH. Structural mechanism for HIV-1 TAR loop recognition by Tat and the super elongation complex. Proc Natl Acad Sci U S A. 2018 Dec 18;115(51):12973-12978. doi: 10.1073/pnas.1806438115. Epub 2018 Dec 4. PubMed PMID: 30514815; PubMed Central PMCID: PMC6305006.
 
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.
 
Shah PS, Link N, Jang GM, Sharp PP, Zhu T, Swaney DL, Johnson JR, Von Dollen J, Ramage HR, Satkamp L, Newton B, Hüttenhain R, Petit MJ, Baum T, Everitt A, Laufman O, Tassetto M, Shales M, Stevenson E, Iglesias GN, Shokat L, Tripathi S, Balasubramaniam V, Webb LG, Aguirre S, Willsey AJ, Garcia-Sastre A, Pollard KS, Cherry S, Gamarnik AV, Marazzi I, Taunton J, Fernandez-Sesma A, Bellen HJ, Andino R, Krogan NJ. Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis. Cell. 2018 Dec 13; 175(7):1931-1945.e18. PMID: 30550790.
 
Tambe A, East-Seletsky A, Knott GJ, Doudna JA, O'Connell MR. RNA Binding and HEPN-Nuclease Activation Are Decoupled in CRISPR-Cas13a. Cell Rep. 2018 Jul 24;24(4):1025-1036. doi: 10.1016/j.celrep.2018.06.105. PubMed PMID: 30044970; PubMed Central PMCID: PMC6085867.
 
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.
 
Dang B, Wu H, Mulligan VK, Mravic M, Wu Y, Lemmin T, Ford A, Silva DA, Baker D, DeGrado WF. De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures. Proc Natl Acad Sci U S A. 2017 Oct 10;114(41):10852-10857. doi: 10.1073/pnas.1710695114. Epub 2017 Sep 25. PubMed PMID: 28973862; PubMed Central PMCID: PMC5642715.
 
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

Faust TB, Binning JM, Gross JD, Frankel AD. Making Sense of Multifunctional Proteins: Human Immunodeficiency Virus Type 1 Accessory and Regulatory Proteins and Connections to Transcription. Annu Rev Virol. 2017 Sep 29;4(1):241-260. doi: 10.1146/annurev-virology-101416-041654. Review. PMC5750048

Ivry SL, Meyer NO, Winter MB, Bohn MF, Knudsen GM, O'Donoghue AJ, Craik CS. Global substrate specificity profiling of post-translational modifying enzymes. Protein Sci. 2018 Mar;27(3):584-594. doi: 10.1002/pro.3352. Epub 2017 Dec 8. Review. PubMed PMID: 29168252; PubMed Central PMCID: PMC5818756.

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

Metcalf B, Chuang C, Dufu K, Patel MP, Silva-Garcia A, Johnson C, Lu Q, Partridge JR, Patskovska L, Patskovsky Y, Almo SC, Jacobson MP, Hua L, Xu Q, Gwaltney SL 2nd, Yee C, Harris J, Morgan BP, James J, Xu D, Hutchaleelaha A, Paulvannan K, Oksenberg D, Li Z. Discovery of GBT440, an Orally Bioavailable R-State Stabilizer of Sickle Cell Hemoglobin. ACS Med Chem Lett. 2017 Jan 23;8(3):321-326. doi: 10.1021/acsmedchemlett.6b00491. eCollection 2017 Mar 9. PubMed PMID: 28337324; PubMed Central PMCID: PMC5346980.
 
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: e00237-17PMC5432865

Pužar Dominkuš P, Ferdin J, Plemenitaš A, Peterlin BM, Lenassi M. Nef is secreted in exosomes from Nef.GFP-expressing and HIV-1-infected human astrocytes. J Neurovirol. 2017 Oct;23(5):713-724. doi: 10.1007/s13365-017-0552-x. Epub 2017 Jul 31. PubMed PMID: 28762184; PubMed Central PMCID: PMC6010353.
 
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

Tsvetanova NG, Trester-Zedlitz M, Newton BW, Riordan DP, Sundaram AB, Johnson JR, Krogan NJ, von Zastrow M. G Protein-Coupled Receptor Endocytosis Confers Uniformity in Responses to Chemically Distinct Ligands. Mol Pharmacol. 2017 Feb;91(2):145-156. doi: 10.1124/mol.116.106369. Epub 2016 Nov 22. PubMed PMID: 27879340; PubMed Central PMCID: PMC5267521.

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.

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