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John Gross, PhD

TitleProfessor
SchoolUCSF School of Pharmacy
DepartmentPharmaceutical Chemistry
Address600 16th St
San Francisco CA 94158
Phone415-514-4402
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    Collapse Biography 
    Collapse Education and Training
    Harvard Medical School, Boston, MAPostdoctoral2003Biological Chemistry
    Massachusetts Institute of Technology, Cambridge, MAPh.D.1998Chemistry
    University of the South, Sewanee, TNB.S.1992Chemistry

    Collapse Overview 
    Collapse Overview
    We investigate molecular machines that coordinate gene expression or antiviral immunity. Research areas include : i- RNA decay enzymes that act in mRNA quality control and gene regulatory pathways, and ii- nucleic acid based immune systems that protect animals from viruses and neutralization of these systems by viral accessory proteins. We use tools from molecular biophysics to understand the structure and regulatory conformational dynamics in these systems with the ultimate goal of defining molecular mechanisms and avenues for structure based drug design.


    Collapse Research 
    Collapse Research Activities and Funding
    Conformational Control of Heterochromatin Formation by the HP-1 Protein from Fission Yeast
    NIH/NIGMS R01GM121962Sep 30, 2017 - Jun 30, 2021
    Role: Principal Investigator
    Developing Small Molecule Screens for Vif-APOBEC3 antagonists
    NIH/NIAID R21AI118528May 1, 2015 - Apr 30, 2017
    Role: Principal Investigator
    A Combined 600 MHz NMR Console for Studies of Cell Extracts and Biological Solids
    NIH/NCRR S10RR026415Sep 13, 2010 - Mar 12, 2013
    Role: Principal Investigator
    Structure and Function of the Decapping Enzyme Complex
    NIH/NIGMS R01GM078360Dec 1, 2008 - Feb 28, 2019
    Role: Principal Investigator
    HARC Center: HIV Accessory and Regulatory Complexes
    NIH/NIGMS P50GM082250Aug 27, 2007 - Aug 31, 2022
    Role: Co-Investigator
    Bio-Organic Biomedical Mass Spectrometry Resource
    NIH P41RR001614Mar 1, 1982 - May 31, 2015
    Role: Co-Investigator

    Collapse ORNG Applications 
    Collapse Websites
    Collapse In The News
    Collapse Twitter

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
    List All   |   Timeline
    1. Paquette DR, Tibble RW, Daifuku TS, Gross J. Control of mRNA decapping by autoinhibition. Nucleic Acids Res. 2018 Mar 29. PMID: 29618050.
      View in: PubMed
    2. Mugridge JS, Tibble RW, Ziemniak M, Jemielity J, Gross J. Structure of the activated Edc1-Dcp1-Dcp2-Edc3 mRNA decapping complex with substrate analog poised for catalysis. Nat Commun. 2018 Mar 20; 9(1):1152. PMID: 29559651.
      View in: PubMed
    3. Binning JM, Smith AM, Hultquist JF, Craik CS, Caretta N, Campbell MG, Burton L, La Greca F, McGregor MJ, Ta HM, Bartholomeeusen K, Peterlin BM, Krogan NJ, Sevillano N, Cheng Y, Gross J. Fab-based inhibitors reveal ubiquitin independent functions for HIV Vif neutralization of APOBEC3 restriction factors. PLoS Pathog. 2018 Jan; 14(1):e1006830. PMID: 29304101.
      View in: PubMed
    4. DR Paquette, JS Mugridge, DE Weinberg, and JD Gross. Application of a Schizosaccharomyces pombe Edc1-fused Dcp1-Dcp2 decapping enzyme for transcription start site mapping. RNA. 2018; 24(2):251-257.
    5. Faust TB, Binning JM, Gross J, 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. PMID: 28961413.
      View in: PubMed
    6. Isaac RS, Sanulli S, Tibble R, Hornsby M, Ravalin M, Craik CS, Gross J, Narlikar GJ. Biochemical Basis for Distinct Roles of the Heterochromatin Proteins Swi6 and Chp2. J Mol Biol. 2017 Nov 24; 429(23):3666-3677. PMID: 28942089.
      View in: PubMed
    7. Sinha KK, Gross J, Narlikar GJ. Distortion of histone octamer core promotes nucleosome mobilization by a chromatin remodeler. Science. 2017 01 20; 355(6322). PMID: 28104838.
      View in: PubMed
    8. Kim DY, Gross J. CBFß and HIV Infection. Adv Exp Med Biol. 2017; 962:415-431. PMID: 28299671.
      View in: PubMed
    9. Weinberg DE, Gross J. Molecular biology: Messenger RNAs marked for longer life. Nature. 2017 01 19; 541(7637):293-294. PMID: 28002405.
      View in: PubMed
    10. Mugridge JS, Ziemniak M, Jemielity J, Gross J. Structural basis of mRNA-cap recognition by Dcp1-Dcp2. Nat Struct Mol Biol. 2016 Nov; 23(11):987-994. PMID: 27694842.
      View in: PubMed
    11. Ziemniak M, Mugridge JS, Kowalska J, Rhoads RE, Gross J, Jemielity J. Two-headed tetraphosphate cap analogs are inhibitors of the Dcp1/2 RNA decapping complex. RNA. 2016 Apr; 22(4):518-29. PMID: 26826132; PMCID: PMC4793208 [Available on 04/01/17].
    12. Jayaraman B, Mavor D, Gross J, Frankel AD. Thermodynamics of Rev-RNA interactions in HIV-1 Rev-RRE assembly. Biochemistry. 2015 Oct 27; 54(42):6545-54. PMID: 26422686; PMCID: PMC4801481.
    13. 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 J, 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. PMID: 25981045; PMCID: PMC4613747.
    14. Ni W, Xu SL, Tepperman JM, Stanley DJ, Maltby DA, Gross J, Burlingame AL, Wang ZY, Quail PH. A mutually assured destruction mechanism attenuates light signaling in Arabidopsis. Science. 2014 Jun 06; 344(6188):1160-1164. PMID: 24904166; PMCID: PMC4414656.
    15. Aglietti RA, Floor SN, McClendon CL, Jacobson MP, Gross J. Active site conformational dynamics are coupled to catalysis in the mRNA decapping enzyme Dcp2. Structure. 2013 Sep 03; 21(9):1571-80. PMID: 23911090; PMCID: PMC3769517.
    16. Watson LC, Kuchenbecker KM, Schiller BJ, Gross J, Pufall MA, Yamamoto KR. The glucocorticoid receptor dimer interface allosterically transmits sequence-specific DNA signals. Nat Struct Mol Biol. 2013 Jul; 20(7):876-83. PMID: 23728292; PMCID: PMC3702670.
    17. Mugridge JS, Gross J. Judge, jury, and executioner: DXO functions as a decapping enzyme and exoribonuclease in pre-mRNA quality control. Mol Cell. 2013 Apr 11; 50(1):2-4. PMID: 23582258; PMCID: PMC3665275.
    18. Fraser JS, Gross J, Krogan NJ. From systems to structure: bridging networks and mechanism. Mol Cell. 2013 Jan 24; 49(2):222-31. PMID: 23352243; PMCID: PMC3558917.
    19. Kim DY, Kwon E, Hartley PD, Crosby DC, Mann S, Krogan NJ, Gross J. CBFß stabilizes HIV Vif to counteract APOBEC3 at the expense of RUNX1 target gene expression. Mol Cell. 2013 Feb 21; 49(4):632-44. PMID: 23333304; PMCID: PMC3582769.
    20. Markley JL, Akutsu H, Asakura T, Baldus M, Boelens R, Bonvin A, Kaptein R, Bax A, Bezsonova I, Gryk MR, Hoch JC, Korzhnev DM, Maciejewski MW, Case D, Chazin WJ, Cross TA, Dames S, Kessler H, Lange O, Madl T, Reif B, Sattler M, Eliezer D, Fersht A, Forman-Kay J, Kay LE, Fraser J, Gross J, Kortemme T, Sali A, Fujiwara T, Gardner K, Luo X, Rizo-Rey J, Rosen M, Gil RR, Ho C, Rule G, Gronenborn AM, Ishima R, Klein-Seetharaman J, Tang P, van der Wel P, Xu Y, Grzesiek S, Hiller S, Seelig J, Laue ED, Mott H, Nietlispach D, Barsukov I, Lian LY, Middleton D, Blumenschein T, Moore G, Campbell I, Schnell J, Vakonakis IJ, Watts A, Conte MR, Mason J, Pfuhl M, Sanderson MR, Craven J, Williamson M, Dominguez C, Roberts G, Günther U, Overduin M, Werner J, Williamson P, Blindauer C, Crump M, Driscoll P, Frenkiel T, Golovanov A, Matthews S, Parkinson J, Uhrin D, Williams M, Neuhaus D, Oschkinat H, Ramos A, Shaw DE, Steinbeck C, Vendruscolo M, Vuister GW, Walters KJ, Weinstein H, Wüthrich K, Yokoyama S. In support of the BMRB. Nat Struct Mol Biol. 2012 Sep; 19(9):854-60. PMID: 22955930.
      View in: PubMed
    21. Kwon E, Kim DY, Ngo TD, Gross CA, Gross J, Kim KK. The crystal structure of the periplasmic domain of Vibrio parahaemolyticus CpxA. Protein Sci. 2012 Sep; 21(9):1334-43. PMID: 22760860; PMCID: PMC3631362.
    22. Floor SN, Borja MS, Gross J. Interdomain dynamics and coactivation of the mRNA decapping enzyme Dcp2 are mediated by a gatekeeper tryptophan. Proc Natl Acad Sci U S A. 2012 Feb 21; 109(8):2872-7. PMID: 22323607; PMCID: PMC3286934.
    23. Jäger S, Kim DY, Hultquist JF, Shindo K, LaRue RS, Kwon E, Li M, Anderson BD, Yen L, Stanley D, Mahon C, Kane J, Franks-Skiba K, Cimermancic P, Burlingame A, Sali A, Craik CS, Harris RS, Gross J, Krogan NJ. Vif hijacks CBF-ß to degrade APOBEC3G and promote HIV-1 infection. Nature. 2011 Dec 21; 481(7381):371-5. PMID: 22190037; PMCID: PMC3310910.
    24. Borja MS, Piotukh K, Freund C, Gross J. Dcp1 links coactivators of mRNA decapping to Dcp2 by proline recognition. RNA. 2011 Feb; 17(2):278-90. PMID: 21148770; PMCID: PMC3022277.
    25. Kwon E, Kim DY, Gross CA, Gross J, Kim KK. The crystal structure Escherichia coli Spy. Protein Sci. 2010 Nov; 19(11):2252-9. PMID: 20799348; PMCID: PMC3005795.
    26. Floor SN, Jones BN, Hernandez GA, Gross J. A split active site couples cap recognition by Dcp2 to activation. Nat Struct Mol Biol. 2010 Sep; 17(9):1096-101. PMID: 20711189; PMCID: PMC2933276.
    27. Nayak A, Berry B, Tassetto M, Kunitomi M, Acevedo A, Deng C, Krutchinsky A, Gross J, Antoniewski C, Andino R. Cricket paralysis virus antagonizes Argonaute 2 to modulate antiviral defense in Drosophila. Nat Struct Mol Biol. 2010 May; 17(5):547-54. PMID: 20400949; PMCID: PMC3815677.
    28. Harigaya Y, Jones BN, Muhlrad D, Gross J, Parker R. Identification and analysis of the interaction between Edc3 and Dcp2 in Saccharomyces cerevisiae. Mol Cell Biol. 2010 Mar; 30(6):1446-56. PMID: 20086104; PMCID: PMC2832485.
    29. Harjes E, Gross PJ, Chen KM, Lu Y, Shindo K, Nowarski R, Gross J, Kotler M, Harris RS, Matsuo H. An extended structure of the APOBEC3G catalytic domain suggests a unique holoenzyme model. J Mol Biol. 2009 Jun 26; 389(5):819-32. PMID: 19389408; PMCID: PMC2700007.
    30. Lampe JN, Floor SN, Gross J, Nishida CR, Jiang Y, Trnka MJ, Ortiz de Montellano PR. Ligand-induced conformational heterogeneity of cytochrome P450 CYP119 identified by 2D NMR spectroscopy with the unnatural amino acid (13)C-p-methoxyphenylalanine. J Am Chem Soc. 2008 Dec 03; 130(48):16168-9. PMID: 18998650; PMCID: PMC2645923.
    31. Floor SN, Jones BN, Gross J. Control of mRNA decapping by Dcp2: An open and shut case? RNA Biol. 2008 Oct-Dec; 5(4):189-92. PMID: 18971632; PMCID: PMC2699264.
    32. Campbell LA, Faivre EJ, Show MD, Ingraham JG, Flinders J, Gross J, Ingraham HA. Decreased recognition of SUMO-sensitive target genes following modification of SF-1 (NR5A1). Mol Cell Biol. 2008 Dec; 28(24):7476-86. PMID: 18838537; PMCID: PMC2593425.
    33. Neher SB, Bradshaw N, Floor SN, Gross J, Walter P. SRP RNA controls a conformational switch regulating the SRP-SRP receptor interaction. Nat Struct Mol Biol. 2008 Sep; 15(9):916-23. PMID: 19172744; PMCID: PMC2767265.
    34. Deshmukh MV, Jones BN, Quang-Dang DU, Flinders J, Floor SN, Kim C, Jemielity J, Kalek M, Darzynkiewicz E, Gross J. mRNA decapping is promoted by an RNA-binding channel in Dcp2. Mol Cell. 2008 Feb 15; 29(3):324-36. PMID: 18280238.
      View in: PubMed
    35. Jones BN, Quang-Dang DU, Oku Y, Gross J. A kinetic assay to monitor RNA decapping under single- turnover conditions. Methods Enzymol. 2008; 448:23-40. PMID: 19111169.
      View in: PubMed
    36. Toyama BH, Kelly MJ, Gross J, Weissman JS. The structural basis of yeast prion strain variants. Nature. 2007 Sep 13; 449(7159):233-7. PMID: 17767153.
      View in: PubMed
    37. Deshmukh MV, Oku Y, Gross J. Backbone and sidechain methyl Ile (delta1), Leu and Val resonance assignments of the catalytic domain of the yeast mRNA decapping enzyme, Dcp2. Biomol NMR Assign. 2007 Jul; 1(1):17-8. PMID: 19636815.
      View in: PubMed
    38. Moerke NJ, Aktas H, Chen H, Cantel S, Reibarkh MY, Fahmy A, Gross J, Degterev A, Yuan J, Chorev M, Halperin JA, Wagner G. Small-molecule inhibition of the interaction between the translation initiation factors eIF4E and eIF4G. Cell. 2007 Jan 26; 128(2):257-67. PMID: 17254965.
      View in: PubMed
    39. von der Haar T, Oku Y, Ptushkina M, Moerke N, Wagner G, Gross J, McCarthy JE. Folding transitions during assembly of the eukaryotic mRNA cap-binding complex. J Mol Biol. 2006 Mar 03; 356(4):982-92. PMID: 16405910.
      View in: PubMed
    40. He C, Hus JC, Sun LJ, Zhou P, Norman DP, Dötsch V, Wei H, Gross J, Lane WS, Wagner G, Verdine GL. A methylation-dependent electrostatic switch controls DNA repair and transcriptional activation by E. coli ada. Mol Cell. 2005 Oct 07; 20(1):117-29. PMID: 16209950.
      View in: PubMed
    41. Chatwood LL, Müller J, Gross J, Wagner G, Lippard SJ. NMR structure of the flavin domain from soluble methane monooxygenase reductase from Methylococcus capsulatus (Bath). Biochemistry. 2004 Sep 28; 43(38):11983-91. PMID: 15379538.
      View in: PubMed
    42. von der Haar T, Gross J, Wagner G, McCarthy JE. The mRNA cap-binding protein eIF4E in post-transcriptional gene expression. Nat Struct Mol Biol. 2004 Jun; 11(6):503-11. PMID: 15164008.
      View in: PubMed
    43. Gross J, Moerke NJ, von der Haar T, Lugovskoy AA, Sachs AB, McCarthy JE, Wagner G. Ribosome loading onto the mRNA cap is driven by conformational coupling between eIF4G and eIF4E. Cell. 2003 Dec 12; 115(6):739-50. PMID: 14675538.
      View in: PubMed
    44. Bennett AE, Gross J, Wagner G. Broadband 13C-13C adiabatic mixing in solution optimized for high fields. J Magn Reson. 2003 Nov; 165(1):59-79. PMID: 14568517.
      View in: PubMed
    45. Gross J, Gelev VM, Wagner G. A sensitive and robust method for obtaining intermolecular NOEs between side chains in large protein complexes. J Biomol NMR. 2003 Mar; 25(3):235-42. PMID: 12652135.
      View in: PubMed
    46. Lugovskoy AA, Degterev AI, Fahmy AF, Zhou P, Gross J, Yuan J, Wagner G. A novel approach for characterizing protein ligand complexes: molecular basis for specificity of small-molecule Bcl-2 inhibitors. J Am Chem Soc. 2002 Feb 20; 124(7):1234-40. PMID: 11841292.
      View in: PubMed
    47. JL Battiste, JD Gross, and G Wagner. Global Fold Determination of large proteins using site-directed spin labeling. Protein NMR for the Millenium. 2002; 79-101.
    48. Gross J, Matsuo H, Fletcher M, Sachs AB, Wagner G. Interactions of the eukaryotic translation initiation factor eIF4E. Cold Spring Harb Symp Quant Biol. 2001; 66:397-402. PMID: 12762042.
      View in: PubMed
    49. Hershey PE, McWhirter SM, Gross J, Wagner G, Alber T, Sachs AB. The Cap-binding protein eIF4E promotes folding of a functional domain of yeast translation initiation factor eIF4G1. J Biol Chem. 1999 Jul 23; 274(30):21297-304. PMID: 10409688.
      View in: PubMed
    50. Hong M, Gross J, Hu W, Griffin RG. Determination of the peptide torsion angle phi by 15N chemical shift and 13Calpha-1Halpha dipolar tensor correlation in solid-state MAS NMR. J Magn Reson. 1998 Nov; 135(1):169-77. PMID: 9799691.
      View in: PubMed
    51. DE Warschawski, JD Gross, and RG Griffin. Effects of membrane peptide dynamics on high-resolution magic-angle spinning NMR. Journal de Chimie Physique et de Physico-Chimie Biologique. 1998; 95(2):460-466.
    52. JD Gross, PR Costa, and RG Griffin. Tilted n-fold symmetric radio frequency pulse sequences: Applications to CSA and heteronuclear dipolar recoupling in homonuclear dipolar coupled spin networks. The Journal of Chemical Physics. 1998; 108(17):7286-7293.
    53. Hong M, Gross J, Rienstra CM, Griffin RG, Kumashiro KK, Schmidt-Rohr K. Coupling amplification in 2D MAS NMR and its application to torsion angle determination in peptides. J Magn Reson. 1997 Nov; 129(1):85-92. PMID: 9405219.
      View in: PubMed
    54. JD Gross, DE Warschawski, and RG Griffin. Dipolar recoupling in MAS NMR: a probe for segmental order in lipid bilayers. Journal of the American Chemical Society. 1997; 119(4):796-802.
    55. M Hong, JD Gross, and RG Griffin. Site-Resolved Determination of Peptide Torsion Angle phi from the relative orientation of backbone NH and CH bonds by solid-state NMR. The Journal of Physical Chemistry B. 1997; 101(30):5869-5874.
    56. M Hong, JD Gross, CM Rienstra, RG Griffin, KK Kumashiro, K Schmidt-Rohr. Coupling amplification in 2D MAS NMR and its application to torsion angle determination in peptides. Journal of Magnetic Resonance. 1997; 129(1):85-92.
    57. PR Costa, JD Gross, M Hong, and RG Griffin. Solid-state NMR measurement of psi in peptides: a NCCN 2Q-heteronuclear local field experiment. Chemical Physics Letters. 1997; 280(1-2):95-103.
    58. JD Gross, PR Costa, JP Dubacq, DE Warschawski, PN Lirsac, PF Devaux, and RG Griffin. Multidimensional NMR in lipid systems. Coherence transfer through J couplings under MAS. Journal of Magnetic Resonance Series B. 1995; 106:190.
    59. AC Bach, CJ Eyermann, JD Gross, MJ Bower, RL Harlow, PC Weber, WF DeGrado. Structural studies of a family of high affinity ligands for GPIIb/IIIa. Journal of the American Chemical Society. 1994; 116(8):3207-3219.
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