Don Kirkpatrick

Scientist, Protein Chemistry

POSTDOC MENTOR

"By applying the leading edge technology to biology's most challenging questions, we hope to make medical breakthroughs that impact the lives or patients."

• 6
  years at Genentech
• 18
  publications (2010-12)

I joined Genentech in 2007 after completing a postdoc in the area of mass spectrometry proteomics. My role as a Scientist is to develop and implement new technologies so that we might explore biology beyond the current boundaries of our understanding.

Advances in mass spectrometry have revolutionized the study of cellular proteins, allowing us to elucidate the molecular mechanisms of disease and the effects of therapeutic agents at a depth and scale unthinkable even a decade ago. As is true across Genentech, the research in our group is fast paced and highly collaborative, drawing on the expertise of some of the world's leading experts in biochemistry, cell biology and disease indications. By applying the leading edge technology to biology's most challenging questions, we hope to make medical breakthroughs that impact the lives or patients.

• My Focus

  My research focuses on using mass spectrometry to characterize the proteins present in cells and tissues. Quantitative analysis of cellular proteins and post-translational modifications by mass spectrometry is an effective way to differentiate between biological states. By coupling stable isotope labeling technologies and computational approaches with mass spectrometry proteomics, we have begun to define tissue specific protein-protein interactions, profile signal transduction networks operating through post-translational modifications, and to survey the proteome of cells and tissues in a global and quantitative manner.

  Many of our efforts focus on proteins that sense biological stimuli, transmit essential signals, or convert signals into function. One area of particular interest is the ubiquitin proteasome pathway. Disruption of ubiquitin system has been shown to be an underlying cause of diseases as diverse as cancer, neurodegeneration, and immune dysfunction. While the basic biochemistry of the protein ubiquitination has been elegantly described, much remains to be learned about how ubiquitin modifies the activity other proteins, which enzymes remove ubiquitin from its target substrates, and how these processes change during disease progression and/or therapeutic response. Advances in mass spectrometry offer the opportunity to unravel many of these mysteries.

• Publications

  • OTUB1 modulates c-IAP1 stability to regulate signalling pathways

    EMBO Journal, 2013, ISSN: 0261-4189

    Goncharov, Tatiana; Niessen, Kyle; de Almagro, Maria Cristina; Izrael-Tomasevic, Anita; Fedorova, Anna V; Varfolomeev, Eugene; Arnott, David; Deshayes, Kurt; Kirkpatrick, Donald S; Vucic, Domagoj

     View on PubMed

  • A Novel Peptide-Based SILAC Method to Identify the Posttranslational Modifications Provides Evidence for Unconventional Ubiquitination in the ER-Associated Degradation Pathway

    International Journal of Proteomics, 2013, ISSN: 2090-2166

    Anania, Veronica; Bustos, Daisy; Lill, Jennie; Kirkpatrick, Donald; Coscoy, Laurent

     View on PubMed

  • HectD1 E3 Ligase Modifies Adenomatous Polyposis Coli (APC) with Polyubiquitin to Promote the APC-Axin Interaction

    The Journal of biological chemistry, 2012, ISSN: 0021-9258

    Tran, Hoanh; Bustos, Daisy; Yeh, Ronald; Rubinfeld, Bonnee; Lam, Cynthia; Shriver, Stephanie; Zilberleyb, Inna; Lee, Michelle W; Phu, Lilian; Sarkar, Anjali A; Zohn, Irene E; Wertz, Ingrid E; Kirkpatrick, Donald S; Polakis, Paul

     View on PubMed

  • Ser1292 Autophosphorylation Is an Indicator of LRRK2 Kinase Activity and Contributes to the Cellular Effects of PD Mutations

    Science Translational Medicine, 2012, ISSN: 1946-6234

    Sheng, Zejuan; Zhang, Shuo; Bustos, Daisy; Kleinheinz, Tracy; Le Pichon, Claire E; Dominguez, Sara L; Solanoy, Hilda O; Drummond, Jason; Zhang, Xiaolin; Ding, Xiao; Cai, Fang; Song, Qinghua; Li, Xianting; Yue, Zhenyu; van der Brug, Marcel P; Burdick, Daniel J; Gunzner-Toste, Janet; Chen, Huifen; Liu, Xingrong; Estrada, Anthony A; Sweeney, Zachary K; Scearce-Levie, Kimberly; Moffat, John G; Kirkpatrick, Donald S; Zhu, Haitao

     View on PubMed

  • Loss of the Tumor Suppressor BAP1 Causes Myeloid Transformation

    Science, 2012, ISSN: 0036-8075

    Dey, Anwesha; Seshasayee, Dhaya; Noubade, Rajkumar; French, Dorothy M; Liu, Jinfeng; Chaurushiya, Mira S; Kirkpatrick, Donald S; Pham, Victoria C; Lill, Jennie R; Bakalarski, Corey E; Wu, Jiansheng; Phu, Lilian; Katavolos, Paula; Lafave, Lindsay M; Abdel-Wahab, Omar; Modrusan, Zora; Seshagiri, Somasekar; Dong, Ken; Lin, Zhonghua; Balazs, Mercedesz; Suriben, Rowena; Newton, Kim; Hymowitz, Sarah; Garcia-Manero, Guillermo; Martin, Flavius; Levine, Ross L; Dixit, Vishva M

     View on PubMed

  • Complementary Proteomic Tools for the Dissection of Apoptotic Proteolysis Events

    Journal of Proteome Research, 2012, ISSN: 1535-3893

    Pham, Victoria C.; Pitti, Robert; Anania, Veronica G.; Bakalarski, Corey E.; Bustos, Daisy; Jhunjhunwala, Suchit; Phung, Qui T.; Yu, Kebing; Forrest, William F.; Kirkpatrick, Donald S.; Ashkenazi, Avi; Lill, Jennie R.

     View on PubMed

  • Complementary Proteomic Tools for the Dissection of Apoptotic Proteolysis Events.

    Journal of Proteome Research, 2012, ISSN:

    Pham VC; Pitti R; Anania VG; Bakalarski CE; Bustos D; Jhunjhunwala S; Phung QT; Yu K; Forrest WF; Kirkpatrick DS; Ashkenazi A; Lill JR.

     View on PubMed

  • Engineering and Structural Characterization of a Linear-Polyubiquitin-Specific Antibody

    Journal of Molecular Biology, 2011, ISSN: 0022-2836

    Matsumoto, Marissa L; Dong, Ken C; Yu, Christine; Phu, Lilian; Gao, Xinxin; Hannoush, Rami N; Hymowitz, Sarah G; Kirkpatrick, Donald S; Dixit, Vishva M; Kelley, Robert F

     View on PubMed

  • Preparation of Distinct Ubiquitin Chain Reagents of High Purity and Yield

    Structure, 10 Aug 2011, vol. 19, no. 8, p. 1053-63, ISSN: 1878-4186.

    Dong, Ken C; Helgason, Elizabeth; Yu, Christine; Phu, Lilian; Arnott, David P; Bosanac, Ivan; Compaan, Deanne M; Huang, Oscar W; Fedorova, Anna V; Kirkpatrick, Donald S; Hymowitz, Sarah G; Dueber, Erin C

     View on PubMed

  • Ubiquitin Ligase RNF146 Regulates Tankyrase and Axin to Promote Wnt Signaling

    PLoS ONE, {PLoS-ONE}, 2011, vol. 6, no. 7, article number: e22595, 35 refs, eISSN: 1932-6203. Publisher: Public Library of Science, 185 Berry Street, Suite 1300, San Francisco, CA 94107, USA.

    Callow, Marinella G; Tran, Hoanh; Phu, Lilian; Lau, Ted; Lee, James; Sandoval, Wendy N; Liu, Peter S; Bheddah, Sheila; Tao, Janet; Lill, Jennie R; Hongo, Jo Anne; Davis, David; Kirkpatrick, Donald S; Polakis, Paul; Costa, Mike

     View on PubMed

  • Improved quantitative mass spectrometry methods for characterizing complex ubiquitin signals

    Molecular & Cellular Proteomics, 2011, ISSN: 1535-9476

    Phu, L.; Izrael-Tomasevic, A.; Matsumoto, M.L.; Bustos, D.; Dynek, J.N.; Fedorova, A.V.; Bakalarski, C.E.; Arnott, D.; Deshayes, K.; Dixit, V.M.; Kelley, R.F.; Vucic, D.; Kirkpatrick, D.S.

  • A novel acetylation of β-tubulin by San modulates microtubule polymerization via down-regulating tubulin incorporation.

    Molecular Biology of the Cell, 2010, ISSN: 1939-4586

    Chu, C.W.; Hou, F.; Zhang, J.; Phu, L.; Loktev, A.V.; Kirkpatrick, D.S.; Jackson, P.K.; Zhao, Y.; Zou, H.

  • c-IAP1 and UbcH5 promote K11-linked polyubiquitination of RIP1 in TNF signalling.

    EMBO Journal, 2010, ISSN: 1460-2075

    Dynek, J.N.; Goncharov, T.; Dueber, E.C.; Fedorova, A.V.; Izrael-Tomasevic, A.; Phu, L.; Helgason, E.; Fairbrother, W.J.; Deshayes, K.; Kirkpatrick, D.S.; Vucic, D.

  • Ubiquitin Binding to A20 ZnF4 Is Required for Modulation of NF-κB Signaling.

    Molecular Cell, 2010, ISSN: 1097-2765

    Bosanac, I.; Wertz, I.E.; Pan, B.; Yu, C.; Kusam, S.; Lam, C.; Phu, L.; Phung, Q.; Maurer, B.; Arnott, D.; Kirkpatrick, D.S.; Dixit, V.M.; Hymowitz, S.G.

  • Improved quantitative mass spectrometry methods for characterizing complex ubiquitin signals.

    Molecular & Cellular Proteomics, 2010, ISSN: 1535-9484

    Phu, L.; Izrael, T.A.; Matsumoto, M.L.; Bustos, D.J.; Dynek, J.N.; Fedorova, A.V.; Bakalarski, C.E.; Arnott, D.; Deshayes, K.; Dixit, V.M.; Kelley, R.F.; Vucic, D.; Kirkpatrick, D.S.

  • K11-Linked Polyubiquitination in Cell Cycle Control Revealed by a K11 Linkage-Specific Antibody.

    Molecular Cell, 2010, ISSN: 1097-4164

    Matsumoto, M.; Wickliffe, K.; Dong, K.; Yu, C.; Bosanac, I.; Bustos, D.; Phu, L.; Kirkpatrick, D.; Hymowitz, S.; Rape, M.; Kelley, R.; Dixit, V.

  • GPS navigation of the protein-stability landscape.

    Nature Biotechnology, 2009, ISSN: 1087-0156

    Kirkpatrick, D.S.; Dixit, V.M.

  • Ubiquitin binding modulates IAP antagonist-stimulated proteasomal degradation of c-IAP1 and c-IAP2¹.

    Biochemical Journal, 2009, ISSN: 1470-8728

    Blankenship, J.W.; Varfolomeev, E.; Goncharov, T.; Fedorova, A.V.; Kirkpatrick, D.S.; Izrael-Tomasevic, A.; Phu, L.; Arnott, D.; Aghajan, M.; Zobel, K.; Bazan, J.F.; Fairbrother, W.J.; Deshayes, K.; Vucic, D.

• Education
  • Harvard Medical School, Cell Biology, Postdoctoral Fellow – 2003
  • University of Arizona, Pharmacology and Toxicology, Ph.D. – 2003
  • University of Oklahoma, Biochemistry, B.S. – 1998