Alma Burlingame, PhD

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
Alma Burlingame, PhD

Professor, Departments of Chemistry and Pharmaceutical Chemistry, UCSF

alb@cgl.ucsf.edu

Phone: (415) 476-5641, 476-4893 (voice)
Box 0446, UCSF
San Francisco, CA 94143-0446

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Cancer Center Membership

Program Member » Non-aligned

Research Summary

My group has long-standing, extensive expertise and experience in mass spectrometry, proteomics and systems biology, especially focused on sequencing, identification and study of unknown proteins, and the detection, assignment and site-specific dynamics of posttranslational modifications of proteins, particularly OGlcNAcylation, phosphorylation, acetylation, methylation and ubiquitinylation. Over many years we have collaborated with the neurobiological community extensively, including structural characterization of the GPI membrane anchor of the prion protein, structure of the lysyl oxidase co-factor, identification and PTM regulation of proteins in the retrograde signaling complexes in damaged axons, the O-GlcNAc/phosphorylation dynamics at the murine synapse, identification of new proteins involved in the Nodes of Ranvier, etc.

In addition to the work in proteomics and epigenetics above, we have focused significant effort on other studies concerning the architecture of protein complexes and machines for which angstrom resolution structural information has not yet been tractable. For example we have developed a new lysine-lysine cross-linking strategy based on chemical reductive amination that provides comprehensive sequence and cross-link site assignments using electron transfer dissociation (ETD). This information provides accurate distance constraints that complement cryoEM and computer modeling efforts. In parallel software algorithms and scoring strategies have been developed that greatly facilitates the assignment of cross-linked peptides in general. Very recently we have initiated a thrust into development and application of methodology to measure protein complexes directly in the gas phase using a newly acquired high mass Orbitrap Exactive instrument (m/z < 22,000). This effort will complement our long-standing work on chemical cross-linking of protein complexes and machines.

Finally, we have developed a general suite of programs and software tools required for processing large scale mass spectral data sets (HCD, ETD, etc) and stable isotopic labeling experiments (SILAC, iTRAQ, etc) called Protein Prospector.

Education

University of Rhode Island, Kingston, RI, B.S. 1959, Chemistry
MIT, Cambridge, MA, Ph.D., 1962, Chemistry, Physics


Professional Experience

  • 1963-68
    Asst. Professor of Chemistry, U. C. Berkeley, Dept. of Chemistry & Space Sciences Lab
  • 1968-72
    Assoc. Research Chemist, Space Sciences Lab., U.C. Berkeley
  • 1972-84
    Research Chemist, Space Sciences Lab., U.C. Berkeley
  • 1973-84
    Director, Biomedical Mass Spectrometry Resource, Space Sciences Lab., U. C. Berkeley
  • 1978-81
    Adjunct Professor of Chemistry & Pharmaceutical Chemistry, U. C. San Francisco
  • 1978-present
    Director, Biomedical Mass Spectrometry Resource, School of Pharmacy, U. C. San Francisco
  • 1980-present
    Member, The Liver Center, School of Medicine, U. C. San Francisco
  • 1981-present
    Professor of Chemistry & Pharmaceutical Chemistry, U. C. San Francisco
  • 1993-94
    Visiting Professor, Ludwig Institute for Cancer Research, London, UK
  • 1996-2003
    Professor of Biochemistry, University College, London
  • 2006-present
    Member, UCSF Helen Diller Family Comprehensive Cancer Center

Honors & Awards

  • 1970-72
    Guggenheim Fellow, Karolinska Institute, Stockholm
  • 1990-
    Elected Fellow, American Association for the Advancement of Science1999-2006
    Deputy Editor, Molecular and Cellular Proteomics
  • 2002-04
    Physiological Chemistry Study Section CSR, NIH
  • 2006-
    Co-editor, Molecular and Cellular Proteomics

Selected Publications

  1. Discrete spatial organization of TGFß receptors couples receptor multimerization and signaling to cellular tension. Elife. 2015; 4.
    View on PubMed
  2. The Brassinosteroid-Activated BRI1 Receptor Kinase Is Switched off by Dephosphorylation Mediated by Cytoplasm-Localized PP2A B' Subunits. Mol Plant. 2016 Jan 4; 9(1):148-57.
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  3. A non-synonymous single-nucleotide polymorphism associated with multiple sclerosis risk affects the EVI5 interactome. Hum Mol Genet. 2015 Oct 3.
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  4. Oligomerization between BSU1 Family Members Potentiates Brassinosteroid Signaling in Arabidopsis. Mol Plant. 2015 Sep 29.
    View on PubMed
  5. Molecular architecture of the yeast Mediator complex. Elife. 2015; 4.
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  6. Isolation and analyses of axonal ribonucleoprotein complexes. Methods Cell Biol. 2016; 131:467-86.
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  7. Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes. J Am Soc Mass Spectrom. 2015 Sep 1.
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  8. Deconvolution Method for Specific and Nonspecific Binding of Ligand to Multiprotein Complex by Native Mass Spectrometry. Anal Chem. 2015 Aug 18; 87(16):8541-6.
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  9. Tau post-translational modifications in wild-type and human amyloid precursor protein transgenic mice. Nat Neurosci. 2015 Aug; 18(8):1183-9.
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  10. Erratum: The ubiquitin-modifying enzyme A20 restricts ubiquitination of the kinase RIPK3 and protects cells from necroptosis. Nat Immunol. 2015 Jun 18; 16(7):785.
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  11. On Credibility, Clarity, and Compliance. Mol Cell Proteomics. 2015 Jul; 14(7):1731-3.
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  12. A ribonucleoprotein complex protects the interleukin-6 mRNA from degradation by distinct herpesviral endonucleases. PLoS Pathog. 2015 May; 11(5):e1004899.
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  13. The ubiquitin-modifying enzyme A20 restricts ubiquitination of the kinase RIPK3 and protects cells from necroptosis. Nat Immunol. 2015 Jun; 16(6):618-27.
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  14. Minireviews revisited. Mol Cell Proteomics. 2015 Mar; 14(3):455.
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  15. A20 Restricts Ubiquitination of Pro-Interleukin-1ß Protein Complexes and Suppresses NLRP3 Inflammasome Activity. Immunity. 2015 Jan 20; 42(1):55-67.
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  16. Mass spectrometry-based detection and assignment of protein posttranslational modifications. ACS Chem Biol. 2015 Jan 16; 10(1):63-71.
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  17. Human Liver Cytochrome P450 3A4 Ubiquitination: MOLECULAR RECOGNITION BY UBC7-gp78 AUTOCRINE MOTILITY FACTOR RECEPTOR AND UbcH5a-CHIP-Hsc70-Hsp40 E2-E3 UBIQUITIN LIGASE COMPLEXES. J Biol Chem. 2015 Feb 6; 290(6):3308-32.
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  18. NGF and ProNGF: Regulation of neuronal and neoplastic responses through receptor signaling. Adv Biol Regul. 2015 May; 58:16-27.
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  19. MST3 Kinase Phosphorylates TAO1/2 to Enable Myosin Va Function in Promoting Spine Synapse Development. Neuron. 2014 Dec 3; 84(5):968-82.
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  20. Oncogene mimicry as a mechanism of primary resistance to BRAF inhibitors. Cell Rep. 2014 Aug 21; 8(4):1037-48.
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