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

UCSF Profiles | Burlingame Lab Website

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. Doll S, Urisman A, Oses-Prieto JA, Arnott D, Burlingame AL. Quantitative proteomics reveals fundamental regulatory differences in oncogenic HRAS and IDH1 driven astrocytoma. Mol Cell Proteomics. 2016 Nov 10.
    View on PubMed
  2. Barrette AM, Roberts JK, Chapin C, Egan EA, Segal MR, Oses-Prieto JA, Chand S, Burlingame AL, Ballard PL. Antiinflammatory Effects of Budesonide in Human Fetal Lung. Am J Respir Cell Mol Biol. 2016 Nov; 55(5):623-632.
    View on PubMed
  3. Bu SL, Liu C, Liu N, Zhao JL, Ai LF, Chi H, Li KL, Chien CW, Burlingame AL, Zhang SW, Wang ZY. Immuno-purification mass spectrometry identifies protein phosphatase 2A (PP2A) and BIN2/GSK3 as regulators of AKS transcription factors in Arabidopsis. Mol Plant. 2016 Oct 18.
    View on PubMed
  4. Kim S, Maynard JC, Sasaki Y, Strickland A, Sherman DL, Brophy PJ, Burlingame AL, Milbrandt J. Schwann Cell O-GlcNAc Glycosylation Is Required for Myelin Maintenance and Axon Integrity. J Neurosci. 2016 Sep 14; 36(37):9633-46.
    View on PubMed
  5. Robinson PJ, Trnka MJ, Bushnell DA, Davis RE, Mattei PJ, Burlingame AL, Kornberg RD. Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex. Cell. 2016 Sep 8; 166(6):1411-1422.e16.
    View on PubMed
  6. Maynard JC, Burlingame AL, Medzihradszky KF. Cysteine S-linked N-acetylglucosamine (S-GlcNAcylation), A New Post-translational Modification in Mammals. Mol Cell Proteomics. 2016 Nov; 15(11):3405-3411.
    View on PubMed
  7. Levin RS, Hertz NT, Burlingame AL, Shokat KM, Mukherjee S. Innate immunity kinase TAK1 phosphorylates Rab1 on a hotspot for posttranslational modifications by host and pathogen. Proc Natl Acad Sci U S A. 2016 Aug 1.
    View on PubMed
  8. Perry RB, Rishal I, Doron-Mandel E, Kalinski AL, Medzihradszky KF, Terenzio M, Alber S, Koley S, Lin A, Rozenbaum M, Yudin D, Sahoo PK, Gomes C, Shinder V, Geraisy W, Huebner EA, Woolf CJ, Yaron A, Burlingame AL, Twiss JL, Fainzilber M. Nucleolin-Mediated RNA Localization Regulates Neuron Growth and Cycling Cell Size. Cell Rep. 2016 Aug 9; 16(6):1664-76.
    View on PubMed
  9. Lee S, Shang Y, Redmond SA, Urisman A, Tang AA, Li KH, Burlingame AL, Pak RA, Jovicic A, Gitler AD, Wang J, Gray NS, Seeley WW, Siddique T, Bigio EH, Lee VM, Trojanowski JQ, Chan JR, Huang EJ. Activation of HIPK2 Promotes ER Stress-Mediated Neurodegeneration in Amyotrophic Lateral Sclerosis. Neuron. 2016 Jul 6; 91(1):41-55.
    View on PubMed
  10. Burlingame AL. On Strengthening the MCP Editorial Leadership. Mol Cell Proteomics. 2016 Jul; 15(7):2214-6.
    View on PubMed
  11. Wei CQ, Chien CW, Ai LF, Zhao J, Zhang Z, Li KH, Burlingame AL, Sun Y, Wang ZY. The Arabidopsis B-box protein BZS1/BBX20 interacts with HY5 and mediates strigolactone regulation of photomorphogenesis. J Genet Genomics. 2016 Sep 20; 43(9):555-63.
    View on PubMed
  12. Posch C, Sanlorenzo M, Vujic I, Oses-Prieto JA, Cholewa BD, Kim ST, Ma J, Lai K, Zekhtser M, Esteve-Puig R, Green G, Chand S, Burlingame AL, Panzer-Grümayer R, Rappersberger K, Ortiz-Urda S. Phosphoproteomic Analyses of NRAS(G12) and NRAS(Q61) Mutant Melanocytes Reveal Increased CK2a Kinase Levels in NRAS(Q61) Mutant Cells. J Invest Dermatol. 2016 May 29.
    View on PubMed
  13. Sanlorenzo M, Vujic I, Posch C, Ma J, Lin K, Lai K, Lee D, Vujic M, Oses-Prieto JA, Chand S, Rodriguez-Peralto JL, Burlingame A, Ortiz-Urda S. Oncogenic KIT mutations in different exons lead to specific changes in melanocyte phospho-proteome. J Proteomics. 2016 Jul 20; 144:140-7.
    View on PubMed
  14. To TL, Medzihradszky KF, Burlingame AL, DeGrado WF, Jo H, Shu X. Photoactivatable protein labeling by singlet oxygen mediated reactions. Bioorg Med Chem Lett. 2016 Jul 15; 26(14):3359-63.
    View on PubMed
  15. Lewis BA, Burlingame AL, Myers SA. Human RNA Polymerase II Promoter Recruitment in Vitro Is Regulated by O-Linked N-Acetylglucosaminyltransferase (OGT). J Biol Chem. 2016 Jul 1; 291(27):14056-61.
    View on PubMed
  16. Li C, Gu L, Gao L, Chen C, Wei CQ, Qiu Q, Chien CW, Wang S, Jiang L, Ai LF, Chen CY, Yang S, Nguyen V, Qi Y, Snyder MP, Burlingame AL, Kohalmi SE, Huang S, Cao X, Wang ZY, Wu K, Chen X, Cui Y. Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis. Nat Genet. 2016 Jun; 48(6):687-93.
    View on PubMed
  17. Xu SL, Medzihradszky KF, Wang ZY, Burlingame AL, Chalkley RJ. N-Glycopeptide Profiling in Arabidopsis Inflorescence. Mol Cell Proteomics. 2016 Jun; 15(6):2048-54.
    View on PubMed
  18. Myers SA, Peddada S, Chatterjee N, Friedrich T, Tomoda K, Krings G, Thomas S, Maynard J, Broeker M, Thomson M, Pollard K, Yamanaka S, Burlingame AL, Panning B. SOX2 O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells. Elife. 2016; 5.
    View on PubMed
  19. Portnoy V, Lin SH, Li KH, Burlingame A, Hu ZH, Li H, Li LC. saRNA-guided Ago2 targets the RITA complex to promoters to stimulate transcription. Cell Res. 2016 Mar; 26(3):320-35.
    View on PubMed
  20. Roh SH, Kasembeli M, Galaz-Montoya JG, Trnka M, Lau WC, Burlingame A, Chiu W, Tweardy DJ. Chaperonin TRiC/CCT Modulates the Folding and Activity of Leukemogenic Fusion Oncoprotein AML1-ETO. J Biol Chem. 2016 Feb 26; 291(9):4732-41.
    View on PubMed

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