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. 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.
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  2. 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.
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  3. 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.
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  4. 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.
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  5. 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.
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  6. 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.
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  7. Zhang B, Wang X, Zhao Z, Wang R, Huang X, Zhu Y, Yuan L, Wang Y, Xu X, Burlingame AL, Gao Y, Sun Y, Tang W. OsBRI1 Activates BR Signaling by Preventing Binding between the TPR and Kinase Domains of OsBSK3 via Phosphorylation. Plant Physiol. 2016 Feb; 170(2):1149-61.
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  8. Rys JP, DuFort CC, Monteiro DA, Baird MA, Oses-Prieto JA, Chand S, Burlingame AL, Davidson MW, Alliston TN. Discrete spatial organization of TGFß receptors couples receptor multimerization and signaling to cellular tension. Elife. 2015; 4.
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  9. Wang R, Liu M, Yuan M, Oses-Prieto JA, Cai X, Sun Y, Burlingame AL, Wang ZY, Tang W. 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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  10. Didonna A, Isobe N, Caillier SJ, Li KH, Burlingame AL, Hauser SL, Baranzini SE, Patsopoulos NA, Oksenberg JR. 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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  11. Kim EJ, Youn JH, Park CH, Kim TW, Guan S, Xu S, Burlingame AL, Kim YP, Kim SK, Wang ZY, Kim TW. Oligomerization between BSU1 Family Members Potentiates Brassinosteroid Signaling in Arabidopsis. Mol Plant. 2015 Sep 29.
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  12. Robinson PJ, Trnka MJ, Pellarin R, Greenberg CH, Bushnell DA, Davis R, Burlingame AL, Sali A, Kornberg RD. Molecular architecture of the yeast Mediator complex. Elife. 2015; 4.
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  13. Doron-Mandel E, Alber S, Oses JA, Medzihradszky KF, Burlingame AL, Fainzilber M, Twiss JL, Lee SJ. Isolation and analyses of axonal ribonucleoprotein complexes. Methods Cell Biol. 2016; 131:467-86.
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  14. Lu J, Trnka MJ, Roh SH, Robinson PJ, Shiau C, Fujimori DG, Chiu W, Burlingame AL, Guan S. 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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  15. Guan S, Trnka MJ, Bushnell DA, Robinson PJ, Gestwicki JE, Burlingame AL. 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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  16. Morris M, Knudsen GM, Maeda S, Trinidad JC, Ioanoviciu A, Burlingame AL, Mucke L. 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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  17. Onizawa M, Oshima S, Schulze-Topphoff U, Oses-Prieto JA, Lu T, Tavares R, Prodhomme T, Duong B, Whang MI, Advincula R, Agelidis A, Barrera J, Wu H, Burlingame A, Malynn BA, Zamvil SS, Ma A. 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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  18. Burlingame A, Carr SA, Bradshaw RA, Chalkley RJ. On Credibility, Clarity, and Compliance. Mol Cell Proteomics. 2015 Jul; 14(7):1731-3.
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  19. Muller M, Hutin S, Marigold O, Li KH, Burlingame A, Glaunsinger BA. 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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  20. Onizawa M, Oshima S, Schulze-Topphoff U, Oses-Prieto JA, Lu T, Tavares R, Prodhomme T, Duong B, Whang MI, Advincula R, Agelidis A, Barrera J, Wu H, Burlingame A, Malynn BA, Zamvil SS, Ma A. The ubiquitin-modifying enzyme A20 restricts ubiquitination of the kinase RIPK3 and protects cells from necroptosis. Nat Immunol. 2015 Jun; 16(6):618-27.
    View on PubMed

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