University of California San Francisco
Helen Diller Family Comprehensive Cancer Center
Alma Burlingame, PhD

Alma Burlingame, PhD

Professor, Departments of Chemistry and Pharmaceutical Chemistry, UCSF

Cancer Center Program Memberships

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

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. Liu Y, Trnka MJ, Guan S, Kwon D, Kim DH, Chen JJ, Greer PA, Burlingame AL, Correia MA. A Novel Mechanism For NF-?B Activation Via I?B Aggregation: Implications For Hepatic Mallory-Denk-Body Induced Inflammation. Mol Cell Proteomics. 2020 Sep 10.
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  2. White CW, Fan X, Maynard JC, Wheatley EG, Bieri G, Couthouis J, Burlingame AL, Villeda SA. Age-related loss of neural stem cell O-GlcNAc promotes a glial fate switch through STAT3 activation. Proc Natl Acad Sci U S A. 2020 Aug 26.
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  3. McGilvray PT, Anghel SA, Sundaram A, Zhong F, Trnka MJ, Fuller JR, Hu H, Burlingame AL, Keenan RJ. An ER translocon for multi-pass membrane protein biogenesis. Elife. 2020 Aug 21; 9.
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  4. Maynard JC, Fujihira H, Dolgonos GE, Suzuki T, Burlingame AL. Cytosolic N-GlcNAc proteins are formed by the action of endo-ß-N-acetylglucosaminidase. Biochem Biophys Res Commun. 2020 Oct 01; 530(4):719-724.
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  5. Petkovic M, Oses-Prieto J, Burlingame A, Jan LY, Jan YN. TMEM16K is an interorganelle regulator of endosomal sorting. Nat Commun. 2020 07 03; 11(1):3298.
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  6. Gierasch LM, Davidson NO, Rye KA, Burlingame AL. Opening ASBMB publications freely to all. J Biol Chem. 2020 May 29; 295(22):7814-7815.
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  7. Gierasch LM, Davidson NO, Rye KA, Burlingame AL. Opening ASBMB publications freely to all. J Lipid Res. 2020 Jul; 61(7):969-970.
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  8. Gierasch LM, Davidson NO, Rye KA, Burlingame AL. Opening ASBMB publications freely to all. Mol Cell Proteomics. 2020 06; 19(6):914-915.
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  9. Garcia VJ, Xu SL, Ravikumar R, Wang W, Elliott L, Gonzalez E, Fesenko M, Altmann M, Brunschweiger B, Falter-Braun P, Moore I, Burlingame A, Assaad FF, Wang ZY. TRIPP Is a Plant-Specific Component of the Arabidopsis TRAPPII Membrane Trafficking Complex with Important Roles in Plant Development. Plant Cell. 2020 07; 32(7):2424-2443.
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  10. von Appen A, LaJoie D, Johnson IE, Trnka MJ, Pick SM, Burlingame AL, Ullman KS, Frost A. LEM2 phase separation promotes ESCRT-mediated nuclear envelope reformation. Nature. 2020 06; 582(7810):115-118.
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  11. Wilkins JA, Kaasik K, Chalkley RJ, Burlingame AL. Characterization of Prenylated C-terminal Peptides Using a Thiopropyl-based Capture Technique and LC-MS/MS. Mol Cell Proteomics. 2020 06; 19(6):1005-1016.
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  12. Gingras AC, Carr SA, Burlingame AL. Virtual Issue: Technological Innovations. Mol Cell Proteomics. 2020 04; 19(4):572-573.
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  13. Burlingame AL, Carr S, Gingras AC. Compliance Checklists No Longer Required at Initial Manuscript Submission. Mol Cell Proteomics. 2020 04; 19(4):571.
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  14. Yang Z, Guo G, Yang N, Pun SS, Ho TKL, Ji L, Hu I, Zhang J, Burlingame AL, Li N. The change of gravity vector induces short-term phosphoproteomic alterations in Arabidopsis. J Proteomics. 2020 Apr 30; 218:103720.
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  15. Gierasch LM, Davidson NO, Rye KA, Burlingame AL. The Data Must Be Accessible to All. Mol Cell Proteomics. 2020 04; 19(4):569-570.
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  16. Gierasch LM, Davidson NO, Rye KA, Burlingame AL. The data must be accessible to all. J Biol Chem. 2020 Mar 27; 295(13):4371.
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  17. Gierasch LM, Davidson NO, Rye KA, Burlingame AL. The data must be accessible to all. J Lipid Res. 2020 Apr; 61(4):465.
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  18. Cuesta A, Wan X, Burlingame AL, Taunton J. Ligand Conformational Bias Drives Enantioselective Modification of a Surface-Exposed Lysine on Hsp90. J Am Chem Soc. 2020 02 19; 142(7):3392-3400.
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  19. Torii T, Ogawa Y, Liu CH, Ho TS, Hamdan H, Wang CC, Oses-Prieto JA, Burlingame AL, Rasband MN. NuMA1 promotes axon initial segment assembly through inhibition of endocytosis. J Cell Biol. 2020 02 03; 219(2).
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  20. Hamdan H, Lim BC, Torii T, Joshi A, Konning M, Smith C, Palmer DJ, Ng P, Leterrier C, Oses-Prieto JA, Burlingame AL, Rasband MN. Mapping axon initial segment structure and function by multiplexed proximity biotinylation. Nat Commun. 2020 01 03; 11(1):100.
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