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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Additional Websites

• Burlingame Lab Website

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. Shiau C, Trnka MJ, Bozicevic A, Torres IO, Al-Sady B, Burlingame AL, Narlikar GJ, Fujimori DG. Reconstitution of nucleosome demethylation and catalytic properties of a jumonji histone demethylase. Chem Biol. 2013 Apr 18; 20(4):494-9.
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2. Greninger AL, Knudsen GM, Betegon M, Burlingame AL, Derisi JL. ACBD3 Interaction with TBC1 Domain 22 Protein Is Differentially Affected by Enteroviral and Kobuviral 3A Protein Binding. MBio. 2013; 4(2).
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3. Bessat M, Knudsen G, Burlingame AL, Wang CC. A Minimal Anaphase Promoting Complex/Cyclosome (APC/C) in Trypanosoma brucei. PLoS One. 2013; 8(3):e59258.
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4. Myers SA, Daou S, Affar el B, Burlingame A. Electron transfer dissociation (ETD): The mass spectrometric breakthrough essential for O-GlcNAc protein site assignments-a study of the O-GlcNAcylated protein Host Cell Factor C1. Proteomics. 2013 Mar; 13(6):982-91.
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5. Le DD, Cortesi AT, Myers SA, Burlingame AL, Fujimori DG. Site-specific and regiospecific installation of methylarginine analogues into recombinant histones and insights into effector protein binding. J Am Chem Soc. 2013 Feb 27; 135(8):2879-82.
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6. Kaasik K, Kivimäe S, Allen JJ, Chalkley RJ, Huang Y, Baer K, Kissel H, Burlingame AL, Shokat KM, Ptácek LJ, Fu YH. Glucose Sensor O-GlcNAcylation Coordinates with Phosphorylation to Regulate Circadian Clock. Cell Metab. 2013 Feb 5; 17(2):291-302.
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7. Ilagan JO, Chalkley RJ, Burlingame AL, Jurica MS. Rearrangements within human spliceosomes captured after exon ligation. RNA. 2013 Mar; 19(3):400-12.
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8. Choy JW, Bryant C, Calvet CM, Doyle PS, Gunatilleke SS, Leung SS, Ang KK, Chen S, Gut J, Oses-Prieto JA, Johnston JB, Arkin MR, Burlingame AL, Taunton J, Jacobson MP, McKerrow JM, Podust LM, Renslo AR. Chemical-biological characterization of a cruzain inhibitor reveals a second target and a mammalian off-target. Beilstein J Org Chem. 2013; 9:15-25.
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9. Ouellet H, Chow ED, Guan S, Cox JS, Burlingame AL, de Montellano PR. Genetic and Mass Spectrometric Tools for Elucidating the Physiological Function(s) of Cytochrome P450 Enzymes from Mycobacterium tuberculosis. Methods Mol Biol. 2013; 987:79-94.
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10. Just S, Illing S, Trester-Zedlitz M, Lau EK, Kotowski SJ, Miess E, Mann A, Doll C, Trinidad JC, Burlingame AL, von Zastrow M, Schulz S. Differentiation of opioid drug effects by hierarchical multi-site phosphorylation. Mol Pharmacol. 2013 Mar; 83(3):633-9.
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11. Zhuang M, Guan S, Wang H, Burlingame AL, Wells JA. Substrates of IAP Ubiquitin Ligases Identified with a Designed Orthogonal E3 Ligase, the NEDDylator. Mol Cell. 2013 Jan 24; 49(2):273-82.
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12. Bradshaw RA, Chalkley RJ, Biarc J, Burlingame AL. Receptor tyrosine kinase signaling mechanisms: Devolving TrkA responses with phosphoproteomics. Adv Biol Regul. 2013 Jan; 53(1):87-96.
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13. Robinson PJ, Bushnell DA, Trnka MJ, Burlingame AL, Kornberg RD. Structure of the Mediator Head module bound to the carboxy-terminal domain of RNA polymerase II. Proc Natl Acad Sci U S A. 2012 Oct 30; 109(44):17931-5.
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14. Trinidad JC, Thalhammer A, Burlingame AL, Schoepfer R. Activity-dependent Protein Dynamics Define Interconnected Cores of Co-regulated Postsynaptic Proteins. Mol Cell Proteomics. 2013 Jan; 12(1):29-41.
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15. O'Donoghue AJ, Eroy-Reveles AA, Knudsen GM, Ingram J, Zhou M, Statnekov JB, Greninger AL, Hostetter DR, Qu G, Maltby DA, Anderson MO, Derisi JL, McKerrow JH, Burlingame AL, Craik CS. Global identification of peptidase specificity by multiplex substrate profiling. Nat Methods. 2012 Nov; 9(11):1095-100.
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16. Nagano K, Akpan A, Warnasuriya G, Corless S, Totty N, Yang A, Stein R, Zvelebil M, Stensballe A, Burlingame A, Waterfield M, Cramer R, Timms JF, Naaby-Hansen S. Functional Proteomic Analysis of Long-term Growth Factor Stimulation and Receptor Tyrosine Kinase Coactivation in Swiss 3T3 Fibroblasts. Mol Cell Proteomics. 2012 Dec; 11(12):1690-708.
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17. Crawford ED, Seaman JE, Barber AE, David DC, Babbitt PC, Burlingame AL, Wells JA. Conservation of caspase substrates across metazoans suggests hierarchical importance of signaling pathways over specific targets and cleavage site motifs in apoptosis. Cell Death Differ. 2012 Dec; 19(12):2040-8.
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18. Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ. Systematic functional prioritization of protein posttranslational modifications. Cell. 2012 Jul 20; 150(2):413-25.
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19. Shimbo K, Hsu GW, Nguyen H, Mahrus S, Trinidad JC, Burlingame AL, Wells JA. Quantitative profiling of caspase-cleaved substrates reveals different drug-induced and cell-type patterns in apoptosis. Proc Natl Acad Sci U S A. 2012 Jul 31; 109(31):12432-7.
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20. Stowe IB, Mercado EL, Stowe TR, Bell EL, Oses-Prieto JA, Hernández H, Burlingame AL, McCormick F. A shared molecular mechanism underlies the human rasopathies Legius syndrome and Neurofibromatosis-1. Genes Dev. 2012 Jul 1; 26(13):1421-6.
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