UCSF

Ralph Bradshaw

Ralph Bradshaw

Position

Professor of Chemistry and Pharmaceutical Chemistry

Deputy Director, Mass Spectrometry Facility

Email

rab@cgl.ucsf.edu

Education

Ph.D. Biochemistry 1966 Duke University, Durham, NC
B.A. Chemistry 1962 Colby College, Waterville, ME

Work History

2006-Present: Professor, Department of Pharmaceutical Chemistry, UCSF, San Francisco, CA, and Deputy Director, Mass Spectrometry Facility, UCSF, San Francisco, CA.
2006-Present: Professor Emeritus, Department of Physiology and Biophysics, College of Medicine, University of California, Irvine, Irvine, CA.
2004-2005: Parke-Davis Exchange Fellow, Department of Biochemistry, Cambridge University, Cambridge, United Kingdom.
1997-2006: Professor, Department of Physiology and Biophysics, and Department of Anatomy and Neurobiology, College of Medicine, University of California, Irvine, Irvine, CA.
1993-1996: Professor, Department of Biological Chemistry, College of Medicine, University of California, Irvine, Irvine, CA.
1992-1993: Alexander von Humboldt Senior Scientist, Max Planck Institute of Biochemistry, Department of Molecular Biology, Martinsried, Germany.
1982-1993: Professor and Chair, Department of Biological Chemistry, College of Medicine, University of California, Irvine, Irvine, CA.
1977-1978: Josiah Macy Faculty Scholar, Howard Florey Institute, University of Melbourne, Parkville, Victoria, Australia.
1974-1982: Professor, Department of Biological Chemistry, Washington University School of Medicine, St. Louis, MO.
1972-1974: Associate Professor, Department of Biological Chemistry, Washington University School of Medicine, St. Louis, MO.
1969-1972: Assistant Professor, Department of Biological Chemistry, Washington University School of Medicine, St. Louis, MO.
1967-1969: Senior Fellow and Acting Research Assistant Professor, Department of Biochemistry, University of Washington, Seattle, WA.
1966-1967: Research Associate, Department of Chemistry, Indiana University, Bloomington, IN.

Research Interests

My overall research interests are related to the structure/function relationships of proteins. For many years, these have focused on two areas: eukaryotic signal transduction and co/post-translational processing of protein N-termini. We are presently using proteomic/bioinformatic approaches to study both areas primarily through the use of mass spectrometry.

An important segment of cell signaling is dependent on polypeptide growth factors and their receptors. Our recent studies have focused primarily on the TrkA receptor and the downstream phosphorylations that it induces. Utilizing stably transfected chimeric receptors with the ectodomain of the PDGF receptor and the transmembrane and endodomain of the TrkA receptor to define signaling responses, we have quantitatively determined the shifts (both positive and negative) in the phosphoproteome induced after 20 min of stimulation in PC12 cells. These modifications primarily involve serine and threonine residues (tyrosine modifications generally occur at much shorter time points of stimulation). By comparison to other analyses with the EGF receptor in human cells at the same time interval following activation, there was a dramatic similarity in response as judged by the responses of various kinase classes (determined by substrate motifs). We have also used the same paradigm to study the effects of mutating known tyrosine docking sites (Y490 and Y785) on this profile. These analyses revealed that there are additional signaling regions/docking sites on the TrkA endodomain that are not subject to activation by the phosphoryaltion of Y490 or Y785. We are now expanding these studies to determine the profile of Lys-ε-acetylation and O-GlcNAc modification of serine and threonine residues as an overlay study to the phosphoproteomic analysis. The techniques utilized in these studies will also be useful in other applications such as determining the basis of drug resistance in cancer and in the differentiation of stem cells. In addition, in collaboration with the Shokat Laboratory, we have also been addressing the immediate substrates of the TrkA kinase domain utilizing mutants that can utilize special ATP derivatives and bearing the same signaling alterations.

The earliest modifications of proteins following the initiation of protein synthesis are N-terminal modifications that can be divided into three main groups: those that modify the α-amino group, those that modify the side chain of the N-terminal residue and those that involve proteolysis of one or more amino acids. There are more than three dozen such alterations, some of which are quite common and are essentially ubiquitous, and others that are quite rare. Similarly, some occur as co-translational events while others take place only later in the lifetime of the protein, after it is fully synthesized. We have focused on the removal of initiator methionine residues and the acetylation of the Nα-amino group (with or without the methionine). Defects in these modifications have been increasingly tied to various pathologies and form the basis for further investigations.

Select Publications

Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA. Dissecting the roles of tyrosines 490 and 785 of TrkA protein in the induction of downstream protein phosphorylation using chimeric receptors. J Biol Chem. 288(23), 16606-18 (2013). [Pubmed]

Bradshaw RA, Chalkley RJ, Biarc J, Burlingame AL. Receptor tyrosine kinase signaling mechanisms: Devolving TrkA responses with phosphoproteomics. Adv Biol Regul. 53(1), 87-96 (2013). [Pubmed]

Bonissone S, Gupta N, Romine M, Bradshaw RA, Pevzner PA. N-terminal protein processing: a comparative proteogenomic analysis. Mol Cell Proteomics. 12(1), 14-28 (2013). [Pubmed]

Demont Y, Corbet C, Page A, Ataman-Önal Y, Choquet-Kastylevsky G, Fliniaux I, Le Bourhis X, Toillon RA, Bradshaw RA, Hondermarck H. Pro-nerve growth factor induces autocrine stimulation of breast cancer cell invasion through tropomyosin-related kinase A (TrkA) and sortilin protein. J Biol Chem. 287(3), 1923-31 (2012). [Pubmed]

Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA. The induction of serine/threonine protein phosphorylations by a PDGFR/TrkA chimera in stably transfected PC12 cells. Mol Cell Proteomics. 11(5), 15-30 (2012). [Pubmed]

Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA., Receptor Tyrosine Kinase Signaling: A Proteomic Perspective, Adv Enzyme Regulation, 51(1), 1-13 (2010). [Pubmed]

Bradshaw RA and Burlingame AL. From Proteins to Proteomics, IUBMB Life, 57(4-5), 267 - 272 (2005). [Pubmed]