Tom Huxford

Professor, Biochemistry

office: CSL 325A
phone: 619-594-1606
Huxford photo

Huxford Group Page

Curriculum Vitae

  • B.S. Biochemistry, Brigham Young University, Provo, Utah, 1995
  • Ph.D. Chemistry, University of California San Diego, La Jolla, California, 2001, Advisor: Dr. Gourisankar Ghosh
  • Postdoc Structural Biology, University of California San Diego, La Jolla, California, 2005, Fellow of the University of California University-wide AIDS Research Program
  • Assistant and Associate Professor, Department of Chemistry & Biochemistry, San Diego State University, 2005-present
  • Assistant and Associate Professor, Molecular Biology Institute, San Diego State University, 2005-present

Research Interests

In this laboratory we use our knowledge and experience in the area of protein structure and function to determine the chemical mechanisms employed by interesting biological factors. The major focus of the laboratory is in understanding regulation in the transcription factor NF-κB signal transduction pathway. NF-κB is a relatively small class of proteins that respond to diverse stimuli by activating the expression of numerous genes. NF-κB responsive genes include many of the key components of the cellular survival program including inflammatory cytokines, mediators and effectors of both innate and adaptive immunity, and inhibitors of apoptosis. Although proper NF-κB function is integral to a cell's ability to fight off infection and respond to stress, too much of an NF-κB response can contribute to states of chronic inflammation such as arthritis, asthma, multiple sclerosis, and colitis. Recently, it has been shown that chronically inflamed tissues can serve as hotbeds for tumor formation. Cellular processes that recognize and kill tumors in healthy tissues fail to function effectively under the influence of the NF-κB cell survival program. Chronic inflammation due to hyperactive NF-κB has also been shown to contribute to sclerotic formation in arteries and heart disease.

NFkB activation

The prototypical NF-κB functions as a heterodimer of p50 and p65 subunits. NF-κB is present in the cytoplasm of all cells as an inactive factor in complex with a member of the IκB inhibitor protein family. Diverse NF-κB-inducing stimuli lead to activation of the IκB kinase complex (IKK). IKK is a large multisubunit complex that specifically phosphorylates a pair of serine amino acid side chains in the amino-terminal region of NF-κB complex-associated IκB. Once phosphorylated, IκB is recognized by a specific E3 Ubiquitin-protein ligase complex leading to its poly-ubiquitinylation. The 26 S proteasome can then recognize and proteolyze IκB. Removal of IκB renders NF-κB active. It rapidly translocates from the cytoplasm to the nucleus where it binds specifically to DNA elements within the promoter regions of target genes and activates their transcription (Figure 1).

We are currently working on the following two NF-κB-related projects:

  1. IKK structure and function.

    IKK is a multisubunit kinase complex that specifically phosphorylates IκB. Purification of IKK from cytokine-induced HeLa cells revealed that it is composed of three subunits. These are referred to as IKKα (IKK1), IKKβ (IKK2), and IKKgamma (NEMO, FIP3). Although IKKα and IKKβ are highly conserved protein subunits, they differ significantly in their cellular function. For example, the IKKβ subunit has been shown to be responsible for activating NF-κB in response to inflammatory stimuli by catalyzing the attachment of two phosphates near the amino-terminus of the classical IκB proteins. Furthermore, IKKβ itself is subject to phosphorylation-dependent regulation of its own catalytic activity. We are interested in understanding the detailed mechanisms of substrate specificity and phosphorylation-dependent regulation of the IKKβ subunit.

  2. Nuclear IκB structure and function.

    The classical NF-κB inhibitor proteins, IκBα, IκBβ, and IκBε, function primarily in the cell cytoplasm by masking NF-κB nuclear localization signals and blocking DNA binding. However, two additional classes of IκB proteins are also integral to NF-κB regulation. The proteins p105 and p100 play a dual roles as IκB proteins and precursors of the mature NF-κB p50 and p52 subunits, respectively. The identification of a third general class of IκB proteins that function exclusively in the nucleus has been made recently. The nuclear IκB proteins include Bcl-3, IκBζ (MAIL), and IκBNS. These proteins all show similar properties: their expression is regulated by NF-κB; they rapidly accumulate in the nucleus; and they have modulatory effects on NF-κB-dependent expression of specific target genes. We have shown that in contrast to classical IκB proteins, the nuclear IκBζ protein binds preferentially to the NF-κB p50 homodimer. We also found that formation of this protein-protein complex does not remove the NF-κB homodimer from binding to target DNA. We are currently interested in studying how assembly of an IκBζ/NF-κB p50/DNA complex in the nucleus activates the expression of specific NF-κB responsive genes such as the cytokine interleukin-6 (IL-6).

    Other projects in which we are currently involved include:

  3. Structure and function of a muscle assembly co-chaperone

    In collaboration with the students in the laboratory of Dr. Sanford I. Bernstein in the Department of Biology at San Diego State University we are studying the structure and in vitro biochemistry of the factor UNC-45 that functions to help assemble skeletal muscles and to repair the misfolded heads of myosin motor proteins.

  4. Structure and selectivity of anti-lipid antibodies

    The hydrolytic products of membrane sphingolipids are potent signaling molecules. In collaboration with the San Diego-based biotechnology company LPath, Inc. we are studying the structures of antibodies that have been raised to recognize specific biologically active lipids.

  5. Selected Publications

    Full Publication list»
    1. "Probing kinase activation and substrate specificity with an engineered monomeric IKK2," Hauenstein A.V., Rogers W.E., Shaul J.D., Huang D.-B., Ghosh G. & Huxford T. Biochemistry 53 2064-2073, 2014.
    2. "A structural basis for IκB Kinase 2 activation via oligomerization-dependent trans auto-phosphorylation," Polley S., Huang D.-B., Hauenstein A.V., Fusco A.J., Zhong X., Vu D., Schröfelbauer B., Kim Y., Hoffmann A., Verma I.M., Ghosh G. & Huxford T., PLoS Biol. 11 e1001581, 2013.
    3. "Transgenic expression and purification of myosin isoforms using the Drosophila melanogaster indirect flight muscle system," Caldwell J.T., Melkani G.C., Huxford T. & Bernstein S.I. Methods 56 25-32, 2012.
    4. "Biochemical and structural characterization of lysophosphatidic acid binding by a humanized monoclonal antibody," Fleming J.K., Wojciak J.M., Campbell M.A. & Huxford T. J. Mol. Biol. 408 462-476, 2011.
    5. "X-ray crystal structure of the UCS domain-containing UNC-45 myosin chaperone from Drosophila melanogaster," Lee C.F., Hauenstein A.V., Fleming J.K., Gasper W.C., Engelke V., Sankaran B., Bernstein S.I. & Huxford T. Structure 19 397-408, 2011.

    M.S. Theses and Ph.D. Dissertations

    1. Dan V. Trinh, M.S. Thesis 2007. Biochemical characterization of IκBζ interactions with NF-κB/DNA complexes.
    2. Jacob D. Shaul, M.S. Thesis 2008. IKKβ phosphorylates IκBα with CK2-like specificity upon removal of C-terminal elements.
    3. Ghazal Farhang, M.S. Thesis 2008. Assaying transcriptional activation by NF-κB p50 Homodimer/IκBζ complexes on κB DNA promoters.
    4. Michaela S. Norrbom, M.S. Thesis 2008. Expression, purification, and in vitro characterization of the Drosophila melanogaster IκB Kinase β subunit.
    5. Jon K. Fleming, M.S. Thesis 2010. Crystallization and x-ray structure determination of the antigen binding portion of a humanized monoclonal anti-lysophosphatidic acid antibody.
    6. Jesal C. Patel, M.S. Thesis 2010. Biochemical characterization of a phosphate-binding domain in STS-1.
    7. Mark Villaluz, M.S. Thesis 2011. Purification and Kinetic Characterization of Soluble Sphingomyelinases C and D.
    8. Danielle DiTirro, M.S. Thesis 2011. Large-scale expression and characterization of a human multi-subuit IKK complex.
    9. Frank Erasmus, M.S. Thesis 2012. Characterization of metal binding by the anti-sphingosine-1-phosphate metalloantibody LT1002.
    10. Deepthi Anipindi, M.S. Thesis 2012. X-ray crystal structures of two thermostable metal binding variants of Streptococcal Protein Gβ1 domain.
    11. Ashlee King, M.S. Thesis 2013. Crystallization of nucleic acid complexes: NF-κB p50 homodimer bound to G-IRE sequences and Holliday Junctions bound to inhibitors of recombination.
    12. Norman Zhu, Ph.D. Dissertation 2013. Structure and biochemistry of IκBζ: A nuclear IκB protein.
    13. Arthur Hauensten, Ph.D. Dissertation 2013. The role of oligomerization in human IKK2 activation as revealed by structural and biophysical studies.
    14. James T. Caldwell, Ph.D. Dissertation 2013. First x-ray crystal structure of an insect muscle myosin.
    15. Scott W. Lashbrook, M.S. Thesis 2014. In vitro analysis of tyrosine auto-phosporylation by the IKK2 enzyme.
    16. Christy Milani, M.S. Thesis 2015. Ideal DNA binding site spacity by NF-κB p50 homodimer.
Full Publications List