Tom Alber
Tom AlberProfessor of Biochemistry and Molecular Biology **And member, Lawrence Berkeley National Laboratory, Physical Biosciences Division E-mail: tom@ucxray6.berkeley.edu |
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Full Directory InformationResearch Interests
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Our interests focus on defining the molecular logic of regulatory circuits in physiology and disease. An immediate challenge is to understanding how protein interactions control biochemical reactions. To investigate the fundamental problems of molecular recognition and signaling, the primary tools we use are X-ray crystallography, molecular biology, genomics and physical biochemistry.
Current Projects
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Our attack on the principles of regulation employs two distinct strategies. To explore the diversity of regulatory mechanisms, we are determining the crystal structures of signaling proteins, allosteric enzymes and transcriptional regulators. To discover how protein interactions are restricted, we are designing new protein-protein interactions using coiled coils and other pairing motifs.
Regulatory mechanisms and X-ray crystallography. Structural studies lie at the heart of our exploration of regulatory mechanisms. To speed crystallographic work, we developed a program called Elves, which automates the computational steps of X-ray structure determination. In addition, we built collaboratively a shared X-ray beamline at the Lawrence Berkeley National Laboratory. We routinely use this facility for functionally motivated projects and for an international collaboration to explore the structural genomics of tuberculosis. Our focus in this genomics project is to develop new tools to analyze the structural basis of kinase signaling and gene expression in M. tuberculosis.
A major goal is to understand the functions of the 11 Ser/Thr protein kinases (STKs) and the single predicted Ser/Thr phosphatase in M. tuberculosis. This pathogenic bacterium infects one third of the world's population. TB kills over 3 million people annually, more than any other infectious disease. Our biochemical and structural work on the kinase domain of M. tuberculosis PknB showed that prokaryotic and eukaryotic STKs share a remarkably conserved three-dimensional structure and universal mechanisms of regulation and substrate recognition (Young, et al, 2003). We have set the stage to define the mechanisms of signaling, switching and substrate recognition in this small family of STKs.
Ligand-promoted conformational changes are essential to many biochemical switches. Among the most important conformational transitions are those in the allosteric enzymes, including E. coli ATCase. We proposed in collaboration with H. K. Schachman a new hypothesis that ATCase activation entails an increase in overall flexibility rather than a switch to a specific alternative conformation. This "triggered release" model may be a general, simple mechanism for regulating reactions that entail large conformational changes. We are testing this idea by searching for structural polymorphisms in the crystal structures of ATCase mutants that are activated in the absence of ligands.
To investigate mechanisms of cell-cell communication, we are studying signaling through the TNF receptor class. Our cocrystal structure of a fragment of the TNF receptor associated factor, TRAF2, bound to a peptide from the CD40 receptor defined the trimeric TRAF fold and supported a new mechanism of transmembrane signaling. Current studies focus on two important questions: What determines the specificity of TRAF trimerization and how do the TRAFs generate intracellularsignals?
Protein-protein interactions. Subunit oligomerization in 3-4% of proteins is mediated by coiled coils. These structures, which are helical ropes of two or more strands, are especially simple models for studying protein-protein interactions. Our previous studies led to the discovery of amino acid sequence patterns that distinguish two-, three- and four-helical coiled coils. Our ongoing studies aim to define structure/function relationships in coiled coils and discover the sequence features that restrict coiled-coil pairing.
We initially tackled the problem of pairing specificity by analyzing sequence patterns in natural heterodimers. Pairing rules were derived and tested by designing peptides complementary to the coiled coil of the APC tumor suppressor, a protein that is mutated in most colon tumors. The designed peptides showed 30 fM affinity for the target, and they were used in lieu of antibodies for Western blots and affinity purification. Current challenges include generalizing this approach to design ligands that bind other interesting targets and using these designed tags to investigate the functions of the target proteins. We are developing computational and genetic tools to meet these goals.
Selected Publications
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Structure of M. tuberculosis PknB supports a universal activation mechanism for serine/threonine protein kinases. [T.A. Young, B. Delagoutte, J.A. Endrizzi, and T. Alber (2003). Nature Struct. Biol. 10, 168-174]
The TB structural genomics consortium: Providing a structural foundation for drug discovery. [C.W. Goulding, et al. (2002). Curr. Drug Targets _ Infectious Disorders 2, 121-41]
Comparison of in-vivo selection and rational design of heterodimeric coiled coils. [K.M. Arndt, J.N. Pelletier, K.M. Muller, A. Pluckthun and T. Alber (2002). Structure 10, 1235-1248]
Covariance analysis of RNA Recognition Motifs identifies functionally linked amino acids. [S. Crowder, J. Holton and T. Alber (2001). J. Mol. Biol. 310, 793-800]
The many faces of Ras: How small GTP-binding proteins are recognized. [K.D. Corbett and T. Alber (2001). Trends Biochem. Sci. 26, 711-716]
Last Updated 8/30/2004
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