Links for Additional Information

Robert Sauer, Ph.D.

Department of Biology
Salvador E. Luria Professor of Biology

Room 68-571A
617-253-3163 (phone)
617-258-0673 (fax)


B.A. Biophysics, Amherst College 1972
Ph.D. Biochemistry & Molecular Biology, Harvard University 1979
Assistant Professor (1978-1982)
Associate Professor (1982-1987)
Chair, Graduate Program in Biology (1987-1991)
Associate Head, Department of Biology (1989-1998)
Professor, Department of Biology (1987-present)
Head, Department of Biology (1999-2004)
MIT Computational and Systems Biology Initiative (CSBi)

Research Summary

We study the relationships between protein structure, sequence, folding, and function with particular attention to ATP-dependent machines that catalyze protein destruction. All organisms contain ATP-dependent proteases that consist of an AAA+ ATPase and a compartmentalized peptidase. The AAA+ subunits recognize protein substrates, unfold them, and translocate the unfolded polypeptide into the proteolytic chamber of an associated barrel-shaped peptidase for degradation. We focus on the ClpXP and HslUV proteases. ClpX and HslU are homologous hexameric-ring ATPases; ClpP and HslV are non-homologous double-ring peptidases.

The AAA+ ATPase initially grasps protein substrates via an unstructured peptide tag. Substrate selection can be also be regulated by adaptor proteins. For example, the dimeric SspB adaptor binds substrates bearing the ssrA-degradation tag and tethers them to ClpXP for efficient degradation. We have redesigned the ssrA tag to allow more efficient substrate delivery and have designed an SspB-dependent system for temporally controlled degradation of any suitably tagged protein in bacterial cells.

Unfolding of proteins by AAA+ ATPases is a mechanical process that also allows these enzymes to disassemble macromolecular complexes. Current evidence suggests that, following binding of the peptide tag, the enzyme begins to translocate this tag through a central pore, generating a denaturation force when the attached native protein cannot pass through this narrow aperture. Denaturation of native protein substrates by AAA+ machines depends on ATP hydrolysis and on the local stability of the substrate structure immediately adjacent to the degradation tag. ClpX applies an unfolding force iteratively. Depending on the substrate, unfolding of a single substrate can require as few as 10 or as many as 5000 cycles of ATP hydrolysis. This variation occurs because protein substrates that resist denaturation are released from ClpX, resulting in a clutch-like mechanism that prevents stalling of the AAA+ motor when substrates cannot be unfolded. ClpX is a hexamer of identical subunits but allosteric interactions partition its six potential nucleotide-binding sites into three distinct classes. Binding to the degradation tag of protein substrates requires ATP occupancy of one set of sites and ATP/ADP occupancy of a second set of sites. During the normal ATPase cycle, ClpX never passes through an all-ADP state, allowing it to maintain interactions with ClpP and with protein substrates. By linking wild-type and inactive mutant ClpX subunits to form úcovalent hexamers, we found that ATP hydrolysis in a single subunit was sufficient for activity, supporting a probabilistic mechanism of hydrolysis for the subunits of the wild-type enzyme.

Other Research: Protein structure and design
We are using protein design strategies both to dissect structure-function relationships and to develop orthologous synthetic systems that allow specific proteins to be degraded or specific protein complexes to be dismantled in a controlled fashion in cells.

Selected Publications

  • Farrell. C.M., Baker, T.A. & Sauer, R.T. (2007) Altered specificity of a AAA+ protease. Mol. Cell 25, 161-166.
  • McGinness, K.E., Baker, T.A. & Sauer, R.T. (2006) Engineering controllable protein degradation. Mol. Cell 22, 701-707.
  • Bolon, D.N., Grant, R.A., Baker, T.A. & Sauer, R.T. (2005) Specificity versus stability in computational protein design. Proc. Natl. Acad. Sci. USA 102, 12724-12729.
  • Martin, A., Baker, T.A. & Sauer, R.T. (2005) Rebuilt AAA+ motors reveal operating principles for ATP-fueled machines. Nature 437, 1115-1120.
  • Hersch, G.L., Burton, R.E., Bolon, D.N., Baker, T.A. & Sauer, R.T. (2005) Asymmetric interactions of ATP with the AAA+ ClpX6 unfoldase: allosteric control of a protein machine. Cell 121, 1017-1027.
  • Tabtiang, R.K., Cezairliyan, B.O., Grant, R.A, Cochrane, J.C. & Sauer, R.T. (2005) Consolidating critical binding determinants by non-cyclic rearrangement of protein secondary structure. Proc. Natl. Acad. Sci. USA 102, 2305-2309.
  • Bolon, D.N., Wah, D.A., Hersch, G.L., Baker, T.A. & Sauer, R.T. Bivalent tethering of SspB to ClpXP is required for efficient substrate delivery: a protein-design study. Molecular Cell 13, 443-449 (2004).
  • Hayes, C.S. & Sauer, R.T. Cleavage of the A-site mRNA codon during ribosome pausing provides a mechanism for translational quality control. Molecular Cell 12, 903-911 (2003).
  • Kenniston, J.A., Baker, T.A., Fernandez, J.M. & Sauer, R.T. Linkage between ATP consumption and mechanical unfolding during the protein processing reactions of an AAA+ degradation machine. Cell 114, 511-520 (2003).
  • Walsh, N.P., Alba, B.M., Bose, B., Gross, C.A. & Sauer, R.T. OMP peptide signals initiate the envelope-stress response by activating DegS protease through relief of inhibitory interactions mediated by its PDZ domain. Cell 113, 61-71 (2003).
  • Cordes, M.H.J., Burton, R.E., Walsh, N.P., McKnight, C.J. & Sauer, R.T. An Evolutionary Bridge to a New Protein Fold. Nature Structural Biology 7, 1129-1132 (2000).

Last Updated: April 16, 2008