We study the relationships between protein structure, function, sequence, and folding, focusing on molecular machines that degrade or remodel proteins and cellular factors that target proteins for these ATP-dependent reactions. Our experimental tools include biochemistry and single-molecule biophysics, structural biology, protein design and engineering, and molecular genetics.
Protein quality control is an essential cellular function in all kingdoms of life. Proteins that are misfolded, damaged, inactive, or no longer necessary are remodeled and/or degraded. For example, all organisms contain proteolytic machines that consist of an AAA+ ATPase and a compartmentalized peptidase. The AAA+ domains of these multimeric machines form a hexameric ring with a narrow central pore or channel. This hexamer recognizes protein substrates, uses cycles of ATP hydrolysis to unfold these molecules, and translocates the unfolded polypeptide into a sequestered proteolytic chamber for degradation. In some cases, AAA+ enzymes also function as molecular chaperones by mechanisms that are still poorly understood. In collaboration with Tania Baker’s lab, we study a number of different AAA+ proteases and/or chaperones that function in bacteria, archaea, and eukaryotes. These enzymes include ClpX and ClpXP, ClpA and ClpAP, HslU and HslUV, Lon, and Cdc48 and Cdc48•20S. We are probing the rules of substrate recognition, studying regulatory factors that enhance or inhibit recognition of specific substrates, and dissecting the mechanisms by which these energy-dependent enzymes catalyze the mechanical unfolding, translocation, and remodeling of protein substrates.
Iosefson, O., Olivares, A.O., Baker, T.A. & Sauer, R.T. (2015) Dissection of axial-pore loop function during unfolding and translocation by a AAA+ proteolytic machine. Cell Reports 12, 1032-1041.
Stinson, B.M., Baytshtok, V., Schmitz, K.R., Baker, T.A. & Sauer, R.T. (2015) Subunit asymmetry and roles of conformational switching in the hexameric AAA+ ring of ClpX. Nat. Struct. Mol. Biol. 22, 411–416.
Baytshtok, V., Baker, T.A. & Sauer, R.T. (2015) Assaying the kinetics of protein denaturation catalyzed by AAA+ unfolding machines and proteases. Proc. Natl. Acad. Sci. USA 112, 5377–5382.
Schmitz, K.R., Carney, D.W., Sello, J.K. & Sauer, R.T. (2014) The crystal structure of M. tuberculosis ClpP1P2 suggests a model for peptidase activation by AAA+ partner binding and substrate delivery. Proc. Natl. Acad. Sci. USA 111, E4587-4595.
Cordova, J.C, Olivares, A.O., Shin, Y., Stinson, B.M., Calmat, S., Schmitz, K.R., Aubin-Tam, M-E. Baker, T.A., Lang, M.J., & Sauer R.T. (2014) Stochastic but highly coordinated protein unfolding and translocation by the ClpXP proteolytic machine. Cell 158, 647-658.
Kim, S. & Sauer, R.T. (2014) Distinct regulatory mechanisms balance DegP proteolysis to maintain cellular fitness during heat stress. Genes Dev. 28, 902-911.
Lima, S., Guo, M.S., Chaba. R., Gross, C.A. & Sauer, R.T. (2013) Dual molecular signals mediate the bacterial response to outer-membrane stress. Science 340, 837-841.
Stinson, B.M., Nager, A.R., Glynn, S.E., Schmitz, K.R., Baker, T.A, and Sauer, R.T. (2013) Nucleotide binding and conformational switching in the hexameric ring of a AAA+ machine. Cell 153, 628-639.