Bob Sauer's Lab

JOSEPH H. DAVIS

Joseph H. Davis
Graduate Student (2006-2010)
jhdavis [at] mit.edu

Faculty
Massachusetts Institute of Technology
Department of Biology - Davis Lab

Davis JH, Baker TA, Sauer RT. Small-molecule control of protein degradation using split adaptors ACS Chem Biol. 2011 Nov 18;6(11):1205-13. Epub 2011 Sep 8. PMID: 21866931 [PubMed - indexed for MEDLINE]

Kelly JR, Rubin AJ, Davis JH, Ajo-Franklin CM, Cumbers J, Czar MJ, de Mora K, Glieberman AL, Monie DD, Endy D. Measuring the activity of BioBrick promoters using an in vivo reference standard
J Biol Eng. 2009 Mar 20;3:4.

Davis JH, Rubin AJ, Sauer RT. (2010) Design, construction and characterization of a set of insulated bacterial promoters Nucleic Acids Res. 2011 Feb;39(3):1131-41. Epub 2010 Sep 15.
PMID: 20843779 [PubMed - indexed for MEDLINE]

Davis, J.H., Baker, T.A. & Sauer, R.T. (2009) Engineering synthetic adaptors and substrates for controlled ClpXP degradation.
J. Biol. Chem. 14, 21848-21855.

Shin, Y., Davis, J.H., Brau, R.R., Martin, A., Kenniston, J.A., Baker, T.A., Sauer, R.T. & Lang, M.J. (2009) Single-molecule denaturation and degradation of proteins by the AAA+ ClpXP protease.
Proc. Natl. Acad. Sci. USA 106, 19340-19345.

MARY LEE

Mary E. Lee
Graduate Student (2005-2010)

Manager
Blue Matter Consulting

Lee, M.E., Baker, T.A. & Sauer, R.T. (2010) Control of substrate gating and translocation into ClpP by channel residues and ClpX binding. J. Mol. Biol. 399, 707-718. PMID: 20416323 [PubMed - indexed for MEDLINE] PMCID: PMC2885556

EYAL GUR

Eyal Gur
Postdoc (2005-2009)
Email (gure[at]exchange.bgu.ac.il)

Faculty
Ben Gurion University of the Negev
Department of Life Sciences

Gur E, Vishkautzan M, Sauer R.T. (2012) Protein unfolding and degradation by the AAA+ Lon protease. Protein Sci. 21:268-278.

Gur, E. & Sauer, R.T. (2009) Degrons in protein substrates program the speed and operating efficiency of the AAA+ Lon proteolytic machine. Proc. Natl. Acad. Sci USA

Gur, E., Sauer, R.T. (2008) Recognition of misfolded proteins by Lon, a AAA+ protease. Genes Dev. 22(16): 2267-77.

Gur, E. & Sauer, R.T. (2008) Reductive evolution of Mycoplasma forced a proteolytic specificity switch in degradation of ssrA-tagged proteins. Proc. Natl. Acad. Sci. USA 105, 16113-16118.

SARAH BARKOW

Sarah Barkow
Graduate Student (2005-2009)
Email (barkow [at] alum.mit.edu)

Team Lead, Consumer Safety Officer
Food and Drug Administration

Barkow, S.R., Levchenko, I., Baker, T.A. & Sauer, R.T. (2009) Polypeptide translocation by the AAA+ ClpXP protease machine. Chemistry & Biology 16, 605-612.

BRENT CEZAIRLIYAN

Brent Cezairliyan
Graduate Student (2003-2008)
Email bcez [at] alum.mit.edu

Research Fellow
Massachusetts General Hospital
Ausubel Lab

Ahuja, N., Korkin, D., Chaba, R., Cezairliyan, B.O., Sauer, R.T., Kim, K.K., & Gross, C.A. (2009) Analyzing the interaction of RseA and RseB, the two negative regulators of the sigmaE envelope stress response, using a combined bioinformatic and experimental strategy. J Biol Chem. 284,5403-5413.

Cezairliyan, B.O. & Sauer, R.T. (2009) Control of P. aeruginosa AlgW protease cleavage of MucA by peptide signals and MucB. Mol. Micro. 72, 368-379.

Cezairliyan, B.O. & Sauer, R.T. (2007) Inhibition of regulated proteolysis by RseB. Proc. Natl. Acad. Sci. USA 10, 3771-3776 .

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.

ANDREAS MARTIN

Andreas Martin
CSBi Postdoc Fellow (2003-2006 and Research Scientist 2006-2008)
Email (a.martin at berkeley.edu )

Faculty
Univerty of California at Berkeley

Martin, A., Baker, T.A. & Sauer, R.T. (2008) Pore loops of the AAA+ ClpX machine grip substrates to drive translocation and unfolding.Nat. Struct. Mol. Biol. 15, 1147-1151.

Martin, A., Baker, T.A. & Sauer, R.T. (2008) Diverse pore loops of the AAA+ ClpX machine mediate unassisted and adaptor-dependent recognition of ssrA-tagged substrates. Mol. Cell 29, 441-450.

Martin, A., Baker, T.A. & Sauer, R.T. (2007) Protein unfolding by a AAA+ protease: critical dependence on ATP-hydrolysis rates and energy landscapes. Nat. Struct. Mol. Biol. 15, 139-145.

Martin, A., Baker, T.A. & Sauer, R.T. (2007) Distinct static and dynamic interactions control ATPase-peptidase communication in a AAA+ protease. Mol. Cell 27, 41-52.

Martin, A., Baker, T.A. & Sauer, R.T. (2005) Rebuilt AAA+ motors reveal operating principles for ATP-fueled machines. Nature 437, 1115-1120. pubmed citation

SEAN MOORE

Sean D. Moore
Postdoc (2001-2008 )
Email (sean.moore (at) ucf.edu)

Faculty
Burnett School of Biomedical Sciences, UCF College of Medicine
University of Central Florida

Moore, S.D. & Sauer, R.T. (2008) Revisiting the mechanism of macrolide-antibiotic resistance mediated by ribosomal protein L22. Proc. Natl. Acad. Sci. USA (in press).

Moore, S.D., Baker, T.A. & Sauer, R.T. (2008) Forced extraction of targeted components from complex macromolecular assemblies. Proc. Natl. Acad. Sci. USA 105, 11685-11690.

Moore, S.E. & Sauer, R.T. (2007) The tmRNA system for translational surveillance and ribosome rescue. Annu. Rev. Biochem. 76.101-124.Moore, S.D., & Sauer, R.T. (2005) Ribosome rescue: tmRNA tagging activity and capacity in Escherichia coli. Molecular Microbiology 58, 456-66. pubmed citation

Moore, S.D., McGinness, K.E. & Sauer, R.T. (2003) A glimpse into tmRNA-mediated ribosome rescue. Science 300, 72-73.

JOSEPH YAKAMAVICH

Joe Yakamavich
Graduate Student (2003-2007 )
Email (jyak [at] alum.mit.edu )

Shire Biotechnology Company

Yakamavich, J.A., Baker, T.A. & Sauer, R.T. (2008) Asymmetric nucleotide transactions of the HslUV protease. J. Mol. Biol. 380, 946–957. pubmed citation

CHRISTOPHER FARRELL

Christopher Farrell
Graduate Student (2002-2007)
Email (cmf [at] alum.mit.edu)

Principal Scientist
DSM-Microbia

Farrell. C.M., Baker, T.A. & Sauer, R.T. (2007) Altered specificity of a AAA+ protease. Mol. Cell 25, 161-166. pubmed citation

Farrell, C.M., Grossman, A.D. & Sauer, R.T. (2005) Cytoplasmic degradation of ssrA-tagged proteins. Mol. Micro. 57, 1750-1761. pubmed citation

KATHLEEN MCGINNESS

Kathleen E. McGinness
Postdoc Associate and NIH Postdoc Fellow (2001-2006)
Email (kmcginne[at] broadinstitute.org)

Director, In Vitro Pharmacology
Broad Institute

Sundar, S., McGinness, K.E., Baker, T.A. & Sauer, R.T. (2010)
Multiple sequence signals direct recognition and degradation of
protein substrates by the AAA+ protease HslUV. J. Mol. Biol. 403, 420-429.

McGinness, K.E., Bolon, D.N., Kaganovich, M., Baker, T.A. & Sauer, R.T. (2007) Altered tethering of the SspB adaptor to the ClpXP protease causes changes in substrate delivery. J. Biol. Chem. 282, 11465-11473.

McGinness, K.E., Baker, T.A., & Sauer, R.T. (2006) Engineering controllable protein degradation. Mol. Cell 22, 701-707. pubmed. citation

McGinness, K.E. & Sauer, R.T. (2004) Ribosomal protein S1 binds mRNA and tmRNA similarly but plays distinct roles in translation of these molecules. Proc. Natl. Acad. Sci. USA 101, 13454-13459. pubmed citation

Moore, S.D., McGinness, K.E. & Sauer, R.T. (2003) A glimpse into tmRNA-mediated ribosome rescue. Science 300, 72-73.

GREG HERSCH

Greg Hersch
Grad Student (2002-2006)
Email (Hersch [at ] alum.mit.edu)
Head of NBS Strategy and Program Management - Novartis
Basal Area, Switzerland

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. pubmed. citation

Hersch, G.L., Baker, T.A. & Sauer, R.T. (2004) SspB delivery of substrates for ClpXP proteolysis probed by th design of mproved degradation tags. Proc. Natl. Acad. Sci. USA 101 (33) 12136-12141 . pubmed. citation

Bolon, D.N., Wah, D.A., Hersch G.L., Baker T.A., & Sauer, R.T. (2004) Bivalent tethering of SspB to ClpXP is required for efficient substrate deliver: a protein-design study. Mol. Cell, 13, 443-449. pubmed. citation

Joshi, S.A., Hersch, G.L., Baker, T.A. & Sauer, R.T. (2004) Communication between ClpX and ClpP during substrate processing and degradation. Nature Structural & Molecular Biology 11, 404-411. pubmed. citation

DANIEL BOLON

Dan Bolon
Postdoc (2001-2005)
Email (Dan.Bolon [at ]umassmed.edu)

Faculty
University of Massachusetts Medical School-Bolon Lab
Department of Biochemistry and Molecular Pharmacology

McGinness, K.E., Bolon, D.N., Kaganovich, M., Baker, T.A. & Sauer, R.T. (2007) Altered tethering of the SspB adaptor to the ClpXP protease causes changes in substrate delivery. J. Biol. Chem. 282, 11465-11473.

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. pubmed. citation

Bolon, D.N., Grant, R.A., Baker, T.A., & Sauer, R.T. (2004) Nucleotide-dependent substrate handoff from the SspB adaptor to the AAA+ ClpXP protease. Mol. Cell 16, 443-450. pubmed. citation

Bolon, D.N., Wah, D.A., Hersch, G.L., Baker, T.A., & Sauer, R.T. (2004) Bivalent tethering of SspB to ClpXP is required for efficient substrate delivery: a protein-design study. Mol. Cell 13, 443-449. pubmed. citation

Wah, D.A., Levchenko, I., Rieckhof, G.E., Bolon, D.N., Baker, T.A., & Sauer, R.T. (2003) Flexible linkers leash the substrate binding domain of SspB to a peptide module that stabilizes delivery complexes with the AAA+ ClpXP protease. Mol. Cell 12, 355-363. pubmed. citation

CHRISTOPHER HAYES

Christopher Hayes
Postdoc (2000-2004)
Email (chayes [at] lifesci.ucsb.edu)

Faculty
University of California Santa Barbara

Hayes, C.S. & Sauer, R.T. (2003) Toxin-antitoxin pairs in bacteria: Killers or stress regulators? Cell. 112, 2-4. pubmed. citation

Hayes, C.S., & Sauer, R.T. (2003) Cleavage of the A site mRNA codon during ribosome pausing provides a mechanism for translational quality control. Mol. Cell 12, 903-911. pubmed. citation

Hayes, C.S., Bose, B. & Sauer, R.T. (2002) Proline residues at the C terminus of nascent chains induce SsrA tagging during translation termination. J. Biol. Chem. 277, 33825-33832. pubmed. citation

Hayes, C.S., Bose, B. & Sauer, R.T. (2002) Stop codons preceded by rare arginine codons are efficient determinants of SsrA-tagging in Escherichia coli. Proc. Natl. Acad. Sci. USA 99, 3440-3445. pubmed. citation

JON KENNISTON

Jon Kenniston
Graduate Student (2001-2005)
Email (jkenniston [at] dyax.com)

Senior Scientist
Dyax Pharmaceuticals, Inc.

Shin, Y., Davis, J.H., Brau, R.R., Martin, A., Kenniston, J.A., Baker, T.A., Sauer, R.T. & Lang, M.J. (2009) Single-molecule denaturation and degradation of proteins by the AAA+ ClpXP protease. Proc. Natl. Acad. Sci. USA 106, 19340-19345.

Kenniston, J.A., Baker, T.A., & Sauer, R.T. (2005) Partitioning between unfolding and release of native domains during ClpXP degradation determines substrate selectivity and partial processing. Proc. Natl. Acad. Sci. USA 102, 1390-1395. pubmed. citation

Kenniston, J.A., Burton, R.E., Siddiqui S.M., Baker, T.A., & Sauer, R.T. (2004) Effects of local protein stability and the geometric position of the substrate degradation tag on the efficiency of ClpXP denaturation and degradation. J. Struct. Biol. 146, 130-140. pubmed. citation

Kenniston, J.A., Baker, T.A., Fernandez, J.M., & Sauer, R.T. (2003) Linkage between ATP consumption and mechanical unfolding during the protein processing reactions of an AAA+ degradation machine. Cell 114, 511-520. pubmed. citation

Kenniston, J.A., and Sauer, R.T. (2004) Signaling Degradation. Nature Structure and Molecular Biology 11, 800-802. pubmed. citation

SHILPA JOSHI

Shilpa Joshi
Graduate Student (1998-2004)
Email Sajoshi [at] stanford.edu

Senior Research Scientist
Stanford University
Scott Boyd's Lab

Joshi, S.A., Hersch, G.L., Baker, T.A. & Sauer, R.T. (2004) Communication between ClpX and ClpP during substrate processing and degradation. Nature Structural & Molecular Biology 11, 404-411. pubmed. citation

Joshi, S.A., Baker, T.A. & Sauer, R.T. (2003) C-terminal domain mutations in ClpX uncouple substrate binding from an engagement step required for unfolding. Mol. Micro. 48, 67-76. pubmed. citation

RANDALL BURTON

Randall Burton
Postdoc (1998-2005)
Email (rburton0830 [at] gmail.com)

Research Scientist
US Genomics

Burton, R.E., Baker, T.A., Sauer, R.T. (2005) Nucleotide-dependent substrate recognition by the AAA+ HsIUV protease. Nature Structural and Molecular Biology, 12: 245-251. pubmed citation

Kenniston, J.A., Burton, R.E., Siddiqui, S.M., Baker, T.A. & Sauer, R.T. (2004) Effects of local protein stability and the geometric position of the substrate degradation tag on the efficiency of ClpXP denaturation and degradation. J. Struct. Biol. 146, 130-140. pubmed citation

Burton, R.E., Baker, T.A. & Sauer, R.T. (2003) Energy-dependent degradation: Linkage between ClpX-catalyzed nucleotide hydrolysis and protein-substrate processing. Protein Sci. 12, 893-902. pubmed citation

Burton, R.E., Siddiqui, S.M., Kim, Y.I., Baker, T.A. & Sauer, R.T. (2001) Effects of protein stability and structure on substrate processing by the ClpXP unfolding and degradation machine. EMBO Journal 20, 3092-3100. pubmed citation

Cordes, M.H.J., Burton, R.E., Walsh, N.P., McKnight, C.J. & Sauer, R.T. (2000) An Evolutionary Bridge to a New Protein Fold. Nature Structural Biology 7, 1129-1132. pubmed citation

Kim, Y.I., Burton, R.E., Burton, B.M., Sauer, R.T. & Baker, T.A. (2000) Dynamics of Substrate Denaturation and Translocation by the ClpXP Degradation Machine. Molecular Cell 5, 639-648. pubmed citation

DAVID WAH

David Wah
Postdoc (2000-2004)
Email (wahdavid [at] gmail.com)

Mount Sinai Innovation Partners

Levchenko, I., Grant, R.A., Wah, D.A., Sauer, R.T., & Baker, T.A. (2003) Structure of a delivery protein for an AAA+ protease in complex with a peptide degradation tag. Mol. Cell 12, 365-372. pubmed. citation

Wah, D.A., Levchenko, I., Rieckhof, G.E., Bolon, D.N., Baker, T.A., & Sauer, R.T. (2003) Flexible linkers leash the substrate binding domain of SspB to a peptide module that stabilizes delivery complexes with the AAA+ ClpXP protease. Mol. Cell 12, 355-363. pubmed. citation

Wah, D.A., Levchenko, I., Baker, T.A., & Sauer, R.T. (2002) Characterization of a specificity factor for an AAA+ ATPase: Assembly of SspB dimers with ssrA-tagged proteins and the ClpX hexamer Chem. Biol. 9, 1237-1245. pubmed. citation

Bolon, D.N., Wah, D.A., Hersch G.L., Baker T.A., & Sauer, R.T. (2004) Bivalent tethering of SspB to ClpXP is required for efficient substrate deliver: a protein-design study. Mol. Cell, 13, 443-449. pubmed. citation

SHARI SPECTOR

Shari Spector
Postdoc Sauer/Biology and Tidor/EECS/BE Labs (1999-2003)
Email :

Business Development Manager
Chemical Biology and Bioacatives
MilliporeSigma

Spector, S., Sauer, R.T., & Tidor, B. (2004) Computational and experimental probes of symmetry mismatches in the Arc repressor-DNA complex. J Mol. Biol. 340, 253-261. pubmed citation

Spector, S., Flynn, J.M., Tidor, B., Baker, T.A., & Sauer, R.T. (2003) Expression of N-formylated proteins in Escherichia coli. Protein Expr. Purif. 32, 317-322. pubmed citation

BIJOU BOSE

Bijou Bose
Technical Assistant , Sauer Lab (2000-2003) and
Graduate Student , Alan Grossman Lab (2003-2009) Massachusetts Institute of Technology

Email (bbose [at] alum.mit.edu)

Microbiologist
Evelo Biosciences

Hayes, C.S., Bose, B. & Sauer, R.T. (2002) Proline residues at the C terminus of nascent chains induce SsrA tagging during translation termination. J. Biol. Chem. 277, 33825-33832. pubmed. citation

Hayes, C.S., Bose, B. & Sauer, R.T. (2002) Stop codons preceded by rare arginine codons are efficient determinants of SsrA-tagging in Escherichia coli. Proc. Natl. Acad. Sci. USA 99, 3440-3445. pubmed. citation

RAMON TABTIANG

NO PHOTO AVAILABLE

Ramon Tabtiang, Esq.
Postdoc (1998-2003)
Email (tabtiang at fr.com)

Lawyer
Fish and Richardson

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. pubmed. citation

TONY ANDERSON

Tony Anderson
Graduate Student (1998-2002)
Email (tanderson9 [at] mgh.harvard.edu)

Medical Doctor
Department of Anesthesia

Massachusetts General Hospital

Anderson, T.A. & Sauer, R.T. (2003) Role of an Ncap Residue in Determining the Stability and Operator-Binding Affinity of Arc Repressor, Biophys. Chem. 100, 341-350. pubmed. citation

CATHERINE SMITH

Catherine Smith
Postdoc (1997-2001)
Email (catksmith [at] yahoo.com)

Director, External Discovery and PreclinicalSciences, Oncology
Merck Research Laboratories

Smith, C.K., Wohnert, J., Sauer, R.T. & Schwalbe, H. (2001) Assignments of the 1H, 13C, and 15N resonances of the substrate-binding SSD domain from Lon protease. Journal of Biomolecular NMR 21, 387-388. pubmed. citation

Smith, C.K., Baker, T.A., & Sauer, R.T. (1999) Lon and Clp Family Proteases and Chaperones Share Homologous Substrate-Recognition Domains. Proc. Natl. Acad. Sci. USA 96, 6678-6682. pubmed. citation

Levchenko, I., Smith, C.K., Walsh, N.P., Sauer, R.T. & Baker, T.A. (1997) PDZ-like Domains Mediate Binding Specificity in the Clp/Hsp100 Family of Chaperones and Protease Regulatory Subunits. Cell 91, 939-947. pubmed. citation

MIKE NOHAILE

Michael Nohaile
Postdoc (1997-2000)
Email (nohaile [at] alum.mit.edu)

Head of Molecular Diagnostics
Novartis

Nohaile, M.J., Hendsch, Z.S., Tidor, B. & Sauer, R.T. (2001) Altering Dimerization Specificity by Changes in Surface Electrostatics. Proc. Natl. Acad. Sci. USA 98, 3109-3114. pubmed. citation

Hendsch, Z.S., Nohaile, M.J., Sauer, R.T., & Tidor, B. (2001) Preferential Heterodimer Formation Via Undercompenstated Electrostatic Interactions. J. Amer. Chem. Soc. 123, 1264-1265. pubmed. citation

EHUD GAZIT

Ehud Gazit
Postdoc (1997-2000)
Email (ehudg [at] post.tau.ac.il)

Faculty
Tel-Aviv University
Department of Molecular Microbiology and Biotechnology

Gazit, E. & Sauer, R.T. (1999) The Doc Toxin and Phd Antidote Proteins of the Bacteriophage P1 Plasmid Addiction System Form a Heterotrimeric Complex. J. Biol. Chem. 274,16813-16818. pubmed. citation

Gazit, E. & Sauer, R.T. (1999) Stability and DNA Binding of the Phd Protein of the Phage P1 Plasmid Addiction System. J. Biol. Chem. 274, 2652-2657. pubmed citation

JOHN LO

NO PHOTO AVAILABLE

John Lo
Graduate Student (1997-2000)
Email (johnlo at alum.mit.edu)
Novartis

Lo, J., Baker, T.A. & Sauer, R.T. (2001) Characterization of the N-terminal Repeat Domain of E. coli ClpA—a Class I Clp/HSP100 ATPase. Protein Science 10, 551-559. pubmed. citation

Singh SK, Rozycki J, Ortega J, Ishikawa T, Lo J, Steven AC, Maurizi MR. (2001) Functional domains of the ClpA and ClpX molecular chaperones identified by limited proteolysis and deletion analysis. J Biol Chem. 276, 29420-29419. pubmed. citation