Clp


 

SAUER LAB

BIOLOGY DEPARTMENT
Alumni (1997-2010)
(reverse listing - please scroll down)

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JOSEPH H. DAVIS

 

JHDavis

 

Joseph H. Davis
Graduate Student (2006-2010)

Email (jhdavis [at] alum.mit.edu or jhdavis [at] scripps.edu

Postdoctoral Associate
The Scripps Research Institute Williamson Lab

JHDavisImage

 

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

MEL

Mary E. Lee
Graduate Student (2005-2010)


 

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

 

Eyal Gur
Postdoc (2005-2009)

Email (gure [at bgu.ac.il)


Faculty

Ben Gurion University of the Negev

protease gear

 

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: 2267-2277.

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

Sarah Barkow
Graduate Student (2005-2009)

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

 

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

BCEZ

 

Brent Cezairliyan
Graduate Student (2003-2008)

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

Postdoc Associate
Massachusetts General Hospital
Ausubel Lab

BCEZ

Cezairliyan, B.O. & Sauer, R.T. (2008) 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. pubmed.citation

 

ANDREAS MARTIN

AMartin

 

Andreas Martin
CSBi Postdoc Fellow (2003-2006 and Research Scientist 2006-2008)

Email (a.martin at berkeley.edu
)

Faculty
Univerty of California at Berkeley

AMartin

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

SMoore

 

Sean D. Moore
Postdoc (2001-2008 )

Email (semoore at mail.ucf.edu
)

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


SMoore

 

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

JoeYakamavich

Joe Yakamavich
Graduate Student (2003-2007 )

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

Senior Scientist
AbbVie

 

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

CHRISTOPHER FARRELL

CFarrell

 

Christopher Farrell
Graduate Student (2002-2007)

Email (cmf at alum.mit.edu
)

Scientist
Microbia

 

CFarrell

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

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

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

KATHLEEN MCGINNESS

KMcginness

 

Kathleen E. McGinness
Postdoc Associate and NIH Postdoc Fellow (2001-2006)

Email (
kmcginne [at] broadinstitute.org)

Director, In Vitro Pharmacology
Broad Institute

 

KMcginness

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

GHersch

Greg Hersch
Grad Student (2002-2006)

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

Consultant
Boston Consulting Group

GHersch

 

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

DBolon

 

Dan Bolon
Postdoc (2001-2005)

Email (Dan.Bolon [at ]umassmed.edu)

Faculty
UMass Medical School

DBolon

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

CHayes

 

Christopher Hayes
Postdoc (2000-2004)

Email (
chayes [at] lifesci.ucsb.edu)

Faculty
University of California Santa Barbara

CHayes

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

JKenniston

 

Jon Kenniston
Graduate Student (2001-2005)

Email (jkenniston [at] dyax.com
)

Dyax Corporation

JKenniston

 

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

SJoshi

 

Shilpa Joshi
Graduate Student (1998-2004)

Email (sajoshi [at] stanford.edu)

Visiting Scientist
Stanford University
Scott Boyd's Lab

 

SJoshi

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

RBurton

 

Randall Burton
Postdoc (1998-2005)

Email (rburton0830 [at] gmail.com)

Research Scientist
US Genomics

RBurton

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

DWah

 

David Wah
Postdoc (2000-2004)

Email ()

Faculty

DWah

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

SSpector

 

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

Email ()

Research Scientist
Millipore Corporation

SSpector

 

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

 

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)

Fellow
Harvard University, Department of Molecular and Cellular Biology

Bijou Bose

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

 

RTabtiang

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

TAnderson

 

Tony Anderson
Graduate Student (1998-2002)

Email (tanthonya at yahoo.com)



University of California, San Francisco

TAnderson

 

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

CSmith

 

Catherine Smith
Postdoc (1997-2001)

Email (catherine_smith3 at merck.com or catksmith at yahoo.com)

Director, External Discovery and PreclinicalSciences, Oncology
Merck Research Laboratories

KSmith

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

MNohaile

Michael Nohaile
Postdoc (1997-2000)

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

Head of Molecular Diagnostics
Novartis

 

MNohaile

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

EGazit

 

Ehud Gazit
Postdoc (1997-2000)

Email (ehudg [at] post.tau.ac.il)

Faculty
Tel-Aviv University

EGazit

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

 

JLo

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

 

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Sauer Lab, Massachusetts Institute of Technology
77 Massachusetts Avenue, 68-571
Cambridge, MA 02139
Telephone: 617.253.6077, Fax: 617.258.0673


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