Bob Sauer's Lab

VIRGINIA CORNISH

Virginia Cornish
Postdoc (1996-1999)
Email (vc114 at columbia.edu)

Faculty
Columbia University, City of New York

Lin, H., Abida, W.A., Sauer, R.T. & Cornish, V.W. (2000) Dexamethasone-Methotrexate: An Efficient Chemical Inducer of Protein Dimerization In Vivo. J. Amer. Chem. Soc. 122, 4247-4248. pubmed. citation

PETER CHIVERS

Peter Chivers
Postdoc (1996-2003)
Email (chivers at wustl.edu)

Faculty
Washington University in St. Louis

Chivers, P.T. & Sauer, R.T. (2002) NikR repressor: high-affinity nickel binding to the C-terminal domain regulates binding to operator DNA. Chem. & Biol. 9, 1141-1148. pubmed. citation

Chivers, P.T. & Sauer, R.T. (2000) Regulation of High-Affinity Nickel Uptake in Bacteria: Ni2+-Dependent Interaction of NikR with Wild-type and Mutant Operator Sites. J. Biol. Chem. 275, 19735-19741. pubmed. citation

Chivers, P.T. & Sauer, R.T. (1999) NikR is a ribbon-helix-helix DNA-binding protein. Protein Science 8, 2494-2500. pubmed. citation

NATHAN WALSH

Nate Walsh
Graduate Student (1996-2002)
Email (nwalsh at ensemblediscovery.com)

Senior Informatics Scientist
Ensemble Discovery Corporation

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

Cordes, M.J., Walsh, N., McKnight, J. & Sauer, R.T. (1999) Evolution of a Protein Fold In Vitro. Science 284, 325-327. 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

ERIC ROCHE

Eric Roche
Graduate Student (1995-2001)
Email (eric.roche at healthpoint.com)

Biology Scientist
DFB Pharmaceuticals

Roche, E.D. & Sauer, R.T. (2001) Identification of endogenous SsrA-tagged proteins reveals tagging at positions corresponding to stop codons. J. Biol Chem. 276, 28509-28515. pubmed. citation

Karzai, A.W., Roche, E.D. & Sauer, R.T. (2000) The SsrA-SmpB System for Protein Tagging, Directed Degradation, and Ribosome Rescue. Nature Structural Biology 7, 449-455. pubmed. citation

Roche, E.D. & Sauer, R.T. (1999) SsrA-mediated Tagging Caused by Rare Codons and tRNA Scarcity. EMBO J. 18, 4579-4589. pubmed. citation

Gottesman, S., Roche, E., Zhou, Y.N., & Sauer, R.T. (1998) The ClpXP and ClpAP proteases degrade proteins with C-terminal peptide tails added by the SsrA tagging system. Genes & Development 12, 1338-1347. pubmed. citation

ALOK SRIVASTAVA

Alok Srivastava
Graduate Student (1995-2002)
Email (alok.srivastava at gmail.com)

Nidaan, Inc.

Srivastava, A.K., & Sauer, R.T. (2002) Mutational Studies of Protein Stability and Folding of the Hyperstable MYL Arc Repressor Variant. Biophys.Chem. pubmed. citation

Srivastava, A.K. & Sauer, R.T. (2000) Evidence for Partial Secondary Structure Formation in the Transition State for Arc Repressor Refolding and Dimerization. Biochemistry 39, 8308-8314. pubmed. citation

WALI KARZAI

Wali Karzai
Postdoc (1995-2001)
Email (akarzai at ms.cc.sunysb.edu)

Faculty
Stony Brook University

Barends, S., Karzai, A.W., Sauer, R.T., Wower, J. & Kraal, B. (2001) Simultaneous and Functional Binding of SmpB and EF-TU to the Alanyl Acceptor Arm of tmRNA. J. Mol. Biol. 314, 9-21. pubmed. citation

Karzai, A.W. & Sauer, R.T. (2001) Protein Factors Associated with the SsrA•SmpB Tagging and Ribosome Rescue Complex. Proc. Natl. Acad. Sci. USA 98, 3040-3044. pubmed. citation

Karzai, A.W., Roche, E.D. & Sauer, R.T. (2000) The SsrA-SmpB System for Protein Tagging, Directed Degradation, and Ribosome Rescue. Nature Structural Biology 7, 449-455. pubmed. citation

Karzai, A.W. & Sauer, R.T. (1999) SmpB, A Unique RNA-Binding Protein Essential for the Peptide-Tagging Activity of SsrA (tmRNA). EMBO J. 18, 3793-3799. pubmed. citation

Schildbach, J.F., Karzai, A.W., Raumann, B.E. & Sauer, R.T. (1999) Origins of DNA Binding Specificity: Role of Protein Contacts with the DNA Backbone. Proc. Nat. Acad. Sci. USA 96, 811-817. pubmed. citation

DENNIS RENTZEPERIS

Dennis Rentzeperis
Postdoc (1994-1997)
Email (drentze1 at prdus.jnj.com)

Research Scientist
Johnson & Johnson PRD, L.L.C.

Rentzeperis, D., Jonsson, T., & Sauer, R.T. (1999) Acceleration of the Refolding of Arc Repressor by Nucleic Acids and Other Polyanions. Nature Structural Biology 6, 569 - 573. pubmed. citation

Robinson, C.R., Rentzeperis, D., Silva, J.R., & Sauer, R.T. (1997) Formation of a Denatured Dimer Limits the Thermal Stability of Arc Repressor. J. Mol. Biol. 273, 692-700. pubmed. citation

MATT CORDES

Matthew Cordes
Postdoc (1994-1997)
Email (cordes at u.arizona.edu)

Faculty
The University of Arizona

Cordes, M.H.J., Walsh, N.P., McKnight,C.J.&. Sauer R.T. (2003) Solution structure of switch Arc, a mutant with 310 helices replacing a wild-type onβ-ribbon, Journal of Molecular Biology 326, 899-909. 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. citationCordes, M.J., Walsh, N., McKnight, J. & Sauer, R.T. (1999) Evolution of a Protein Fold In Vitro. Science 284, 325-327. pubmed. citation Cordes, M.J. & Sauer, R.T. (1999) Tolerance of a Protein to Multiple Hydrophobic to Polar Surface Substitutions. Protein Science 8, 318-325. pubmed. citationCordes, M.H.J., Davidson, A.R. & Sauer, R.T. (1996) Sequence Space, Folding, and Protein Design. Curr. Opinion Struct. Biol. 6, 3-10. pubmed. citation.

ARIE BERGGRUN

Arie Berggrun
Graduate Student (1994-1997)
Email (aberggrun at amip.com)

AM Investment Partners

Berggrun, A. & Sauer, R.T. (2001) Contributions of Distinct Quaternary Contacts to Cooperative Operator Binding by Mnt Repressor. Proc. Natl. Acad. Sci. USA 98, 2301-2305. pubmed citation

Berggrun, A. & Sauer, R.T. (2000) Interaction of Arg2 in Mnt’s N-terminal Arm with the Central and Flanking Regions of the mnt Operator. J. Mol. Biol. 301, 959-973. pubmed citation

THORLAKUR JONSSON

Thor Jonsson
Postdoc (1994-1996)
Email (thorlakur.jonsson at decode.is)

Research Scientist
deCODE Genetics

Rentzeperis, D., Jonsson, T., & Sauer, R.T. (1999) Acceleration of the Refolding of Arc Repressor by Nucleic Acids and Other Polyanions. Nature Structural Biology 6, 569 - 573. pubmed. citation

Hendsch, Z.S., Jonsson, T., Sauer, R.T. & Tidor, B. (1996) Protein Stabilization By Removal of Unsatisfied Polar Groups: Computational Approaches and Experimental Tests. Biochemistry 35, 7621-7625. pubmed. citation

Jonsson, T., Waldburger, C.D. & Sauer, R.T. (1996) Nonlinear Free Energy Relationships in Arc Repressor Unfolding Imply Existence of Unstable, Native-like Folding Intermediates. Biochemistry 35, 4795-4802. pubmed. citation

Waldburger, C.D., Jonsson, T. & Sauer, R.T. (1996) Barriers to protein folding: Formation of buried polar interactions is a slow step in acquisition of structure. Proc. Natl. Acad. Sci U.S.A. 93, 2629-2634. pubmed. citation

HARALD KOLMAR

Harald Kolmar
Visiting Faculty (1994-1996)
Email (Kolmar at Biochemie-TUD.de)

Faculty
Darmstadt Technical University

Kolmar, H., Waller, P.R.H., & Sauer, R.T. (1996) The DegP and DegQ periplasmic endoproteases of Escherichia coli: Specificity for cleavage sites and substrate conformation. J. Bact. 178, 5925-5929. pubmed. citation

CLIFF ROBINSON

Cliff Robinson
Postdoc (1994-1996)
Email (cliffrobinson at jhu.edu)

Faculty
University of Delaware

Robinson, C.R. & Sauer, R.T. (2000) Striking Stabilization of Arc Repressor by an Engineered Disulfide Bond. Biochemistry 39, 12494-12502. pubmed. citation

Robinson, C.R. & Sauer, R.T.(1998) Optimizing the Stability of Single-Chain Proteins by Linker Length and Composition Mutagenesis. Proc. Natl. Acad. Sci. USA 95, 5929-5934. pubmed. citation

Schildbach, J.F., Robinson, C.R. & Sauer, R.T. (1998) Biophysical characterization of the TraY protein of Escherichia coli F factor. J. Biol. Chem. 273, 1329-1333. pubmed. citation

Robinson, C.R., Rentzeperis, D., Silva, J.R., & Sauer, R.T. (1997) Formation of a Denatured Dimer Limits the Thermal Stability of Arc Repressor. J. Mol. Biol. 273, 692-700. pubmed. citation

Robinson, C.R. & Sauer, R.T. (1996) Equilibrium Stability and Sub-Millisecond Refolding of a Designed Single-Chain Arc Repressor. Biochemistry 35, 13878-13884. pubmed. citation

Robinson, C.R. & Sauer, R.T. (1996) Covalent Attachment of Arc Repressor Subunits by a Peptide Linker Enhances Affinity for Operator DNA. Biochemistry 35, 109-116. pubmed. citation

LYDIA GREGORET

Lydia Gregoret
Postdoc (1993-1997)
Email (lydia.gregoret at alum.bu.edu)

Doctoral Student (Au.D., class of 2013)
Northeastern University

Gregoret, L.M. & Sauer, R.T. (1998) Tolerance of a protein helix to multiple alanine and valine substitutions. Folding & Design 3, 119-126. pubmed. citation

Gregoret, L. and Sauer, R.T. (1993) Additivity of Mutant Effects Assessed by Binomial Mutagenesis. Proc. Nat. Acad. Sci. USA 90, 4246-4250. pubmed. citation

TRACY SMITH SCHMIDT

Tracy (Smith) Schmidt
Graduate Student (1992-1996)
Email (tracysmithschmidt at yahoo.com)

Sciencewriter

Smith, T.L. & Sauer, R.T. (1996) Role of Operator Subsites in Arc Repression. J. Mol. Biol. 264, 233-242. pubmed. citation

Smith, T.L. & Sauer, R.T. (1996) Dual Regulation of Open-Complex Formation and Promoter Clearance by Arc Explains a Novel Repressor to Activator Switch. Proc. Nat. Acad. Sci. USA 93, 8868-8872. pubmed. citation

Smith, T.L. & Sauer, R.T. (1995) P22 Arc Repressor: Role of Cooperativity in Repression and Binding to Operators with Altered Half-Site Spacing. J. Mol. Biol. 249, 729-742. pubmed. citation

Brown, B.M., Milla, M.E., Smith, T.L. & Sauer, R.T. (1994) Scanning Mutagenesis of Arc Repressor as a Functional Probe of Operator Recognition. Nature Struct. Biol. 1, 164-168. pubmed. citation

JOEL SCHILDBACH

Joel Schildbach
Postdoc (1992-1996)
Email (joel at jhu.edu)

Faculty
The Johns Hopkins University

Schildbach, J.F., Karzai, A.W., Raumann, B.E. & Sauer, R.T. (1999) Origins of DNA Binding Specificity: Role of Protein Contacts with the DNA Backbone. Proc. Nat. Acad. Sci. USA 96, 811-817. pubmed. citation

Schildbach, J.F., Robinson, C.R. & Sauer, R.T. (1998) Biophysical characterization of the TraY protein of Escherichia coli F factor. J. Biol. Chem. 273, 1329-1333. pubmed. citation

Sauer, R.T., Milla, M.E., Waldburger, C.D., Brown, B.M. & Schildbach, J.F. (1996) Sequence Determinants of Folding and Stability for the P22 Arc Repressor Dimer. FASEB Journal 10, 42-48. pubmed. citation

Schildbach, J.F., Milla, M.E., Jeffrey, P.D., Raumann, B.E., & Sauer, R.T. (1995) Crystal Structure, Folding, and Operator Binding of the Hyperstable Arc Repressor Mutant PL8. Biochemistry 34, 1405-1412. pubmed. citation

Waldburger, C.D., Schildbach, J.F., & Sauer, R.T. (1995) Are Buried Salt Bridges Important for Protein Stability and Conformational Specificity. Nature Structural Biology 2, 122-128. pubmed. citation

CAREY WALDBURGER

Carey D. Waldburger
Postdoc (1992-1996)
Email (Waldburgerc at wpunj.edu)

Faculty
William Paterson University of New Jersey

Waldburger, C.D. & Sauer, R.T. (1996) Signal Detection by the PhoQ Sensor-Transmitter: Characterization of the Sensor Domain and a Response- Impaired Mutant that Identifies Ligand-Binding Determinants. J. Biol. Chem. 271, 26630- 26636. pubmed. citation

Jonsson, T., Waldburger, C.D. & Sauer, R.T. (1996) Nonlinear Free Energy Relationships in Arc Repressor Unfolding Imply Existence of Unstable, Native-like Folding Intermediates. Biochemistry 35, 4795-4802. pubmed. citation

Waldburger, C.D., Jonsson, T. & Sauer, R.T. (1996) Barriers to protein folding: Formation of buried polar interactions is a slow step in acquisition of structure. Proc. Natl. Acad. Sci U.S.A. 93, 2629-2634. pubmed. citation

Sauer, R.T., Milla, M.E., Waldburger, C.D., Brown, B.M. & Schildbach, J.F. (1996) Sequence Determinants of Folding and Stability for the P22 Arc Repressor Dimer. FASEB Journal 10, 42-48. pubmed. citation

Milla, M.E., Brown, B.M., Waldburger, C.D. & Sauer, R.T. (1995) P22 Arc Repressor: Transition State Properties Inferred from Mutational Effects on the Rates of Protein Unfolding and Refolding. Biochemistry 34, 13914-13919. pubmed. citation

Waldburger, C.D. & Sauer, R.T. (1995) Domains of Mnt Repressor: Roles in Tetramer Formation, Protein Stability, and Operator DNA Binding. Biochemistry 34, 13109-13116. pubmed. citation

Waldburger, C.D., Schildbach, J.F., & Sauer, R.T. (1995) Are Buried Salt Bridges Important for Protein Stability and Conformational Specificity. Nature Structural Biology 2, 122-128. pubmed. citation

PATRICK WALLER

Patrick R.H. Waller
Graduate Student (1992-1996)
Email (pwaller at wolfgreenfield.com)

Shareholder and Member of the
Biotechnology Group
Wolf, Greenfield & Sacks, PC

Kolmar, H., Waller, P.R.H., & Sauer, R.T. (1996) The DegP and DegQ periplasmic endoproteases of Escherichia coli: Specificity for cleavage sites and substrate conformation. J. Bact. 178, 5925-5929. pubmed. citation

Keiler, K.C., Waller, P.R.H. & Sauer, R.T. (1996) Role of a peptide- tagging system in degradation of proteins translated from damaged mRNA. Science 271, 990-993. pubmed. citation

Waller, P.R.H. & Sauer, R.T. (1996) Characterization of degQ and degS, Escherichia coli genes encoding homologs of the DegP protease. J. Bact. 178, 1146-1153. pubmed. citation

ALAN DAVIDSON

Alan Davidson
Postdoc (1991-1995)
Email (alan.davidson at utoronto.ca)

Faculty
University of Toronto

Cordes, M.H.J., Davidson, A.R. & Sauer, R.T. (1996) Sequence Space, Folding, and Protein Design. Curr. Opinion Struct. Biol. 6, 3-10. pubmed citation

Davidson, A.R., Lumb, K.J. & Sauer, R.T. (1995) Cooperatively Folded Proteins in Random Sequence Libraries. Nature Structural Biology 2, 856-863. pubmed citation

Davidson, A.R. and Sauer, R.T. (1994) Folded Proteins Occur Frequently in Libraries of Random Amino Acid Sequences. Proc. Natl. Acad. Sci. USA 91, 2146-2150. pubmed citation

MARCOS MILLA

Marcos Milla
Postdoc (1990-1993)
Email (marcos.milla at roche.com)

Director, Department of Biochemical Pharmacology
Roche Palo Alto LLC

Sauer, R.T., Milla, M.E., Waldburger, C.D., Brown, B.M. & Schildbach, J.F. (1996) Sequence Determinants of Folding and Stability for the P22 Arc Repressor Dimer. FASEB Journal 10, 42-48. pubmed. citation

Milla, M.E., Brown, B.M., Waldburger, C.D. & Sauer, R.T. (1995) P22 Arc Repressor: Transition State Properties Inferred from Mutational Effects on the Rates of Protein Unfolding and Refolding. Biochemistry 34, 13914-13919. pubmed. citation

Schildbach, J.F., Milla, M.E., Jeffrey, P.D., Raumann, B.E., & Sauer, R.T. (1995) Crystal Structure, Folding, and Operator Binding of the Hyperstable Arc Repressor Mutant PL8. Biochemistry 34, 1405-1412. pubmed. citation

Milla, M.E. & Sauer, R.T. (1995) Critical Side-Chain Interactions at a Subunit Interface in the Arc Repressor Dimer Biochemistry 34, 3344-3351. pubmed. citation

Milla, M.E., Brown, B.M., & Sauer, R.T. (1994) Protein stability effects of a complete set of alanine substitutions in Arc repressor. Nature Struct. Biol. 1, 518-523. pubmed. citation

Brown, B.M., Milla, M.E., Smith, T.L. & Sauer, R.T. (1994) Scanning Mutagenesis of Arc Repressor as a Functional Probe of Operator Recognition. Nature Struct. Biol. 1, 164-168.

Milla, M.E. and Sauer, R.T. (1994) P22 Arc Repressor: Folding Kinetics of a Single Domain, Dimeric Protein. Biochemistry 33, 1125-1133. pubmed. citation

Milla, M.E., Brown, B.M, and Sauer, R.T. (1993) P22 Arc Repressor: Enhanced Expression of Unstable Mutants by Addition of Polar C-terminal Sequences. Protein Science 2, 2198-2205. pubmed. citation

SUSAN MARQUSEE

Susan Marqusee
Postdoc (1990-1992)
Email (marqusee at calmail.berkeley.edu)

Faculty
University of California Berkeley

Marqusee, S. and Sauer, R.T. (1994) Dissection of Protein Stability: the Relative Contributions of Secondary and Tertiary Interactions Involving a Salt Bridge-Hydrogen Bond Network in the N-terminal Domain of l Repressor. Protein Science 3, 2217-2225. pubmed. citation

SARAH ADES

Sarah Ellen Ades
Graduate Student (1990-1995)
Email (sea10 at psu.edu)

Faculty
Pennsylvania State University

Tucker-Kellogg, L., Rould, M.A., Chambers, K.A., Ades, S.E., Sauer, R.T. & Pabo, C.O. (1997) Engrailed (Gln50ÆLys) homeodomain-DNA complex at 1.9 Å resolution: structural basis for enhanced affinity and altered specificity. Structure 5,1047-1054. pubmed. citation

Ades, S.E. & Sauer, R.T. (1995) Specificity of Minor-Groove and Major-Groove Interactions in a Homeodomain-DNA Complex, Biochemistry 34, 14601- 14608. pubmed. citation

*Ades, S.E. & Sauer, R.T. (1994) Differential DNA Binding Specificity of the Engrailed Homeodomain: the Role of Residue 50. Biochemistry 33, 9187- 9194. pubmed. citation

KEN KEILER

Kenneth Keiler
Graduate Student (1990-1995)
Email (kkeiler at psu.edu)

Faculty
Pennsylvania State University

Keiler Lab

Keiler, K. & Sauer, R.T. (2002) Tsp and Related C-terminal Processing Proteases. in The Enzymes, Vol. 22 Co- and Posttranslational Proteolysis of Proteins (Ross E. Dalbey, David S. Sigman eds.) Third Edition, Academic Press, 373-386.

Keiler, K C. & Sauer, R.T. (1998) "Tail-specific protease" in Handbook of Proteolytic Enzymes (Woessner, F, Barrett, A.J., Rawlings, N.D., eds.). Academic Press, Orlando, FL.

Keiler, K.C., Waller, P.R.H. & Sauer, R.T. (1996) Role of a peptide- tagging system in degradation of proteins translated from damaged mRNA. Science 271, 990-993.

Keiler, K C. & Sauer, R.T. (1996) Sequence Determinants of C-terminal Substrate Recognition by the Tsp Protease. J. Biol. Chem. 271, 2589-2593.
Keiler, K C. & Sauer, R.T. (1995) Identification of Active-Site Residues of the Tsp Protease J. Biol. Chem. 270, 28864-28868.

Keiler, K.C., Silber, K.R., Downard, K.M., Papayannopoulos, I.A., Biemann, K., & Sauer, R.T. (1995) C-terminal Specific Protein Degradation: Activity and Substrate Specificity of the Tsp Protease. Protein Science 4, 1507-1515.

Silber, K.R., Keiler, K.C. and Sauer, R.T. (1992). Tsp; a tail-specific protease that selectively degrades proteins with non-polar C-termini. Proc. Natl. Acad. Sci. USA 89, 295-299.

BRIGITTE RAUMANN

Brigitte Raumann
Graduate Student (1989-1995)
Email (brigitte_raumann at yahoo.com)

Lead Scientist
Biostudio

Schildbach, J.F., Karzai, A.W., Raumann, B.E. & Sauer, R.T. (1999) Origins of DNA Binding Specificity: Role of Protein Contacts with the DNA Backbone. Proc. Nat. Acad. Sci. USA 96, 811-817. pubmed. citation

Raumann, B.E., Knight, K.L. & Sauer, R.T. (1995) Dramatic Changes in DNA-Binding Specificity Caused By Single Residue Substitutions in an Arc/Mnt Hybrid Repressor. Nature Structural Biology 2, 1115-1122. pubmed. citation

Schildbach, J.F., Milla, M.E., Jeffrey, P.D., Raumann, B.E., & Sauer, R.T. (1995) Crystal Structure, Folding, and Operator Binding of the Hyperstable Arc Repressor Mutant PL8. Biochemistry 34, 1405-1412. pubmed. citation

Raumann, B.E., Rould, M.A., Pabo, C.O. & Sauer, R.T. (1994) DNA Recognition by b-sheets in the Arc Repressor-Operator Crystal Structure. Nature 367, 754-757. pubmed. citation

Raumann, B.E., Brown, B.M. & Sauer, R.T. (1994) Major Groove DNA Recognition by b-sheets: The Ribbon-Helix-Helix Family of Gene Regulatory Proteins. Curr. Opin. Struct. Biol. 4, 36-43. pubmed. citation

DAVID WAUGH

David S. Waugh
(Postdoc 1989-1991)
Email (waughd at ncifcrf.gov)

Faculty
National Cancer Institute

Waugh, D.S. and Sauer, R.T. (1994) A Novel Class of Fok I Restriction Endonuclease Mutants that Cleave Hemi-methylated Substrates. J. Biol. Chem. 269, 12298-12303. pubmed. citation

Waugh, D.S. and Sauer, R.T. (1993) Single amino acid substitutions uncouple the sequence specific DNA binding and strand scission activities of Fok I endonuclease. Proc. Natl. Acad. Sci. USA 90, 9596-9600. pubmed. citation