Recent Publications

2014 - 2013 - 2012 - 2011 - 2010 - 2009 - 2008 - 2007 - 2006 - 2005 - 2004 - 2003 - 2002 - 2001 - 2000 - (pre-2000)

Cordova JC, Olivares AO, Shin Y, Stinson BM, Calmat S, Schmitz KR, Aubin-Tam ME, Baker TA, Lang MJ, Sauer RT (2014) Stochastic but Highly Coordinated Protein Unfolding and Translocation by the ClpXP Proteolytic Machine. Cell. 158(3):647-58. [Pubmed Citation]

Al-Furoukh N, Kardon JR, Kruger M, Szibor M, Baker TA, Braun T (2014) NOA1, a Novel ClpXP Substrate, Takes an Unexpected Nuclear Detour Prior to Mitochondrial Import. PLoS One. 9(7):e103141. [Pubmed Citation]

de Regt AK, Yin Y, Withers TR, Wang X, Baker TA, Sauer RT, Yu HD (2014) Overexpression of CupB5 activates alginate overproduction in Pseudomonas aeruginosa by a novel AlgW-dependent mechanism. Mol Microbiol. 93(3):415-25. [Pubmed Citation]

Barthelme D, Chen JZ, Grabenstatter J, Baker TA, Sauer RT (2014) Architecture and assembly of the archaeal Cdc48*20S proteasome. Proc Natl Acad Sci U S A 111(17):E1687-94. [Pubmed Citation]

Wohlever ML, Baker TA, Sauer RT (2014) Roles of the N domain of the AAA+ Lon protease in substrate recognition, allosteric regulation and chaperone activity. Mol Microbiol.91(1):66-78. [Pubmed Citation]

Vieux EF, Wohlever ML, Chen JZ, Sauer RT, Baker TA (2013) Distinct quaternary structures of the AAA+ Lon protease control substrate degradation. Proc Natl Acad Sci U S A.[Epub ahead of print] [Pubmed Citation]

Stinson BM, Nager AR, Glynn SE, Schmitz KR, Baker TA, Sauer RT (2013) Nucleotide binding and conformational switching in the hexameric ring of a AAA+ machine. Cell 153(3):628-39. [Pubmed Citation]

Wohlever ML, Nager AR, Baker TA, Sauer RT (2013) Protein Eng Des Sel.26(4):299-305 [Pubmed Citation]

Peterson CN, Levchenko I, Rabinowitz JD, Baker TA, Silhavy TJ (2012) RpoS proteolysis is controlled directly by ATP levels in Escherichia coli. Genes Dev.26(6):548-53 [Pubmed Citation]

Landgraf D, Okumus B, Chien P, Baker TA, Paulsson J (2012) Segregation of molecules at cell division reveals native protein localization. Nat Methods.9(5):480-2 [Pubmed Citation]

Glynn SE, Nager AR, Baker TA, Sauer RT (2012) Dynamic and static components power unfolding in topologically closed rings of a AAA+ proteolytic machine. Nat Struct Mol Biol.19(6):616-22 [Pubmed Citation]

Sundar S, Baker TA, Sauer RT (2011) The I domain of the AAA+ HslUV protease coordinates substrate binding, ATP hydrolysis, and protein degradation. Protein Sci.[Epub ahead of print][ Pubmed Citation]

Davis JH, Baker TA, Sauer RT (2011) Small-Molecule Control of Protein Degradation Using Split Adaptors. ACS Chem Biol.[Epub ahead of print][ Pubmed Citation]

Abel S, Chien P, Wassmann P, Schirmer T, Kaever V, Laub MT, Baker TA, Jenal U (2011) Regulatory Cohesion of Cell Cycle and Cell Differentiation through Interlinked Phosphorylation and Second Messenger Networks. Mol Cell.[Epub ahead of print][ Pubmed Citation]

Nager AR, Baker TA, Sauer RT (2011) Stepwise Unfolding of a β Barrel Protein by the AAA+ ClpXP Protease. J Mol Biol.[Epub ahead of print][ Pubmed Citation]

Roman-Hernandez G, Hou JY, Grant RA, Sauer RT, Baker TA (2011) The ClpS Adaptor Mediates Staged Delivery of N-End Rule Substrates to the AAA+ ClpAP Protease. Mol Cell. 43(2):217-28[ Pubmed Citation]

Baker Ta, Sauer RT. (2011) ClpXP, an ATP-powered unfolding and protein-degradation machine. Biochim Biophys Acta. [Epub ahead of print][ Pubmed Citation]

Aubin-Tam ME, Olivares AO, Sauer RT, Baker TA, Lang MJ. (2011) Single-molecule protein unfolding and translocation by an ATP-fueled proteolytic machine. Cell. 145(2):257-67[ Pubmed Citation]

Sauer RT, Baker TA. (2011) AAA+ Proteases: ATP-Fueled Machines of Protein Destruction. Annu Rev Biochem. [Epub ahead of print][ Pubmed Citation]

Meyer AS, Baker TA (2011) Proteolysis in the Escherichia coli heat shock response: a player at many levels. Curr Opin Microbiol. 14(2):194-9 Pubmed Citation]

Sundar S, McGinness KE, Baker TA, Sauer RT (2010) Multiple sequence signals direct recognition and degradation of protein substrates by the AAA+ protease HslUV. J Mol Biol. [Epub ahead of print] [ Pubmed Citation]

Lee ME, Baker TA, Sauer RT(2010) Control of Substrate Gating and Translocation into ClpP by Channel Residues and ClpX Binding. J Mol Biol. 403(3):420-9[ Pubmed Citation]

Bissonnette SA, Rivera-Rivera I, Sauer RT, Baker TA (2010) The IbpA and IbpB small heat-shock proteins are substrates of the AAA+ Lon protease. Mol Microbiol. [Epub ahead of print] [ Pubmed Citation]

Abdelhakim AH, Sauer RT, and Baker TA (2010) The AAA+ ClpX machine unfolds a keystone subunit to remodel the Mu transpososome. Proc Natl Acad Sci U S A 219(2):242-54. [ Pubmed Citation]

Chowdhury T, Ebrahim S, Chien P, Sauer RT, and Baker TA (2010) Versatile modes of peptide recognition by the ClpX N domain mediate alternative adaptor-binding specificities in different bacterial species. Protein Sci. 219(2):242-54. [ Pubmed Citation]

Glynn SE, Baker TA, and Sauer RT (2009) Crystal structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine. Cell 139(4):744-56. [ Pubmed Citation]

Shin Y, Davis JH, Brau RR, Martin A, Kenniston JA, Baker TA, Sauer RT, Lang MJ. (2009) Single-molecule denaturation and degradation of proteins by the AAA+ ClpXP protease. Proc Natl Acad Sci U S A 106(46):19340-5.[ Pubmed Citation]

Pruteanu M, Baker TA (2009). Proteolysis in the SOS response and metal homeostasis in Escherichia coli. Res Microbiol. 160(9):677-83.[ Pubmed Citation]

Davis JH, Baker TA, and Sauer RT (2009). Engineering synthetic adaptors and substrates for controlled ClpXP degradation. J Biol Chem. 284(33):21848-55.[ Pubmed Citation]

Barkow SR, Levchenko I, Baker TA, and Sauer RT (2009). Polypeptide translocation by the AAA+ ClpXP protease machine. Chem Biol. 16(6):605-12.[ Pubmed Citation]

Roman-Hernandez G, Grant RA, Sauer RT, Baker TA(2009) Molecular basis of substrate selection by the N-end rule adaptor protein ClpS. proc Natl Acad Sci U S A Jun 2;106(22):8888-93. Epub 2009 May 18. [ Pubmed Citation]

Pruteanu M and Baker TA (2009) Controlled degradation by ClpXP protease tunes the levels of the excision repair protein UvrA to the extent of DNA damage. Mol Microbiol. 71(4), 912ñ924.[ Pubmed Citation]

Wang KH, Roman-Hernandez G, Grant RA, Sauer RT, and Baker TA (2008) The molecular basis of N-end rule recognition. Mol Cell. 32(3):406-14.[ Pubmed Citation]

Martin A, Baker TA, and Sauer RT (2008) Pore loops of the AAA+ ClpX machine grip substrates to drive translocation and unfolding. Nat Struct Mol Biol. 15(11):1147-51 [ Pubmed Citation]

Schweidenback CT and Baker TA (2008) Inaugural Article: Dissecting the roles of MuB in Mu transposition: ATP regulation of DNA binding is not essential for target delivery. Proc Natl Acad Sci U S A. 105(34):12101-7 [ Pubmed Citation]

Moore SD , Baker TA, and Sauer RT (2008) Forced extraction of targeted components from complex macromolecular assemblies. Proc Natl Acad Sci U S A. 105(33):11685-90. [ Pubmed Citation]

Yakamavich JA, Baker TA, and Sauer RT (2008) Asymmetric Nucleotide Transactions of the HslUV Protease. J Biol Chem. 380(5):946-57. [ Pubmed Citation]

Wang KH, Oakes ES, Sauer RT, and Baker TA (2008) Tuning the strength of a bacterial N-end rule degradation signal. J Biol Chem. 283(36):24600-7 [ Pubmed Citation]

Abdelhakim A, Oakes EC, Sauer RT, and Baker TA (2008) Unique contacts direct high-priority recognition of the tetrameric Mu transposase-DNA complex by the AAA+ unfoldase ClpX. Mol. Cell 30:39-50. [ Pubmed Citation]

Martin A, Baker TA, and Sauer RT (2008) Diverse Pore Loops of the AAA+ ClpX Machine Mediate Unassisted and Adaptor-Dependent Recognition of ssrA-Tagged Substrates. Mol Cell. 29(4):441-50 [ PubMed Citation ]

Hou JY, Sauer RT and Baker TA (2008) Distinct structural elements of the adaptor ClpS are required for regulating degradation by ClpAP. Nature Structural & Mol. Biol. 15(3):288-94 [ PubMed Citation ]

Martin A, Baker TA, and Sauer RT (2008) Protein unfolding by AAA+ protease: critical dependence on ATP-hydrolysis rates, energy landscapes, and substrate engagement. Nature Structural & Mol. Biol. 15(2): 139 - 145 [ PubMed Citation ]

Lemberg KM, Schweidenback CTH and Baker TA (2007) The dynamic Mu transpososome: MuB activation prevents dIsintegration. J Mol. Biol. 374: 1158-1171[ PubMed Citation ]

Chien P, Grant RA, Sauer RT, and Baker TA (2007)Structure and substrate specificity of a SspB ortholog: design implications for AAA+ adaptors. Structure 15: 1296-1305 [ PubMed Citation ]

Martin A, Baker TA and Sauer RT (2007) Distinct static and dynamic interactions control ATPase-peptidase communication in a AAA+ protease. Mol Cell 27:41-52. [PubMed Citation]

Chien P, Perchuk BS, Laub MT, Sauer RT and Baker TA (2007) Direct and adaptor-mediated substrate recognition by an essential AAA+ protease. Proc. Natl. Acad. Sci. USA. 104:6590-5. [PubMed Citation]

McGinness KE, Bolon DN, Kaganovich M, Baker TA and Sauer RT (2007)  Altered tethering of the SspB adaptor to the ClpXP protease causes changes in substrate delivery. J Biol Chem. 282:11465-73. [PubMed Citation]

Pruteanu M, Neher SB and Baker TA  (2007)  Ligand-controlled proteolysis of the Escherichia coli transcriptional regulator ZntR. J Bacteriol. 189:3017-25. [PubMed Citation]

Wang KH, Sauer RT and Baker TA  (2007)  ClpS modulates but is not essential for bacterial N-end rule degradation. Genes Dev.21:403-408. [PubMed Citation]

Farrell CM, Baker TA and Sauer RT†(2007) Altered specificity of a AAA+ protease. Mol Cell. 25:161-6. [PubMed Citation]

Chaba R, Grigorova IL, Flynn JM, Baker TA and Gross CA†(2007)†Design principles of the proteolytic cascade governing the sigmaE-mediated envelope stress response in Escherichia coli: keys to graded, buffered, and rapid signal transduction. Genes Dev.21:124-36. [PubMed Citation]

Baker TA and Sauer RT  (2006) ATP-dependent proteases of bacteria: recognition logic and operating principles. Trends Biochem Sci. 31:647-653. [PubMed Citation]

McGinness KE, Baker TA and Sauer RT (2006) Engineering Controllable Protein Degradation. Mol Cell 22:701-707. [PubMed Citation]

Neher SB, VillÈn J, Oakes EC, Bakalarski CE, Sauer RT, Gygi SP and Baker TA (2006) Proteomic profiling of ClpXP substrates after DNA damage reveals extensive instability within SOS regulon. Mol Cell 22:193ñ204. [PubMed Citation]

Martin A, Baker TA and Sauer RT   (2005) Rebuilt AAA + motors reveal operating principles for ATP-fuelled machines. Nature 437:1115-20. [PubMed Citation]

Bolon DN, Grant RA, Baker TA and Sauer RT (2005) Specificity versus stability in computational protein design. Proc. Natl. Acad. Sci. USA 102:12724-9. [PubMed Citation]

Burton BM and Baker TA (2005) Remodeling protein complexes: insights from the AAA+ unfoldase ClpX and Mu transposase. Protein Sci. 14:1945-54. [PubMed Citation]

Hersch GL, Burton RE, Bolon DN, Baker TA and Sauer RT (2005) Asymmetric interactions of ATP with the AAA+ ClpX6 unfoldase: allosteric control of a protein machine. Cell 121:1017-1027. [PubMed Citation]

Levchenko I, Grant RA, Flynn JM, Sauer RT and Baker TA   (2005)   Versatile modes of peptide recognition by the AAA+ adaptor protein SspB. Nat Struct Mol Biol. 12:520-525. [PubMed Citation]

Kenniston JA, Baker TA, and Sauer RT   (2005)   Partitioning between unfolding and release of native domains during ClpXP degradation determines substrate selectivity and partial processing. Proc. Natl. Acad. Sci. USA 102:1390-5. [PubMed Citation]

Burton RE, Baker TA and Sauer RT   (2005) Nucleotide-dependent substrate recognition by the AAA+ HslUV protease. Nat Struct Mol Biol. 12:245-51. [PubMed Citation]

Bolon DN, Grant RA, Baker TA and Sauer RT   (2004)   Nucleotide-dependent substrate handoff from the SspB adaptor to the AAA+ ClpXP protease. Mol Cell 16:343-50. [PubMed Citation]

Sauer RT, Bolon DN, Burton BM, Burton RE, Flynn JM, Grant RA, Hersch GL, Joshi SA, Kenniston JA, Levchenko I, Neher SB, Oakes ES, Siddiqui SM, Wah DA, and Baker TA   (2004) Sculpting the proteome with AAA(+) proteases and disassembly machines. Cell 119:9-18. [PubMed Citation]

Flynn JM, Levchenko I, Sauer RT and Baker TA   (2004)   Modulating substrate choice: the SspB adaptor delivers a regulator of the extracytoplasmic-stress response to the AAA+ protease ClpXP for degradation. Genes Dev. 18:2292-2301. [PubMed Citation]

Hersch GL, Baker TA and Sauer RT   (2004)   SspB delivery of substrates for ClpXP proteolysis probed by the design of improved degradation tags. Proc. Natl. Acad. Sci. USA 101:12136-12141. [PubMed Citation]

Siddiqui SM, Sauer RT and Baker TA   (2004)   Role of the protein-processing pore of ClpX, an AAA+ ATPase, in recognition and engagement of specific protein substrates. Genes Dev . 18:369-74. [PubMed Citation]

Joshi SA, Hersch GL, Baker TA and Sauer RT   (2004)   Communication between ClpX and ClpP during substrate processing and degradation. Nat Struct Mol Biol . 11:404-11. [PubMed Citation]

Kenniston JA, Burton RE, Siddiqui SM, Baker TA and Sauer RT   (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. 146:130-40. [PubMed Citation]

Bolon DN, Wah DA, Hersch GL, Baker TA and Sauer RT   (2004)   Bivalent tethering of SspB to ClpXP is required for efficient substrate delivery: a protein-design study. Mol Cell. 13:443-9. [PubMed Citation]

Williams,TL and Baker TA   (2004)   Reorganization of the Mu transpososome active sites during a cooperative transition between DNA cleavage and joining. J Biol Chem. 279:5135-45. [PubMed Citation]

Spector S, Flynn JM, Tidor B, Baker TA and Sauer RT   (2003)   Expression of N-formylated proteins in Escherichia coli . Protein Expr. Purif. 32: 317-322. [PubMed Citation]

Goldhaber-Gordon I, Early MH and Baker TA.   (2003)   MuA transposase separates DNA sequence recognition from catalysis.   Biochem. 42: 14633-42. [PubMed Citation]

Neher SB, Sauer RT and Baker TA   (2003) Distinct peptide signals in the UmuD and UmuD´ subunits of the UmuD/D´ heterodimer mediate tethering and substrate-processing by the ClpXP protease. Proc. Natl. Acad. Sci. USA 100: 13219-24. [PubMed Citation]

Wah DA, Levchenko I, Rieckhof GE, Bolon DN, Baker TA and Sauer RT   (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]

Levchenko I, Grant RA, Wah DA, Sauer RT and Baker TA   (2003)   Structure of a delivery protein for an AAA+ protease in complex with a peptide degradation tag. Mol. Cell 12: 365-372. [PubMed Citation]

Coros CJ, Sekino Y, Baker TA and Chaconas G   (2003)   Effect of mutations in the C-terminal domain of Mu B on DNA binding and interactions with Mu A transposase. J Biol Chem. 278: 31210-7. [PubMed Citation]

Kenniston JA, Baker TA, Fernandez JM and Sauer RT   (2003)   Linkage between ATP consumption and mechanical unfolding during the protein processing reactions of an AAA+ degradation machine. Cell 114: 511-20. [PubMed Citation]

Goldhaber-Gordon I, Early MH and Baker TA   (2003) The terminal nucleotide of the Mu genome controls catalysis of DNA strand transfer. Proc. Natl. Acad. Sci. USA . 100:7509-14. [PubMed Citation]

Burton RE, Baker TA and Sauer RT   (2003)   Energy-dependent degradation: linkage between ClpX-catalyzed nucleotide hydrolysis and protein-substrate processing. Protein Science 12: 893 - 902. [PubMed Citation]

Burton BM and Baker TA   (2003)   Mu transpososome architecture ensures that unfolding by ClpX or proteolysis by ClpXP remodels but does not destroy the complex. Chem Biol. 10:463-72. [PubMed Citation]

Joshi SA, Baker TA and Sauer RT.   (2003)   C-terminal domain mutations in ClpX uncouple substrate binding from an engagement step required for unfolding. Mol Microbiol. 48: 67-76. [PubMed Citation]

Neher SB, Flynn JM, Sauer RT and Baker TA   (2003)   Latent ClpX-recognition signals ensure LexA destruction after DNA damage. Genes and Development 17: 1084-1089. [PubMed Citation]

Sokolsky TD and Baker TA (2003) DNA gyrase requirements distinguish the alternate pathways of Mu transposition. Mol Microbiol. 47:397-409 [PubMed Citation]

Flynn JM, Neher SB, Kim YI, Sauer RT and Baker TA   (2003)   Proteomic discovery of cellular substrates of the ClpXP protease reveals five classes of ClpX-recognition signals. Mol Cell. 11: 671-83. [PubMed Citation]

Wah DA, Levchenko I, Baker TA and Sauer RT   (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]

Goldhaber-Gordon I, Early MH, Gray MK, and Baker TA   (2002)   Sequence and positional requirements for DNA sites in a Mu transpososome.   J. Biol. Chem. 277:7703-7712 [PubMed Citation].

Goldhaber-Gordon I, Williams TL, and Baker TA   (2002)   DNA recognition sites activate MuA transposase to perform transposition of non-Mu DNA.   J. Biol. Chem . 277: 7694-7702. [PubMed Citation]

Kim Y-I, Levchenko I, Fraczkowska K, Woodruff RV, Sauer RT, and Baker TA   (2001)   Molecular determinants of complex formation between Clp/Hsp100 ATPases and the ClpP peptidase.   Nature Structural Biology 8: 230-233. [PubMed Citation]

Lo JH, Baker TA, and Sauer RT   (2001)   Characterization of the N-terminal repeat domain of Escherichia coli ClpA-A class I Clp/HSP100 ATPase.   Protein Science 10: 551-559. [PubMed Citation]

Roldan LAS, and Baker TA   (2001)   Differential role of the Mu B protein in phage Mu integration versus replication: mechanistic insights into two transposition pathways.   Mol Microbiol 40: 141-55. [PubMed Citation]

Burton BM, Williams TL, and Baker TA   (2001)   ClpX-mediated remodeling of Mu transpososomes: selective unfolding of subunits destabilizes the entire complex.   Mol Cell. 8: 449-54. [PubMed Citation]

Flynn JM, Levchenko I, Seidel M, Wickner SH, Sauer RT, and Baker TA   (2001)   Overlapping recognition determinants within the ssrA degradation tag allow modulation of proteolysis.   Proc Natl Acad Sci U S A 11: 10584-9. [PubMed Citation]

Burton RE, Siddiqui SM, Kim Y-I, Baker TA, and Sauer RT   (2001)   Effects of protein stability and structure on substrate processing by the ClpXP unfolding and degradation machine.   EMBO J . 20: 3092-100. [PubMed Citation]

Rice PA, and Baker TA   (2001)   Comparative architecture of transposase and integrase complexes. Nat Struct Biol. 8: 302-307. [PubMed Citation]

Mizuuchi K, and Baker TA   (2001)   Chemical mechanisms for mobilizing DNA.   In Mobile DNA II (NL Craig et al., ed.), American Society of Microbiology, Washington, D.C., pp. 12-23.

Kim Y-I, Burton RE, Burton BM, Sauer RT, and Baker TA   (2000)   Dynamics of substrate denaturation and translocation by the ClpXP degradation machine.   Molecular Cell 5: 639-648. [PubMed Citation]

Levchenko I, Seidel M, Sauer RT, and Baker TA   (2000)   A specificity-enhancing factor for the ClpXP degradation machine.   Science 289: 2354-6. [PubMed Citation]

Williams TL, and Baker TA   (2000)   Transposase team puts a headlock on DNA.   Science 289: 73-4. [PubMed Citation]

Goldhaber-Gordon IM, and Baker TA   (2000)   Non-homologous recombination: simplicity in complexity.   Keystone Symposium on Transposition and Other Genome Rearrangements, Santa Fe, NM, USA, 27 January - 2 February.   Trends in Genetics 16:201-202