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Peer Reviewed Papers, Books, Chapters

Year Title Citation Authors
1. 2010 Control of Substrate Gating and Translocation into ClpP by Channel Residues and ClpX Binding. J Mol Biol. [Epub ahead of print]
2. 2010 The IbpA and IbpB small heat-shock proteins are substrates of the AAA+ Lon protease. Mol Microbiol. [Epub ahead of print]
3. 2009 The AAA+ ClpX machine unfolds a keystone subunit to remodel the Mu transpososome. Proc Natl Acad Sci U S A (accepted)
4. 2009 The IbpA and IbpB small heat-shock proteins are substrates of the AAA+ Lon protease Mol Microbiol. (in revision)
5. 2009 Singlemolecule denaturation and degradation of proteins by the AAA+ ClpXP protease. Proc Natl Acad Sci U S A 106(46): 19340-19345
6. 2009 Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine Cell 139(4): 744-56.
7. 2009 Engineering synthetic adaptors and substrates for controlled ClpXP degradation J Biol Chem. 284(33):21848-55.
8. 2009 Polypeptide translocation by the AAA+ ClpXP protease machine. Chem Biol. 16(6): 605-12
9. 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): 912-24
10. 2009 Molecular basis of substrate selection by the N-end rule adaptor protein ClpS Proc Natl Acad Sci U S A 106(22): 8888-93
11. 2009 Versatile modes of peptide recognition by the ClpX N domain mediate alternative adaptor-binding specificities in different bacterial species. Protein Science (accepted).
12. 2008 Distinct structural elements of the adaptor proteins ClpS are required for activation and inhibition of degradation by AAA+ protease ClpAP Nat Struct Mol. Biol 15: 288-94.
13. 2008 The molecular basis of Nend rule recognition. Mol Cell 32: 406-14
14. 2008 Pore loops of the AAA+ ClpX machine grip substrates to drive translocation and unfolding. Nat Struct Mol Biol. 15: 1147-51
15. 2008 Dissecting the roles of MuB in Mu transposition: ATP regulation of DNA binding is not essential for target delivery Proc Natl Acad Sci USA 105: 12101-7.
16. 2008 Forced extraction of targeted components from complex macromolecular assemblies. Proc Natl Acad Sci USA 105: 11685-90
17. 2008 Asymmetric Nucleotide Transactions of the HslUV Protease J Mol Biol. 380: 946-57
18. 2008 Tuning the strength of a bacterial N-end rule degradation signal. J Biol Chem. 283: 24600-7.
19. 2008 Diverse pore loops of the AAA+ ClpX machine mediate unassisted and adaptor-dependent recognition of ssrA-tagged substrates Mol. Cell 29: 441-50
20. 2008 Unique contacts direct high-priority recognition of the tetrameric Mu transposase-DNA complex by the AAA+ unfoldase ClpX. Mol. Cell 30: 39-50.
21. 2008 Protein unfolding by AAA+ protease: critical dependence on ATP-hydrolysis rates, energy landscapes, and substrate engagement Nat Struct Mol Biol. 15: 139-145
22. 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
23. 2007 The dynamic Mu transpososome: MuB activation prevents disintegration. J. Mol. Biol. 374: 1158-1171
24. 2007 Structure and substrate specificity of a SspB ortholog: design implications for AAA+ adaptors. Structure 15: 1296-1305
25. 2007 Distinct static and dynamic interactions control ATPasepeptidase communication in a AAA+ protease Mol Cell 27: 41-52
26. 2007 Direct and adaptor-mediated substrate recognition by an essential AAA+ protease. Proc. Natl. Acad. Sci. USA 104: 6590-5.
27. 2007 Altered tethering of the SspB adaptor to the ClpXP protease causes changes in substrate delivery. J Biol Chem. 282: 11465-73.
28. 2007 Ligand-controlled proteolysis of the Escherichia coli transcriptional regulator ZntR J Bacteriol. 189: 3017-25.
29. 2007 ClpS modulates but is not essential for bacterial N-end rule degradation. Genes Dev. 21: 403-8.
30. 2007 Altered specificity of a AAA+ protease. Mol Cell 25: 161-6.
31. 2006 ATP-dependent proteases of bacteria: recognition logic and operating principles. Trends Biochem Sci. 31: 647-653
32. 2006 Engineering Controllable Protein Degradation Mol Cell 22: 701–707.
33. 2006 Proteomic profiling of ClpXP substrates after DNA damage reveals extensive instability within SOS regulon. Mol Cell 22: 193–204.
34. 2005 Remodeling protein complexes: insights from the AAA+ unfoldase ClpX and Mu transposase. Protein Sci. 14: 1945-54
35. 2005 Asymmetric interactions of ATP with the AAA+ ClpX6 unfoldase: allosteric control of a protein machine. Cell 121: 1017-1027.
36. 2005 Versatile modes of peptide recognition by the AAA+ adaptor protein SspB. Nat Struct Mol Biol. 12: 520-525
37. 2005 Nucleotide-dependent substrate recognition by the AAA+ HslUV protease. Nat Struct Mol Biol. 12: 245-51
38. 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.
39. 2005 Rebuilt AAA + motors reveal operating principles for ATPfuelled machines Nature 437: 1115-20
40. 2005 Specificity versus stability in computational protein design Proc. Natl. Acad. Sci. USA 102: 12724-9
41. 2004 Bivalent tethering of SspB to ClpXP is required for efficient substrate delivery: a protein-design study. Mol Cell 13: 443-9.
42. 2004 Nucleotide-dependent substrate handoff from the SspB adaptor to the AAA+ ClpXP protease. Mol Cell 16: 343-50
43. 2004 Sculpting the proteome with AAA(+) proteases and disassembly machines Cell 119: 9-18.
44. 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
45. 2004 SspB delivery of substrates for ClpXP proteolysis probed by the design of improved degradation tags. Proc. Natl. Acad. Sci. USA 101: 12136-12141
46. 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
47. 2004 Communication between ClpX and ClpP during substrate processing and degradation. Nat Struct Mol Biol. 11: 404-11
48. 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
49. 2004 Reorganization of the Mu transpososome active sites during a cooperative transition between DNA cleavage and joining J Biol Chem. 279: 5135-45
50. 2003 Latent ClpX-recognition signals ensure LexA destruction after DNA damage. Genes Dev. 17: 1084-1089
51. 2003 Proteomic discovery of cellular substrates of the ClpXP protease reveals five classes of ClpX-recognition signals Mol Cell 11: 671-83
52. 2003 DNA gyrase requirements distinguish the alternate pathways of Mu transposition. Mol Microbiol. 47:397-409
53. 2003 C-terminal domain mutations in ClpX uncouple substrate binding from an engagement step required for unfolding. Mol Microbiol. 48: 67-76
54. 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.
55. 2003 Energy-dependent degradation: linkage between ClpXcatalyzed nucleotide hydrolysis and protein-substrate processing Protein Science 12: 893 - 902
56. 2003 The terminal nucleotide of the Mu genome controls catalysis of DNA strand transfer. Proc. Natl. Acad. Sci. USA 100:7509-14
57. 2003 Linkage between ATP consumption and mechanical unfolding during the protein processing reactions of an AAA+ degradation machine Cell 114: 511-20.
58. 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.
59. 2003 Structure of a delivery protein for an AAA+ protease in complex with a peptide degradation tag. Mol. Cell 12: 365-372
60. 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
61. 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
62. 2003 MuA transposase separates DNA sequence recognition from catalysis. Biochem. 42: 14633-42
63. 2003 Expression of N-formylated proteins in Escherichia coli. Protein Expr. Purif. 32: 317-322
64. 2002 Sequence and positional requirements for DNA sites in a Mu transpososome J. Biol. Chem. 277:7703-7712
65. 2002 DNA recognition sites activate MuA transposase to perform transposition of non-Mu DNA. J. Biol. Chem. 277: 7694-7702
66. 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
67. 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
68. 2001 ClpX-mediated remodeling of Mu transpososomes: selective unfolding of subunits destabilizes the entire complex Mol Cell 8: 449-54
69. 2001 Overlapping recognition determinants within the ssrA degradation tag allow modulation of proteolysis Proc Natl Acad Sci USA 11: 10584-9.
70. 2001 Effects of protein stability and structure on substrate processing by the ClpXP unfolding and degradation machine EMBO J. 20: 3092-100.
71. 2001 Chemical mechanisms for mobilizing DNA Mobile DNA II (NL Craig et al., ed.), American Society of Microbiology, Washington, D.C., pp. 12-23
72. 2001 Comparative architecture of transposase and integrase complexes Nat Struct Biol. 8: 302-307.
73. 2001 Molecular determinants of complex formation between Clp/Hsp100 ATPases and the ClpP peptidase. Nature Structural Biology 8: 230-233.
74. 2001 Characterization of the N-terminal repeat domain of Escherichia coli ClpA-A class I Clp/HSP100 ATPase. Protein Science 10: 551-559.
75. 2000 Transposase team puts a headlock on DNA Science 289: 73-4.
76. 2000 Dynamics of substrate denaturation and translocation by the ClpXP degradation machine Molecular Cell 5: 639-648
77. 2000 A specificity-enhancing factor for the ClpXP degradation machine. Science 289: 2354-6
78. 2000 Non-homologous recombination: simplicity in complexity Trends in Genetics 16:201-202
79. 1999 Organization and dynamics of the Mu transpososome: recombination by communication between two active sites. Genes Dev. 13: 2725-2737.
80. 1999 Lon and Clp family proteases and chaperones share homologous substrate-recognition domains. Proc. Natl. Acad. Sci. USA 96: 6678-6682.
81. 1999 Protein unfolding Trapped in the act Nature 401: 29-30.
82. 1998 An ATP-ADP switch in MuB controls progression of the Mutransposition pathway EMBO J 17: 5509-5518.
83. 1998 PDZ-like domains mediate binding specificity in the Clp/Hsp100 family of chaperones and protease regulatory subunits Cell 91: 939-947
84. 1998 Mutational analysis of the Mu transposase J.Biol. Chem. 273: 31358-31365.
85. 1998 Polymerases and the replisome: machines within machines Cell 92: 295-305.
86. 1997 ClpX and MuB interact with overlapping regions of Mutransposase: implications for control of the transposition pathway Genes Dev. 11: 1561-1572
87. 1996 The interwoven architecture of the Mu transposase couples DNA synapsis to catalysis. Cell 85: 257-269
88. 1995 Bacteriophage Mu: a transposing phage that integrates like retroviruses Seminars in Virology 6: 53-63.
89. 1995 Disassembly of the Mu transposase tetramer by the ClpX chaperone. Genes Dev. 9: 2399-2408
90. 1995 Assembly of Phage Mu transpososomes: cooperative transitions assisted by protein and DNA sequence cofactors as scaffolds Cell 83: 375-385
91. 1995 Replication arrest Cell 80: 521-524
92. 1994 Complete transposition requires four active monomers in the Mu transposase tetramer. Genes Dev. 8: 2416-2428
93. 1994 Identification of residues in the Mu transposase essential for catalysis Proc.Natl. Acad Sci USA 91: 6654-6658.
94. 1994 Replication initiation: a new controller in Escherichia coli Current Biology 4: 945-946
95. 1993 Untangling the steps in chromosome segregation Current Biology 3: 94-96.
96. 1993 Division of labor among monomers within the Mu transposase tetramer Cell 74: 723-733
97. 1993 Protein-DNA assemblies controlling lytic development of bacteriophage Mu. Current Opinion in Genetics and Development 3.
98. 1992 Replication, recombination, and red chili amidst the pueblos New Biologist 4: 482-487.
99. 1992 Assembly of the active form of the transposase-Mu DNA complex: a critical control point in Mu transposition. Cell 70: 303-311
100. 1992 DNA-promoted assembly of the active tetramer of the Mu transposase Genes Dev. 6: 2221-2232
101. 1992 Genetics and enzymology of DNA replication in E. coli Ann. Rev. Genetics 24: 447-477.
102. 1991 ...and then there were two. Nature 353: 794-795
103. 1991 MuB protein allosterically activates strand transfer by the transposase of phage Mu. Cell 65: 1003-1013
104. 1991 DNase footprint analysis of the stable synaptic complexes involved in Mu transposition Proc. Natl. Acad. Sci. USA 88, 9031-9035.
105. 1991 Initiation of chromosomal replication Nucleic Acids and Molecular Biology, vol 5 (DMJ Lilly ed.) Springer-Verlag.
106. 1990 Strand separation required for initiation of replication at the chromosomal origin of E. coli is facilitated by a distant RNA-DNA hybrid EMBO J. 9: 2341-2348.
107. 1990 Early events in the enzymatic replication of plasmids containing the origin of the E.coli chromosome. Molecular Mechanisms in DNA Replication and Recombination, (IR Lehman and CC Richardson, eds.) Alan R. Liss, Inc. pp. 227-236.
108. 1989 A collection of strains containing genetically linked alternating antibiotic resistance elements for genetic mapping of Escherichia coli Microbiol. Rev. 53: 1.
109. 1988 Enzymatic replication of plasmids from the origin of the E. coli chromosome Cancer Cells, Vol. 6, Eukaryotic DNA Replication (TJ Kelly and B Stillman, eds.), Cold Spring Harbor Laboratories, Cold Spring Harbor, N.Y.
110. 1988 Transcriptional activation of initiation of replication from the E. coli chromosomal origin: An RNA-DNA hybrid near oriC Cell 55: 113-123.
111. 1987 Helicase action of dnaB protein during replication from the Escherichia coli chromosomal origin in vitro. J. Biol. Chem. 262: 6877-6885
112. 1987 Enzymatic studies of replication of oriC plasmids DNA Replication and Recombination (T Kelly and R McMacken eds.), Alan R. Liss, Inc., New York., pp. 137-149.
113. 1987 In vitro assembly of a prepriming complex at the origin of the Escherichia coli chromosome J. Biol. Chem. 262: 10327-10334
114. 1986 Extensive unwinding of the plasmid template during staged enzymatic initiation of DNA replication from the origin of the Escherichia coli chromosome. Cell 45: 53-64
115. 1986 Complete enzymatic replication of plasmids containing the origin of the Escherichia coli chromosome J. Biol. Chem. 261: 5616-5624.
116. 1985 Analysis of the Escherichia coli heat shock response Microbiology 1985 (L Leive, ed.), American Society of Microbiology,Washington, D.C., pp. 327-331.
117. 1985 Initiation of enzymatic replication at the origin of the Escherichia coli chromosome: contributions of RNA polymerase and primase Proc. Natl. Acad. Sci. USA 82: 3562-3566.
118. 1985 Importance of state of methylation of oriC GATC sites in initiation of DNA replication in Escherichia coli. EMBO J. 4: 1319-1326
119. 1985 Initiation of enzymatic replication at the origin of the Escherichia coli chromosome: primase as the sole priming enzyme Proc. Natl. Acad. Sci. USA 82: 3954-3958.
120. 1984 A gene regulating the heat shock response in E.coli also causes a defect in proteolysis. Proc. Natl. Acad. Sci. USA 81: 6779-6783
121. 1983 MudX, a derivative of Mud1 (lac Apr) which makes stable lacZ fusions at high temperature J. Bacteriol. 156: 970-974


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