Application of the sequential n-step kinetic mechanism to polypeptide translocases

Methods in Enzymology

Volumn 488, Issue C, 2011, Pages 239-264

  Lucius, Aaron L ^a   Miller, Justin M ^a   Rajendar, Burki ^a  

^a UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; CARRIER PROTEIN; MOLECULAR MOTOR; POLYPEPTIDE;

ARTICLE; CASE REPORT; ENZYME MECHANISM; ESCHERICHIA COLI; FLUORESCENCE; HUMAN; KINETICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN BINDING; PROTEIN HYDROLYSIS; QUALITY CONTROL; SEQUENTIAL ANALYSIS;

EID: 78650955824     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-381268-1.00010-0     Document Type: Chapter

References (29)

1. J.A. Ali, and T.M. Lohman Kinetic measurement of the step size of DNA unwinding by Escherichia coli UvrD helicase Science 275 1997 377 380
2. S.M. Block Bead movement by single kinesin molecules studied with optical tweezers Nature 348 1990 348 352
3. E. Eytan ATP-dependent incorporation of 20S protease into the 26S complex that degrades proteins conjugated to ubiquitin Proc. Natl. Acad. Sci. USA 86 1989 7751 7755
4. C.J. Fischer, and T.M. Lohman ATP-dependent translocation of proteins along single-stranded DNA: Models and methods of analysis of pre-steady state kinetics J. Mol. Biol. 344 2004 1265 1286
5. C.J. Fischer Mechanism of ATP-dependent translocation of E. coli UvrD monomers along single-stranded DNA J. Mol. Biol. 344 2004 1287 1309
6. J.R. Glover, and S. Lindquist Hsp104, Hsp70, and Hsp40: A novel chaperone system that rescues previously aggregated proteins Cell 94 1998 73 82
7. P. Goloubinoff Sequential mechanism of solubilization and refolding of stable protein aggregates by a bichaperone network Proc. Natl. Acad. Sci. USA 96 1999 13732 13737
8. J.R. Hoskins Protein binding and unfolding by the chaperone ClpA and degradation by the protease ClpAP Proc. Natl. Acad. Sci. USA 97 2000 8892 8897
9. R. Hough Purification of two high molecular weight proteases from rabbit reticulocyte lysate J. Biol. Chem. 262 1987 8303 8313
10. J. Howard Movement of microtubules by single kinesin molecules Nature 342 1989 154 158
11. E. Jankowsky The DExH protein NPH-II is a processive and directional motor for unwinding RNA Nature 403 2000 447 451
12. Y.I. Kim Dynamics of substrate denaturation and translocation by the ClpXP degradation machine Mol. Cell 5 2000 639 648
13. A. Kornberg, and T.A. Baker DNA Replication 1992 W.H. Freeman New York
14. T.M. Lohman, and K.P. Bjornson Mechanisms of helicase-catalyzed DNA unwinding Annu. Rev. Biochem. 65 1996 169 214
15. T.M. Lohman Non-hexameric DNA helicases and translocases: Mechanisms and regulation Nat. Rev. Mol. Cell Biol. 9 2008 391 401
16. A.L. Lucius DNA unwinding step-size of E. coli RecBCD helicase determined from single turnover chemical quenched-flow kinetic studies J. Mol. Biol. 324 2002 409 428
17. A.L. Lucius General methods for analysis of sequential "n-step" kinetic mechanisms: Application to single turnover kinetics of helicase-catalyzed DNA unwinding Biophys. J. 85 2003 2224 2239
18. A.L. Lucius Fluorescence stopped-flow studies of single turnover kinetics of E. coli RecBCD helicase-catalyzed DNA unwinding J. Mol. Biol. 339 2004 731 750
19. S.W. Matson, and K.A. Kaiser-Rogers DNA helicases Annu. Rev. Biochem. 59 1990 289 329
20. G. Piszczek, J. Rozycki, S.K. Singh, A. Ginsburg, and M.R. Maurizi The molecular chaperone, ClpA, has a single high affinity peptide binding site per hexamer J. Biol. Chem. 280 2005 12221 12230
21. A.M. Pyle Translocation and unwinding mechanisms of RNA and DNA helicases Annu. Rev. Biophys. 37 2008 317 336
22. B. Rajendar, and A.L. Lucius Molecular mechanism of polypeptide translocation catalyzed by the Escherichia coli ClpA protein translocase J. Mol. Biol. 399 2010 665 679
23. T.A. Rapoport Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes Nature 450 2007 663 669
24. B.G. Reid ClpA mediates directional translocation of substrate proteins into the ClpP protease Proc. Natl. Acad. Sci. USA 98 2001 3768 3772
25. K. Svoboda Direct observation of kinesin stepping by optical trapping interferometry Nature 365 1993 721 727
26. T.Q. Uyeda Myosin step size. Estimation from slow sliding movement of actin over low densities of heavy meromyosin J. Mol. Biol. 214 1990 699 710
27. R.D. Vale, and R.J. Fletterick The design plan of kinesin motors Annu. Rev. Cell Dev. Biol. 13 1997 745 777
28. J. Weibezahn Thermotolerance requires refolding of aggregated proteins by substrate translocation through the central pore of ClpB Cell 119 2004 653 665
29. J. Zimmer Structure of a complex of the ATPase SecA and the protein-translocation channel Nature 455 2008 936 943