Quantitative analysis of approaches to measure cooperative phosphate release in polymerized actin

Biophysical Journal

Volumn 103, Issue 11, 2012, Pages 2369-2378

  Burnett, Mark M ^a   Carlsson, Anders E ^a  

^a WASHINGTON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIN; PHOSPHATE;

ALGORITHM; ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; DIMERIZATION; PROTEIN BINDING; ULTRASTRUCTURE;

ACTINS; ALGORITHMS; COMPUTER SIMULATION; DIMERIZATION; MODELS, CHEMICAL; MODELS, MOLECULAR; PHOSPHATES; PROTEIN BINDING;

EID: 84870528309     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2012.10.032     Document Type: Article

References (34)

1. I. Fujiwara, D. Vavylonis, and T.D. Pollard Polymerization kinetics of ADP- and ADP-Pi-actin determined by fluorescence microscopy Proc. Natl. Acad. Sci. 104 2007 8827 8832
2. M.F. Carlier, and D. Pantaloni Direct evidence for ADP-inorganic phosphate-F-actin as the major intermediate in ATP-actin polymerization. Rate of dissociation of inorganic phosphate from actin filaments Biochemistry 25 1986 7789 7792
3. B. Bugyi, and M.-F. Carlier Control of actin filament treadmilling in cell motility Ann. Rev. Biophys. J 39 2010 449 470
4. V.E. Galkin, and A. Orlova E.H. Egelman Structural polymorphism in F-actin Nat. Struct. Mol. Biol. 17 2010 1318 1323
5. D. Pantaloni, and T.L. Hill E.D. Korn A model for actin polymerization and the kinetic effects of ATP hydrolysis Proc. Natl. Acad. Sci. 82 1985 7207 7211
6. D. Vavylonis, Q. Yang, and B. O'Shaughnessy Actin polymerization kinetics, cap structure, and fluctuations Proc. Natl. Acad. Sci. 102 2005 8543 8548
7. E.B. Stukalin, and A.B. Kolomeisky ATP hydrolysis stimulates large length fluctuations in single actin filaments Biophys. J. 90 2006 2673 2685
8. P. Ranjith, and K. Mallick D. Lacoste Role of ATP-hydrolysis in the dynamics of a single actin filament Biophys. J. 98 2010 1418 1427
9. T. Ohm, and A. Wegner Mechanism of ATP hydrolysis by polymeric actin Biochim. Biophys. Acta 1208 1994 8 14
10. U. Pieper, and A. Wegner The end of a polymerizing actin filament contains numerous ATP-subunit segments that are disconnected by ADP-subunits resulting from ATP hydrolysis Biochemistry 35 1996 4396 4402
11. A. Jégou, and T. Niedermayer G. Romet-Lemonne Individual actin filaments in a microfluidic flow reveal the mechanism of ATP hydrolysis and give insight into the properties of profilin PLoS Biol. 9 2011 e1001161
12. D.T. Gillespie Stochastic simulation of chemical kinetics Annu. Rev. Phys. Chem. 58 2007 35 55
13. G. van Rossum, and J. de Boer Interactively testing remote servers using the Python Programming Language CWI Quart 4 1991 283 330
14. T.P. Schulze Efficient kinetic Monte Carlo simulation J. Comput. Phys. 227 2008 2455 2462
15. R. Melki, S. Fievez, and M.-F. Carlier Continuous monitoring of Pi release following nucleotide hydrolysis in actin or tubulin assembly using 2-amino-6-mercapto-7-methylpurine ribonucleoside and purine-nucleoside phosphorylase as an enzyme-linked assay Biochemistry 35 1996 12038 12045
16. L. Blanchoin, and T.D. Pollard Mechanism of interaction of Acanthamoeba actophorin (ADF/Cofilin) with actin filaments J. Biol. Chem. 274 1999 15538 15546
17. D. Sept, and J. Xu J.A. McCammon Annealing accounts for the length of actin filaments formed by spontaneous polymerization Biophys. J. 77 1999 2911 2919
18. C. Salter Error analysis using the variance-covariance matrix J. Chem. Educ. 77 2000 1239
19. J. Hu, and H. Othmer A theoretical analysis of filament length fluctuations in actin and other polymers J. Math. Biol. 63 2011 1001 1049
20. A. Orlova, and A. Shvetsov E. Reisler Actin-destabilizing factors disrupt filaments by means of a time reversal of polymerization Proc. Natl. Acad. Sci. 101 2004 17664 17668
21. T. Oda, and M. Iwasa A. Narita The nature of the globular- to fibrous-actin transition Nature 457 2009 441 445
22. J. Fass, and C. Pak A. Mogilner Stochastic simulation of actin dynamics reveals the role of annealing and fragmentation J. Theor. Biol. 252 2008 173 183
23. M.F. Carlier, D. Pantaloni, and E.D. Korn The mechanisms of ATP hydrolysis accompanying the polymerization of Mg-actin and Ca-actin J. Biol. Chem. 262 1987 3052 3059
24. F.J. Brooks, and A.E. Carlsson Actin polymerization overshoots and ATP hydrolysis as assayed by pyrene fluorescence Biophys. J. 95 2008 1050 1062
25. T. Miyoshi, and T. Tsuji N. Watanabe Actin turnover-dependent fast dissociation of capping protein in the dendritic nucleation actin network: evidence of frequent filament severing J. Cell Biol. 175 2006 947 955
26. J. Berro, V. Sirotkin, and T.D. Pollard Mathematical modeling of endocytic actin patch kinetics in fission yeast: disassembly requires release of actin filament fragments Mol. Biol. Cell 21 2010 2905 2915
27. H.Y. Kueh, W.M. Brieher, and T.J. Mitchison Dynamic stabilization of actin filaments Proc. Natl. Acad. Sci. 105 2008 16531 16536
28. X. Li, R. Lipowsky, and J. Kierfeld Coupling of actin hydrolysis and polymerization: reduced description with two nucleotide states Europhys. Lett. 89 2010 38010
29. T. Niedermayer, and A. Jégou R. Lipowsky Intermittent depolymerization of actin filaments is caused by photo-induced dimerization of actin protomers Proc. Natl. Acad. Sci. 109 2012 10769 10774
30. I. Fujiwara, and S. Takahashi S. Ishiwata Microscopic analysis of polymerization dynamics with individual actin filaments Nat. Cell Biol. 4 2002 666 673
31. J.R. Kuhn, and T.D. Pollard Real-time measurements of actin filament polymerization by total internal reflection fluorescence microscopy Biophys. J. 88 2005 1387 1402
32. T.D. Pollard Rate constants for the reactions of ATP- and ADP-actin with the ends of actin filaments J. Cell Biol. 103 1986 2747 2754
33. L. Blanchoin, and T.D. Pollard Hydrolysis of ATP by polymerized actin depends on the bound divalent cation but not profilin Biochemistry 41 2002 597 602
34. 2+ at the high-affinity and low-affinity sites on the polymerization of actin and associated ATP hydrolysis J. Biol. Chem. 261 1986 10785 10792