A stochastic analysis of actin polymerization in the presence of twinfilin and gelsolin

Journal of Theoretical Biology

Volumn 249, Issue 4, 2007, Pages 723-736

  Matzavinos, Anastasios ^a   Othmer, Hans G ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Actin; Capping protein; Gelsolin; Polymerization; Stochastic simulation algorithm; Twinfilin

Indexed keywords

ACTIN; ADENOSINE DIPHOSPHATE; G ACTIN; GELSOLIN; PROTEIN; TWINFILIN; UNCLASSIFIED DRUG;

ALGORITHM; CALCIUM; EXPERIMENTAL STUDY; FLUORESCENCE; MAMMAL; POLYMERIZATION; PROTEIN; SIMULATION; STOCHASTICITY;

ACTIN POLYMERIZATION; ALGORITHM; ARTICLE; MOLECULAR INTERACTION; PRIORITY JOURNAL; REACTION ANALYSIS; SIMULATION; STOCHASTIC MODEL;

ACTIN CAPPING PROTEINS; ACTINS; ADENOSINE DIPHOSPHATE; ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; GELSOLIN; HUMANS; MICROFILAMENT PROTEINS; PROTEIN-TYROSINE KINASES; STOCHASTIC PROCESSES;

MAMMALIA;

EID: 36248980951     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2007.08.018     Document Type: Article

References (22)

1. Bindschadler M., Osborn E., Dewey C., and McGrath J. A mechanistic model of the actin cycle. Biophys. J. 86 (2004) 2720-2739
2. Blanchoin L., and Pollard T. Hydrolysis of ATP by polymerized actin depends on the bound divalent cation but not profilin. Biochemistry 41 (2002) 597-602
3. Cao Y., Li H., and Petzold L. Efficient formulation of the stochastic simulation algorithm for chemically reacting systems. J. Chem. Phys. 121 9 (2004) 4059-4067
4. E W., Liu D., and Vanden-Eijnden E. Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates. J. Chem. Phys. 123 (2005) 194107
5. Falck S., Paavilainen V., Wear M., Grossmann J., Cooper J., and Lappalainen P. Biological role and structural mechanism of twinfilin-capping protein interaction. EMBO J. 23 (2004) 3010-3019
6. Fass, J., Pak, C., Bamburg, J., Mogilner, A., 2007. Stochastic simulation of actin dynamics reveals the role of annealing and fragmentation. Biophys. J., submitted for publication.
7. Fujiwara I., Vavylonis D., and Pollard T. Polymerization kinetics of ADP- and ADP-Pi-actin determined by fluorescence microscopy. Proc. Natl Acad. Sci. 104 21 (2007) 8827-8832
8. Gadgil C., Lee C., and Othmer H. A stochastic analysis of first-order reaction networks. Bull. Math. Biol. 67 (2005) 901-946
9. Gardiner C. Handbook of Stochastic Methods for Physics, Chemistry and the Natural Sciences. second ed. (1985), Springer, Berlin
10. Gibson M., and Bruck J. Efficient exact stochastic simulation of chemical systems with many species and many channels. J. Phys. Chem. A 104 (2000) 1876-1889
11. Gillespie D. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comput. Phys. 22 (1976) 403-434
12. Gillespie D. Stochastic simulation of chemical kinetics. Annu. Rev. Phys. Chem. 58 (2007) 35-55
13. Helfer E., Nevalainen E., Naumanen P., Romero S., Didry D., Pantaloni D., Lappalainen P., and Carlier M.-F. Mammalian twinfilin sequesters ADP-G-actin and caps filament barbed ends: implications in motility. EMBO J. 25 (2006) 1184-1195
14. Hu J., Matzavinos A., and Othmer H. A theoretical approach to actin filament dynamics. J. Stat. Phys. 128 (2007) 111-138
15. Kuhn J., and Pollard T. Real-time measurements of actin filament polymerization by total internal reflection fluorescence microscopy. Biophys. J. 88 (2005) 1387-1402
16. Moseley J., Okada K., Balcer H., Kovar D., Pollard T., and Goode B. Twinfilin is an actin-filament-severing protein and promotes rapid turnover of actin structures in vivo. J. Cell Sci. 119 (2006) 1547-1557
17. Ojala P., Paavilainen V., Vartiainen M., Tume R., Weeds A.G., and Lappalainen P. The two ADF-H domains of twinfilin play functionally distinct roles in interactions with actin monomers. Mol. Biol. Cell 13 (2002) 3811-3821
18. Paavilainen V., Bertling E., Falck S., and Lappalainen P. Regulation of cytoskeletal dynamics by actin-monomer-binding proteins. Trends Cell Biol. 14 7 (2004) 386-394
19. Pollard T., and Borisy G. Cellular motility driven by assembly and disassembly of actin filaments. Cell 112 (2003) 453-465
20. Selden L., Kinosian H., Estes J., and Gershman L. Impact of profilin on actin-bound nucleotide exchange and actin polymerization dynamics. Biochemistry 38 (1999) 2769-2778
21. Sept D., Xu J., Pollard T., and McCammon J. Annealing accounts for the length of actin filaments formed by spontaneous polymerization. Biophys. J. 77 (1999) 2911-2919
22. Stukalin E., and Kolomeisky A. ATP hydrolysis stimulates large length fluctuations in single actin filaments. Biophys. J. 90 (2006) 2673-2685