Skip to main content
NCBI home page
Biophysical Journal logoLink to Biophysical Journal
. 2001 Aug;81(2):667–674. doi: 10.1016/S0006-3495(01)75731-1

Thermodynamics and kinetics of actin filament nucleation.

D Sept 1, J A McCammon 1
PMCID: PMC1301543  PMID: 11463615

Abstract

We have performed computer simulations and free energy calculations to determine the thermodynamics and kinetics of actin nucleation and thus identify a probable nucleation pathway and critical nucleus size. The binding free energies of structures along the nucleation pathway are found through a combination of electrostatic calculations and estimates of the entropic and surface area contributions. The association kinetics for the formation of each structure are determined through a series of Brownian dynamics simulations. The combination of the binding free energies and the association rate constants determines the dissociation rate constants, allowing for a complete characterization of the nucleation and polymerization kinetics. The results indicate that the trimer is the size of the critical nucleus, and the rate constants produce polymerization plots that agree very well with experimental results over a range of actin monomer concentrations.

Full Text

The Full Text of this article is available as a PDF (312.3 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Antosiewicz J., McCammon J. A., Gilson M. K. The determinants of pKas in proteins. Biochemistry. 1996 Jun 18;35(24):7819–7833. doi: 10.1021/bi9601565. [DOI] [PubMed] [Google Scholar]
  2. Brady G. P., Sharp K. A. Entropy in protein folding and in protein-protein interactions. Curr Opin Struct Biol. 1997 Apr;7(2):215–221. doi: 10.1016/s0959-440x(97)80028-0. [DOI] [PubMed] [Google Scholar]
  3. Buzan J. M., Frieden C. Yeast actin: polymerization kinetic studies of wild type and a poorly polymerizing mutant. Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):91–95. doi: 10.1073/pnas.93.1.91. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Carlier M. F. Actin: protein structure and filament dynamics. J Biol Chem. 1991 Jan 5;266(1):1–4. [PubMed] [Google Scholar]
  5. Cooper J. A., Buhle E. L., Jr, Walker S. B., Tsong T. Y., Pollard T. D. Kinetic evidence for a monomer activation step in actin polymerization. Biochemistry. 1983 Apr 26;22(9):2193–2202. doi: 10.1021/bi00278a021. [DOI] [PubMed] [Google Scholar]
  6. De La Cruz E. M., Mandinova A., Steinmetz M. O., Stoffler D., Aebi U., Pollard T. D. Polymerization and structure of nucleotide-free actin filaments. J Mol Biol. 2000 Jan 21;295(3):517–526. doi: 10.1006/jmbi.1999.3390. [DOI] [PubMed] [Google Scholar]
  7. Elcock A. H., Gabdoulline R. R., Wade R. C., McCammon J. A. Computer simulation of protein-protein association kinetics: acetylcholinesterase-fasciculin. J Mol Biol. 1999 Aug 6;291(1):149–162. doi: 10.1006/jmbi.1999.2919. [DOI] [PubMed] [Google Scholar]
  8. Erickson H. P. Co-operativity in protein-protein association. The structure and stability of the actin filament. J Mol Biol. 1989 Apr 5;206(3):465–474. doi: 10.1016/0022-2836(89)90494-4. [DOI] [PubMed] [Google Scholar]
  9. Estes J. E., Selden L. A., Kinosian H. J., Gershman L. C. Tightly-bound divalent cation of actin. J Muscle Res Cell Motil. 1992 Jun;13(3):272–284. doi: 10.1007/BF01766455. [DOI] [PubMed] [Google Scholar]
  10. Frieden C., Goddette D. W. Polymerization of actin and actin-like systems: evaluation of the time course of polymerization in relation to the mechanism. Biochemistry. 1983 Dec 6;22(25):5836–5843. doi: 10.1021/bi00294a023. [DOI] [PubMed] [Google Scholar]
  11. Frieden C. Polymerization of actin: mechanism of the Mg2+-induced process at pH 8 and 20 degrees C. Proc Natl Acad Sci U S A. 1983 Nov;80(21):6513–6517. doi: 10.1073/pnas.80.21.6513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Gabdoulline R. R., Wade R. C. Brownian dynamics simulation of protein-protein diffusional encounter. Methods. 1998 Mar;14(3):329–341. doi: 10.1006/meth.1998.0588. [DOI] [PubMed] [Google Scholar]
  13. Gabdoulline R. R., Wade R. C. Simulation of the diffusional association of barnase and barstar. Biophys J. 1997 May;72(5):1917–1929. doi: 10.1016/S0006-3495(97)78838-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. García-Moreno B., Dwyer J. J., Gittis A. G., Lattman E. E., Spencer D. S., Stites W. E. Experimental measurement of the effective dielectric in the hydrophobic core of a protein. Biophys Chem. 1997 Feb 28;64(1-3):211–224. doi: 10.1016/s0301-4622(96)02238-7. [DOI] [PubMed] [Google Scholar]
  15. Gilson M. K., Given J. A., Bush B. L., McCammon J. A. The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys J. 1997 Mar;72(3):1047–1069. doi: 10.1016/S0006-3495(97)78756-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Higgs H. N., Blanchoin L., Pollard T. D. Influence of the C terminus of Wiskott-Aldrich syndrome protein (WASp) and the Arp2/3 complex on actin polymerization. Biochemistry. 1999 Nov 16;38(46):15212–15222. doi: 10.1021/bi991843+. [DOI] [PubMed] [Google Scholar]
  17. Higgs H. N., Pollard T. D. Activation by Cdc42 and PIP(2) of Wiskott-Aldrich syndrome protein (WASp) stimulates actin nucleation by Arp2/3 complex. J Cell Biol. 2000 Sep 18;150(6):1311–1320. doi: 10.1083/jcb.150.6.1311. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Holmes K. C., Popp D., Gebhard W., Kabsch W. Atomic model of the actin filament. Nature. 1990 Sep 6;347(6288):44–49. doi: 10.1038/347044a0. [DOI] [PubMed] [Google Scholar]
  19. Horton N., Lewis M. Calculation of the free energy of association for protein complexes. Protein Sci. 1992 Jan;1(1):169–181. doi: 10.1002/pro.5560010117. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Kinosian H. J., Selden L. A., Estes J. E., Gershman L. C. Thermodynamics of actin polymerization; influence of the tightly bound divalent cation and nucleotide. Biochim Biophys Acta. 1991 Apr 8;1077(2):151–158. doi: 10.1016/0167-4838(91)90052-2. [DOI] [PubMed] [Google Scholar]
  21. Kozack R. E., d'Mello M. J., Subramaniam S. Computer modeling of electrostatic steering and orientational effects in antibody-antigen association. Biophys J. 1995 Mar;68(3):807–814. doi: 10.1016/S0006-3495(95)80257-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Machesky L. M., Mullins R. D., Higgs H. N., Kaiser D. A., Blanchoin L., May R. C., Hall M. E., Pollard T. D. Scar, a WASp-related protein, activates nucleation of actin filaments by the Arp2/3 complex. Proc Natl Acad Sci U S A. 1999 Mar 30;96(7):3739–3744. doi: 10.1073/pnas.96.7.3739. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Moraczewska J., Wawro B., Seguro K., Strzelecka-Golaszewska H. Divalent cation-, nucleotide-, and polymerization-dependent changes in the conformation of subdomain 2 of actin. Biophys J. 1999 Jul;77(1):373–385. doi: 10.1016/S0006-3495(99)76896-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Mullins R. D., Heuser J. A., Pollard T. D. The interaction of Arp2/3 complex with actin: nucleation, high affinity pointed end capping, and formation of branching networks of filaments. Proc Natl Acad Sci U S A. 1998 May 26;95(11):6181–6186. doi: 10.1073/pnas.95.11.6181. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Northrup S. H., Thomasson K. A., Miller C. M., Barker P. D., Eltis L. D., Guillemette J. G., Inglis S. C., Mauk A. G. Effects of charged amino acid mutations on the bimolecular kinetics of reduction of yeast iso-1-ferricytochrome c by bovine ferrocytochrome b5. Biochemistry. 1993 Jul 6;32(26):6613–6623. doi: 10.1021/bi00077a014. [DOI] [PubMed] [Google Scholar]
  26. Pollard T. D. Actin. Curr Opin Cell Biol. 1990 Feb;2(1):33–40. doi: 10.1016/s0955-0674(05)80028-6. [DOI] [PubMed] [Google Scholar]
  27. Pollard T. D. Rate constants for the reactions of ATP- and ADP-actin with the ends of actin filaments. J Cell Biol. 1986 Dec;103(6 Pt 2):2747–2754. doi: 10.1083/jcb.103.6.2747. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Rohatgi R., Ma L., Miki H., Lopez M., Kirchhausen T., Takenawa T., Kirschner M. W. The interaction between N-WASP and the Arp2/3 complex links Cdc42-dependent signals to actin assembly. Cell. 1999 Apr 16;97(2):221–231. doi: 10.1016/s0092-8674(00)80732-1. [DOI] [PubMed] [Google Scholar]
  29. Sept D., Elcock A. H., McCammon J. A. Computer simulations of actin polymerization can explain the barbed-pointed end asymmetry. J Mol Biol. 1999 Dec 17;294(5):1181–1189. doi: 10.1006/jmbi.1999.3332. [DOI] [PubMed] [Google Scholar]
  30. Sharp K. A., Nicholls A., Fine R. F., Honig B. Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects. Science. 1991 Apr 5;252(5002):106–109. doi: 10.1126/science.2011744. [DOI] [PubMed] [Google Scholar]
  31. Tamura A., Privalov P. L. The entropy cost of protein association. J Mol Biol. 1997 Nov 14;273(5):1048–1060. doi: 10.1006/jmbi.1997.1368. [DOI] [PubMed] [Google Scholar]
  32. Tobacman L. S., Korn E. D. The kinetics of actin nucleation and polymerization. J Biol Chem. 1983 Mar 10;258(5):3207–3214. [PubMed] [Google Scholar]
  33. Wegner A., Engel J. Kinetics of the cooperative association of actin to actin filaments. Biophys Chem. 1975 Jul;3(3):215–225. doi: 10.1016/0301-4622(75)80013-5. [DOI] [PubMed] [Google Scholar]
  34. Welch M. D., Rosenblatt J., Skoble J., Portnoy D. A., Mitchison T. J. Interaction of human Arp2/3 complex and the Listeria monocytogenes ActA protein in actin filament nucleation. Science. 1998 Jul 3;281(5373):105–108. doi: 10.1126/science.281.5373.105. [DOI] [PubMed] [Google Scholar]
  35. Winter D., Lechler T., Li R. Activation of the yeast Arp2/3 complex by Bee1p, a WASP-family protein. Curr Biol. 1999 May 6;9(9):501–504. doi: 10.1016/s0960-9822(99)80218-8. [DOI] [PubMed] [Google Scholar]
  36. Yarar D., To W., Abo A., Welch M. D. The Wiskott-Aldrich syndrome protein directs actin-based motility by stimulating actin nucleation with the Arp2/3 complex. Curr Biol. 1999 May 20;9(10):555–558. doi: 10.1016/s0960-9822(99)80243-7. [DOI] [PubMed] [Google Scholar]

Articles from Biophysical Journal are provided here courtesy of The Biophysical Society

RESOURCES