Molecular dynamics simulations of Arp2/3 complex activation

Biophysical Journal

Volumn 99, Issue 8, 2010, Pages 2568-2576

  Dalhaimer, Paul ^a,b   Pollard, Thomas D ^a  

^a YALE UNIVERSITY   (United States)

^b University of Tennessee   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 78049352798     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2010.08.027     Document Type: Article

References (23)

1. Pollard, T. D. 2007. Regulation of actin filament assembly by Arp2/3 complex and formins. Annu. Rev. Biophys. Biomol. Struct. 36:451-477.
2. Robinson, R. C., K. Turbedsky, ⋯, T. D. Pollard. 2001. Crystal structure of Arp2/3 complex. Science. 294:1679-1684.
3. Mahaffy, R. E., and T. D. Pollard. 2006. Kinetics of the formation and dissociation of actin filament branches mediated by Arp2/3 complex. Biophys. J. 91:3519-3528.
4. Beltzner, C. C., and T. D. Pollard. 2008. Pathway of actin filament branch formation by Arp2/3 complex. J. Biol. Chem. 283:7135-7144.
5. Rouiller, I., X. P. Xu,., D. Hanein. 2008. The structural basis of actin filament branching by the Arp2/3 complex. J. Cell Biol. 180:887-895.
6. Holmes, K. C., D. Popp, ⋯, W. Kabsch. 1990. Atomic model of the actin filament. Nature. 347:37-44.
7. Oda, T., M. Iwasa, ⋯, A. Narita. 2009. The nature of the globular- to fibrous-actin transition. Nature. 457:441-445.
8. Nolen, B. J., R. S. Littlefield, and T. D. Pollard. 2004. Crystal structures of actin-related protein 2/3 complex with bound ATP or ADP. Proc. Natl. Acad. Sci. USA. 101:15627-15632.
9. Nolen, B. J., and T. D. Pollard. 2007. Insights into the influence of nucleotides on actin family proteins from seven structures of Arp2/3 complex. Mol. Cell. 26:449-457.
10. Boczkowska, M., G. Rebowski, ⋯, R. Dominguez. 2008. X-ray scattering study of activated Arp2/3 complex with bound actin-WCA. Structure. 16:695-704.
11. Guex, N., and M. C. Peitsch. 1997. SWISS-MODEL and the Swiss- PDBViewer: An environment for comparative protein modeling. Electrophoresis. 18:2714-2723.
12. Humphrey, W., A. Dalke, and K. Schulten. 1996. VMD: Visual molecular dynamics. J. Mol. Graph. 14:33-38, 27-28.
13. Jorgensen,W. L., J. Chandrasekhar,., M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
14. Dalhaimer, P., T. D. Pollard, and B. J. Nolen. 2008. Nucleotide-mediated conformational changes of monomeric actin and Arp3 studied by molecular dynamics simulations. J. Mol. Biol. 376:166-183.
15. Phillips, J. C., R. Braun, ⋯, K. Schulten. 2005. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26:1781-1802.
16. Pfaendtner, J., and G. A. Voth. 2008. Molecular dynamics simulation and coarse-grained analysis of the Arp2/3 complex. Biophys. J. 95:5324-5333.
17. Pettersen, E. F., T. D. Goddard, ⋯, T. E. Ferrin. 2004. UCSF CHIMERA-a visualization system for exploratory research and analysis. 25:1605-1612.
18. Sanner, M. F., A. J. Olson, and J. C. Spehner. 1996. Reduced surface: An efficient way to compute molecular surfaces. Biopolymers. 38:305-320.
19. Hayward, S., and H. J. C. Berendsen. 1998. Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme. Proteins. 30:144-154.
20. Graceffa, P., and R. Dominguez. 2003. Crystal structure of monomeric actin in the ATP state. Structural basis of nucleotide-dependent actin dynamics. J. Biol. Chem. 278:34172-34180.
21. Achard, V., J. L. Martiel,., R. Boujemaa-Paterski. 2010. A "primer"- based mechanism underlies branched actin filament network formation and motility. Curr. Biol. 20:423-428.
22. Rodal, A. A., O. Sokolova, ⋯, B. L. Goode. 2005. Conformational changes in the Arp2/3 complex leading to actin nucleation. Nat. Struct. Mol. Biol. 12:26-31.
23. Gournier, H., E. D. Goley, ⋯, M. D. Welch. 2001. Reconstitution of human Arp2/3 complex reveals critical roles of individual subunits in complex structure and activity. Mol. Cell. 8:1041-1052.