ArticleBiophysical journal2008
Molecular dynamics simulation and coarse-grained analysis of the Arp2/3 complex.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Molecular mechanism of Arp2/3 complex activation by nucleation-promoting factors and an actin monomer.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Multiscale simulation of actin filaments and actin-associated proteins.Biophysical reviews · 2018Review
- Conformational changes in Arp2/3 complex induced by ATP, WASp-VCA, and actin filaments.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Structural Basis of Arp2/3 Complex Inhibition by GMF, Coronin, and Arpin.Journal of molecular biology · 2017Article
- Key structural features of the actin filament Arp2/3 complex branch junction revealed by molecular simulation.Journal of molecular biology · 2012Article
- Phosphorylation of the Arp2 subunit relieves auto-inhibitory interactions for Arp2/3 complex activation.PLoS computational biology · 2011Article
- Molecular dynamics simulations of Arp2/3 complex activation.Biophysical journal · 2010Article
- Actin filament remodeling by actin depolymerization factor/cofilin.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Structure and dynamics of the actin filament.Journal of molecular biology · 2010Article
- Defining coarse-grained representations of large biomolecules and biomolecular complexes from elastic network models.Biophysical journal · 2009Article
- Nucleotide-dependent conformational states of actin.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Nucleotide- and activator-dependent structural and dynamic changes of arp2/3 complex monitored by hydrogen/deuterium exchange and mass spectrometry.Journal of molecular biology · 2009Article
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2 authors.
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Abstract
A molecular dynamics investigation and coarse-grained analysis of inactivated actin-related protein (Arp) 2/3 complex is presented. It was found that the nucleotide binding site within Arp3 remained in a closed position with bound ATP or ADP, but opened when simulation with no nucleotide was performed. In contrast, simulation of the isolated Arp3 subunit with bound ATP, showed a fast opening of the nucleotide binding cleft. A homology model for the missing subdomains 1 and 2 of Arp2 was constructed, and it was also found that the Arp2 binding cleft remained closed with bound nucleotide. Within the nucleotide binding cleft a distinct opening and closing period of 10 ns was observed in many of the simulations of Arp2/3 as well as isolated Arp3. Substitution studies were employed, and several alanine substitutions were found to induce a partial opening of the ATP binding cleft in Arp3 and Arp2, whereas only a single substitution was found to induce opening of the ADP binding cleft. It was also found that the nucleotide type did not cause a substantial change on interfacial contacts between Arp3 and the ArpC2, ArpC3 and ArpC4 subunits. Nucleotide-free Arp3 had generally less stable contacts, but the overall contact architecture was constant. Finally, nucleotide-dependent coarse-grained models for Arp3 are developed that serve to further highlight the structural differences induced in Arp3 by nucleotide hydrolysis.
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