ArticleJournal of molecular biology2008
Nucleotide-mediated conformational changes of monomeric actin and Arp3 studied by molecular dynamics simulations.
Article in Journal of molecular biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Actin's functional "switch": Constraining C-terminal conformational flexibility disrupts functionally important communication networks.The Journal of biological chemistry · 2026Article
- The ARP2/3 complex, acting cooperatively with Class I formins, modulates penetration resistance in Arabidopsis against powdery mildew invasion.The Plant cell · 2021Article
- Effects of Nucleotide and End-Dependent Actin Conformations on Polymerization.Biophysical journal · 2020Article
- D-loop Dynamics and Near-Atomic-Resolution Cryo-EM Structure of Phalloidin-Bound F-Actin.Structure (London, England : 1993) · 2020Article
- Charge-dependent interactions of monomeric and filamentous actin with lipid bilayers.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Atomic view into Plasmodium actin polymerization, ATP hydrolysis, and fragmentation.PLoS biology · 2019Article
- 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
- Identification of Wiskott-Aldrich syndrome protein (WASP) binding sites on the branched actin filament nucleator Arp2/3 complex.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Evolution of polymer formation within the actin superfamily.Molecular biology of the cell · 2017Review
- Identification of an ATP-controlled allosteric switch that controls actin filament nucleation by Arp2/3 complex.Nature communications · 2016Article
- Nucleotide regulation of the structure and dynamics of G-actin.Biophysical journal · 2014Article
- ATP and ADP actin states.Biopolymers · 2013Article
- Insertions within the actin core of actin-related protein 3 (Arp3) modulate branching nucleation by Arp2/3 complex.The Journal of biological chemistry · 2013Article
- Structural states and dynamics of the D-loop in actin.Biophysical journal · 2012Article
- 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
- A nucleotide state-sensing region on actin.The Journal of biological chemistry · 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
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3 authors.
Funding
Abstract
Members of the actin family of proteins exhibit different biochemical properties when ATP, ADP-P(i), ADP, or no nucleotide is bound. We used molecular dynamics simulations to study the effect of nucleotides on the behavior of actin and actin-related protein 3 (Arp3). In all of the actin simulations, the nucleotide cleft stayed closed, as in most crystal structures. ADP was much more mobile within the cleft than ATP, despite the fact that both nucleotides adopt identical conformations in actin crystal structures. The nucleotide cleft of Arp3 opened in most simulations with ATP, ADP, and no bound nucleotide. Deletion of a C-terminal region of Arp3 that extends beyond the conserved actin sequence reduced the tendency of the Arp3 cleft to open. When the Arp3 cleft opened, we observed multiple instances of partial release of the nucleotide. Cleft opening in Arp3 also allowed us to observe correlated movements of the phosphate clamp, cleft mouth, and barbed-end groove, providing a way for changes in the nucleotide state to be relayed to other parts of Arp3. The DNase binding loop of actin was highly flexible regardless of the nucleotide state. The conformation of Ser14/Thr14 in the P1 loop was sensitive to the presence of the gamma-phosphate, but other changes observed in crystal structures were not correlated with the nucleotide state on nanosecond timescales. The divalent cation occupied three positions in the nucleotide cleft, one of which was not previously observed in actin or Arp2/3 complex structures. In sum, these simulations show that subtle differences in structures of actin family proteins have profound effects on their nucleotide-driven behavior.
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