ArticleProceedings of the National Academy of Sciences of the United States of America2025
Reaching the full potential of cryo-EM reconstructions with molecular dynamics simulations at 310 K: Actin filaments as an example.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Leiomodin2 is a polymerase at the pointed ends of actin filaments.Nature communications · 2026Article
- Evolutionarily conserved short linear motifs drive actin filament binding.Nature cell biology · 2026Article
- Physical Confinement Modulates the Rate-Limiting Transition in the Release of Phosphate from Actin Filaments.bioRxiv : the preprint server for biology · 2026Article
- Reaching the full potential of cryo-EM reconstructions with molecular dynamics simulations at 310 K: Actin filaments as an example.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
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Abstract
Cryoelectron microscopy (cryo-EM) structures of multiprotein complexes such as actin filaments help explain the mechanisms of assembly and interactions with partner proteins. Yet, rapid cooling during freezing may not preserve the conformations at physiological temperature. All-atom molecular dynamics simulations starting with cryo-EM reconstructions can provide additional insights. For example, at 310 K, adenosinediphosphate (ADP)-actin filaments fluctuate on a nanosecond time scale around higher entropy states with partly twisted subunits and smaller rotations along short-pitch helix than the cryo-EM reconstructions, while cryogenic temperatures favor flattened conformations. In the active site, the positions of Q137 and the catalytic water 1 and activating water 2 optimal for in-line attack on the γ-phosphate of ATP are very rare at 310 K, explaining in part the slow rate of ATP hydrolysis in filaments. This favorable arrangement of the waters is not observed in simulations of actin monomers. At 310 K, subunits in ADP-P
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