ArticleJournal of molecular biology2012
Key structural features of the actin filament Arp2/3 complex branch junction revealed by molecular simulation.
Article in Journal of molecular biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 30 citations in OpenAlex.
- 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
- Steps of actin filament branch formation by Arp2/3 complex investigated with coarse-grained molecular dynamics.Frontiers in cell and developmental biology · 2023Article
- Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction.Nature communications · 2020Article
- A Burst of Genetic Innovation in Drosophila Actin-Related Proteins for Testis-Specific Function.Molecular biology and evolution · 2020Article
- Plastic Deformation and Fragmentation of Strained Actin Filaments.Biophysical journal · 2019Article
- 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
- MCMap-A Computational Tool for Mapping Energy Landscapes of Transient Protein-Protein Interactions.ACS omega · 2018Article
- Two Deafness-Causing Actin Mutations (DFNA20/26) Have Allosteric Effects on the Actin Structure.Biophysical journal · 2016Article
- Crystals of the Arp2/3 complex in two new space groups with structural information about actin-related protein 2 and potential WASP binding sites.Acta crystallographica. Section F, Structural biology communications · 2015Article
- Molecular dynamics simulations of large macromolecular complexes.Current opinion in structural biology · 2015Review
- Function and dynamics of macromolecular complexes explored by integrative structural and computational biology.Current opinion in structural biology · 2014Review
- Actin binding proteins, spermatid transport and spermiation.Seminars in cell & developmental biology · 2014Review
- Article
- MICAL, the flavoenzyme participating in cytoskeleton dynamics.International journal of molecular sciences · 2013Review
- Insertions within the actin core of actin-related protein 3 (Arp3) modulate branching nucleation by Arp2/3 complex.The Journal of biological chemistry · 2013Article
- Two deafness-causing (DFNA20/26) actin mutations affect Arp2/3-dependent actin regulation.The Journal of biological chemistry · 2012Article
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Authors and funding
6 authors at 5 institutions in 1 country.
Funding
Abstract
We investigated the structure, properties and dynamics of the actin filament branch junction formed by actin-related protein (Arp) 2/3 complex using all-atom molecular dynamics (MD) simulations based on a model fit to a reconstruction from electron tomograms. Simulations of the entire structure consisting of 31 protein subunits together with solvent molecules containing ∼3 million atoms were performed for an aggregate time of 175 ns. One 75-ns simulation of the original reconstruction was compared to two 50-ns simulations of alternate structures, showing that the hypothesized branch junction structure is very stable. Our simulations revealed that the interface between Arp2/3 complex and the mother actin filament features a large number of salt bridges and hydrophobic contacts, many of which are dynamic and formed/broken on the timescale of the simulation. The simulations suggest that the DNase binding loops in Arp3, and possibly Arp2, form stabilizing contacts with the mother filament. Unbiased comparison of models sampled from the MD simulation trajectory with the primary experimental electron tomography data identified regions were snapshots from the simulation provide atomic details of the model structures and also pinpoints regions where the initial modeling based on the electron tomogram reconstruction may be suboptimal.
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