{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,20]],"date-time":"2025-09-20T19:34:36Z","timestamp":1758396876987,"version":"3.41.2"},"reference-count":37,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,1,17]],"date-time":"2023-01-17T00:00:00Z","timestamp":1673913600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R35GM136372"],"award-info":[{"award-number":["R35GM136372"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell Dev. Biol."],"abstract":"<jats:p>The nucleation of actin filament branches by the Arp2\/3 complex involves activation through nucleation promotion factors (NPFs), recruitment of actin monomers, and binding of the complex to the side of actin filaments. Because of the large system size and processes that involve flexible regions and diffuse components, simulations of branch formation using all-atom molecular dynamics are challenging. We applied a coarse-grained model that retains amino-acid level information and allows molecular dynamics simulations in implicit solvent, with globular domains represented as rigid bodies and flexible regions allowed to fluctuate. We used recent electron microscopy structures of the inactive Arp2\/3 complex bound to NPF domains and to mother actin filament for the activated Arp2\/3 complex. We studied interactions of Arp2\/3 complex with the activating VCA domain of the NPF Wiskott-Aldrich syndrome protein, actin monomers, and actin filament. We found stable configurations with one or two actin monomers bound along the branch filament direction and with CA domain of VCA associated to the strong and weak binding sites of the Arp2\/3 complex, supporting prior structural studies and validating our approach. We reproduced delivery of actin monomers and CA to the Arp2\/3 complex under different conditions, providing insight into mechanisms proposed in previous studies. Simulations of active Arp2\/3 complex bound to a mother actin filament indicate the contribution of each subunit to the binding. Addition of the C-terminal tail of Arp2\/3 complex subunit ArpC2, which is missing in the cryo-EM structure, increased binding affinity, indicating a possible stabilizing role of this tail.<\/jats:p>","DOI":"10.3389\/fcell.2023.1071977","type":"journal-article","created":{"date-parts":[[2023,1,17]],"date-time":"2023-01-17T05:41:00Z","timestamp":1673934060000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":6,"title":["Steps of actin filament branch formation by Arp2\/3 complex investigated with coarse-grained molecular dynamics"],"prefix":"10.3389","volume":"11","author":[{"given":"Shuting","family":"Zhang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dimitrios","family":"Vavylonis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2023,1,17]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"620","DOI":"10.1016\/S0960-9822(01)00152-X","article-title":"The F-actin side binding activity of the Arp2\/3 complex is essential for actin nucleation and lamellipod extension","volume":"11","author":"Bailly","year":"2001","journal-title":"Curr. Biol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"3308","DOI":"10.1038\/ncomms4308","article-title":"Structural analysis of the transitional state of Arp2\/3 complex activation by two actin-bound WCAs","volume":"5","author":"Boczkowska","year":"2014","journal-title":"Nat. Commun."},{"key":"B3","doi-asserted-by":"publisher","first-page":"16644","DOI":"10.1073\/pnas.0507021102","article-title":"Actin-bound structures of Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 and the implications for filament assembly","volume":"102","author":"Chereau","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B4","doi-asserted-by":"publisher","first-page":"4265","DOI":"10.1073\/pnas.1807028115","article-title":"Mechanism of actin polymerization revealed by cryo-EM structures of actin filaments with three different bound nucleotides","volume":"116","author":"Chou","year":"2019","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B5","doi-asserted-by":"publisher","first-page":"2568","DOI":"10.1016\/j.bpj.2010.08.027","article-title":"Molecular dynamics simulations of Arp2\/3 complex activation","volume":"99","author":"Dalhaimer","year":"2010","journal-title":"Biophysical J."},{"key":"B6","doi-asserted-by":"publisher","first-page":"10059411","DOI":"10.1371\/journal.pcbi.1005941","article-title":"Sequence determinants of protein phase behavior from a coarse-grained model","volume":"14","author":"Dignon","year":"2019","journal-title":"PLOS Comput. Biol."},{"key":"B7","doi-asserted-by":"publisher","first-page":"e2202723119","DOI":"10.1073\/pnas.2202723119","article-title":"Structure of Arp2\/3 complex at a branched actin filament junction resolved by single-particle cryo-electron microscopy","volume":"119","author":"Ding","year":"2022","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B8","doi-asserted-by":"publisher","first-page":"6437","DOI":"10.1038\/s41467-020-20286-x","article-title":"Cryo-electron tomography structure of Arp2\/3 complex in cells reveals new insights into the branch junction","volume":"11","author":"F\u00e4\u00dfler","year":"2020","journal-title":"Nat. Commun."},{"key":"B9","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1016\/j.tcb.2021.10.006","article-title":"Nucleation, stabilization, and disassembly of branched actin networks","volume":"32","author":"Gautreau","year":"2022","journal-title":"Trends Cell Biol."},{"key":"B10","doi-asserted-by":"publisher","first-page":"8159","DOI":"10.1073\/pnas.0911668107","article-title":"An actin-filament-binding interface on the Arp2\/3 complex is critical for nucleation and branch stability","volume":"107","author":"Goley","year":"2010","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B11","doi-asserted-by":"publisher","first-page":"1577","DOI":"10.1007\/s12551-018-0475-7","article-title":"Building a dendritic actin filament network branch by branch: models of filament orientation pattern and force generation in lamellipodia","volume":"10","author":"Holz","year":"2018","journal-title":"Biophys. Rev."},{"key":"B12","doi-asserted-by":"publisher","first-page":"1804","DOI":"10.1002\/1873-3468.13088","article-title":"Computational modeling highlights the role of the disordered Formin Homology 1 domain in profilin-actin transfer","volume":"592","author":"Horan","year":"2018","journal-title":"FEBS Lett."},{"key":"B13","doi-asserted-by":"publisher","first-page":"553","DOI":"10.1016\/j.bpj.2020.06.019","article-title":"Insights into actin polymerization and nucleation using a coarse-grained model","volume":"119","author":"Horan","year":"2020","journal-title":"Biophysical J."},{"key":"B14","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: Visual molecular dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. Graph."},{"key":"B15","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1016\/j.cpc.2008.03.005","article-title":"Accurate and efficient methods for modeling colloidal mixtures in an explicit solvent using molecular dynamics","volume":"179","author":"in \u2019t Veld","year":"2008","journal-title":"Comput. Phys. Commun."},{"key":"B16","doi-asserted-by":"publisher","first-page":"1416","DOI":"10.1016\/j.jmb.2007.11.063","article-title":"Coarse-grained models for simulations of multiprotein complexes: Application to ubiquitin binding","volume":"375","author":"Kim","year":"2008","journal-title":"J. Mol. Biol."},{"key":"B17","doi-asserted-by":"publisher","first-page":"5384","DOI":"10.1021\/acs.jpclett.1c00940","article-title":"Deciphering the molecular terms of Arp2\/3 allosteric regulation from all-atom simulations and dynamical network theory","volume":"12","author":"Laporte","year":"2021","journal-title":"J. Phys. Chem. Lett."},{"key":"B18","doi-asserted-by":"publisher","first-page":"836","DOI":"10.1038\/s41580-022-00508-4","article-title":"Biochemical and mechanical regulation of actin dynamics","volume":"23","author":"Lappalainen","year":"2022","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"B19","doi-asserted-by":"publisher","first-page":"487","DOI":"10.1074\/jbc.m112.406744","article-title":"Insertions within the actin core of actin-related protein 3 (Arp3) modulate branching nucleation by Arp2\/3 complex","volume":"288","author":"Liu","year":"2013","journal-title":"J. Biol. Chem."},{"key":"B20","doi-asserted-by":"publisher","first-page":"E1409","DOI":"10.1073\/pnas.1716622115","article-title":"Identification of Wiskott-Aldrich syndrome protein (WASP) binding sites on the branched actin filament nucleator Arp2\/3 complex","volume":"115","author":"Luan","year":"2018","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B21","doi-asserted-by":"publisher","first-page":"886288","DOI":"10.3389\/fcell.2022.886288","article-title":"Functions of Arp2\/3 complex in the dynamics of epithelial tissues","volume":"10","author":"Martin","year":"2022","journal-title":"Front. Cell Dev. Biol."},{"key":"B22","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1146\/annurev.biophys.29.1.291","article-title":"Comparative protein structure modeling of genes and genomes","volume":"29","author":"Mart\u00ed-Renom","year":"2000","journal-title":"Annu. Rev. Biophys. Biomol. Struct."},{"key":"B23","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1006\/jmbi.1996.0114","article-title":"Residue \u2013 residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading","volume":"256","author":"Miyazawa","year":"1996","journal-title":"J. Mol. Biol."},{"key":"B24","doi-asserted-by":"publisher","first-page":"426","DOI":"10.1016\/j.molcel.2008.10.012","article-title":"Hierarchical regulation of WASP\/WAVE proteins","volume":"32","author":"Padrick","year":"2008","journal-title":"Mol. Cell"},{"key":"B25","doi-asserted-by":"publisher","first-page":"E472","DOI":"10.1073\/pnas.1100236108","article-title":"Arp2\/3 complex is bound and activated by two WASP proteins","volume":"108","author":"Padrick","year":"2011","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B26","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1016\/j.jmb.2011.12.025","article-title":"Key structural features of the actin filament Arp2\/3 complex branch junction revealed by molecular simulation","volume":"416","author":"Pfaendtner","year":"2012","journal-title":"J. Mol. Biol."},{"key":"B27","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1006\/jcph.1995.1039","article-title":"Fast parallel algorithms for short-range molecular-dynamics","volume":"117","author":"Plimpton","year":"1995","journal-title":"J. Comput. Phys."},{"key":"B28","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1146\/annurev.biophys.35.040405.101936","article-title":"Regulation of actin filament assembly by Arp2\/3 complex and formins","volume":"36","author":"Pollard","year":"2007","journal-title":"Annu. Rev. Biophys. Biomol. Struct."},{"key":"B29","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1007\/978-1-4939-7811-3_5","article-title":"Replica exchange molecular dynamics: A practical application protocol with solutions to common problems and a peptide aggregation and self-assembly example","volume-title":"Peptide self-assembly: Methods and protocols","author":"Qi","year":"2018"},{"key":"B30","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1186\/1471-2105-7-382","article-title":"MultiSeq: Unifying sequence and structure data for evolutionary analysis","volume":"7","author":"Roberts","year":"2006","journal-title":"BMC Bioinforma."},{"key":"B31","doi-asserted-by":"publisher","first-page":"12226","DOI":"10.1038\/ncomms12226","article-title":"Identification of an ATP-controlled allosteric switch that controls actin filament nucleation by Arp2\/3 complex","volume":"7","author":"Rodnick-Smith","year":"2016","journal-title":"Nat. Commun."},{"key":"B32","doi-asserted-by":"publisher","first-page":"1009","DOI":"10.1038\/s41594-020-0481-x","article-title":"Cryo-EM reveals the transition of Arp2\/3 complex from inactive to nucleation-competent state","volume":"27","author":"Shaaban","year":"2020","journal-title":"Nat. Struct. Mol. Biol."},{"key":"B33","doi-asserted-by":"crossref","first-page":"1285","DOI":"10.1073\/pnas.1211164110","article-title":"Pathway of actin filament branch formation by Arp2\/3 complex revealed by single-molecule imaging","volume":"110","author":"Smith","year":"2013","journal-title":"PNAS"},{"key":"B34","doi-asserted-by":"publisher","first-page":"718","DOI":"10.3390\/ijms22020718","article-title":"Rounding out the understanding of acd toxicity with the discovery of cyclic forms of actin oligomers","volume":"22","author":"Smith","year":"2021","journal-title":"Int. J. Mol. Sci."},{"key":"B35","doi-asserted-by":"publisher","first-page":"E463","DOI":"10.1073\/pnas.1100125108","article-title":"Structural and biochemical characterization of two binding sites for nucleation-promoting factor wasp-vca on Arp2\/3 complex","volume":"108","author":"Ti","year":"2011","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B36","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/cpbi.3","article-title":"Comparative protein structure modeling using MODELLER","volume":"54","author":"Webb","year":"2016","journal-title":"Curr. Protoc. Bioinforma."},{"key":"B37","doi-asserted-by":"publisher","first-page":"eaaz7651","DOI":"10.1126\/sciadv.aaz7651","article-title":"Cryo-EM structure of NPF-bound human Arp2\/3 complex and activation mechanism","volume":"6","author":"Zimmet","year":"2020","journal-title":"Sci. Adv."}],"container-title":["Frontiers in Cell and Developmental Biology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcell.2023.1071977\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,17]],"date-time":"2023-01-17T05:41:07Z","timestamp":1673934067000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcell.2023.1071977\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,1,17]]},"references-count":37,"alternative-id":["10.3389\/fcell.2023.1071977"],"URL":"https:\/\/doi.org\/10.3389\/fcell.2023.1071977","relation":{},"ISSN":["2296-634X"],"issn-type":[{"type":"electronic","value":"2296-634X"}],"subject":[],"published":{"date-parts":[[2023,1,17]]},"article-number":"1071977"}}