{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T08:36:43Z","timestamp":1774687003667,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1010121","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,5,24]],"date-time":"2022-05-24T00:00:00Z","timestamp":1653350400000}}],"reference-count":92,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2022,5,12]],"date-time":"2022-05-12T00:00:00Z","timestamp":1652313600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004809","name":"Financiadora de Estudos e Projetos","doi-asserted-by":"publisher","award":["01.20.0003.00"],"award-info":[{"award-number":["01.20.0003.00"]}],"id":[{"id":"10.13039\/501100004809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","doi-asserted-by":"publisher","award":["17\/18139-6"],"award-info":[{"award-number":["17\/18139-6"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>The nucleocapsid (N) protein of the SARS-CoV-2 virus, the causal agent of COVID-19, is a multifunction phosphoprotein that plays critical roles in the virus life cycle, including transcription and packaging of the viral RNA. To play such diverse roles, the N protein has two globular RNA-binding modules, the N- (NTD) and C-terminal (CTD) domains, which are connected by an intrinsically disordered region. Despite the wealth of structural data available for the isolated NTD and CTD, how these domains are arranged in the full-length protein and how the oligomerization of N influences its RNA-binding activity remains largely unclear. Herein, using experimental data from electron microscopy and biochemical\/biophysical techniques combined with molecular modeling and molecular dynamics simulations, we show that, in the absence of RNA, the N protein formed structurally dynamic dimers, with the NTD and CTD arranged in extended conformations. However, in the presence of RNA, the N protein assumed a more compact conformation where the NTD and CTD are packed together. We also provided an octameric model for the full-length N bound to RNA that is consistent with electron microscopy images of the N protein in the presence of RNA. Together, our results shed new light on the dynamics and higher-order oligomeric structure of this versatile protein.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1010121","type":"journal-article","created":{"date-parts":[[2022,5,12]],"date-time":"2022-05-12T17:51:15Z","timestamp":1652377875000},"page":"e1010121","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":51,"title":["Structural dynamics of SARS-CoV-2 nucleocapsid protein induced by RNA binding"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8471-207X","authenticated-orcid":true,"given":"Helder Veras","family":"Ribeiro-Filho","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5831-1392","authenticated-orcid":true,"given":"Gabriel Ernesto","family":"Jara","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0783-8378","authenticated-orcid":true,"given":"Fernanda Aparecida Heleno","family":"Batista","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3129-8682","authenticated-orcid":true,"given":"Gabriel Ravanhani","family":"Schleder","sequence":"additional","affiliation":[]},{"given":"Celisa Caldana","family":"Costa Tonoli","sequence":"additional","affiliation":[]},{"given":"Adriana Santos","family":"Soprano","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3699-3927","authenticated-orcid":true,"given":"Samuel Leite","family":"Guimar\u00e3es","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0023-6403","authenticated-orcid":true,"given":"Antonio Carlos","family":"Borges","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1032-4749","authenticated-orcid":true,"given":"Alexandre","family":"Cassago","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3371-1143","authenticated-orcid":true,"given":"Marcio Chaim","family":"Bajgelman","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6949-0947","authenticated-orcid":true,"given":"Rafael Elias","family":"Marques","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7505-2345","authenticated-orcid":true,"given":"Daniela Barretto Barbosa","family":"Trivella","sequence":"additional","affiliation":[]},{"given":"Kleber Gomes","family":"Franchini","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7023-8490","authenticated-orcid":true,"given":"Ana Carolina Migliorini","family":"Figueira","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4602-0256","authenticated-orcid":true,"given":"Celso Eduardo","family":"Benedetti","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1287-8019","authenticated-orcid":true,"given":"Paulo Sergio","family":"Lopes-de-Oliveira","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,5,12]]},"reference":[{"key":"pcbi.1010121.ref001","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1146\/annurev.mi.44.100190.001511","article-title":"Corona Virus: Organization, Replication and Expression of Genome","volume":"44","author":"MMC Lai","year":"1990","journal-title":"Annu Rev Microbiol"},{"key":"pcbi.1010121.ref002","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/S0065-3527(05)64006-7","article-title":"Molecular Interactions in the Assembly of Coronaviruses","volume":"64","author":"CAM de Haan","year":"2005","journal-title":"Adv Virus Res"},{"key":"pcbi.1010121.ref003","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/s41579-020-00468-6","article-title":"Coronavirus biology and replication: implications for SARS-CoV-2","volume":"19","author":"P V\u2019kovski","year":"2021","journal-title":"Nat Rev Microbiol"},{"key":"pcbi.1010121.ref004","doi-asserted-by":"crossref","first-page":"2991","DOI":"10.3390\/v6082991","article-title":"The coronavirus nucleocapsid is a multifunctional protein","volume":"6","author":"R McBride","year":"2014","journal-title":"Viruses"},{"key":"pcbi.1010121.ref005","doi-asserted-by":"crossref","first-page":"4288","DOI":"10.1128\/jvi.62.11.4288-4295.1988","article-title":"Specific interaction between coronavirus leader RNA and nucleocapsid protein","volume":"62","author":"SA Stohlman","year":"1988","journal-title":"J Virol"},{"key":"pcbi.1010121.ref006","doi-asserted-by":"crossref","first-page":"12683","DOI":"10.1128\/JVI.78.22.12683-12688.2004","article-title":"The Nucleoprotein Is Required for Efficient Coronavirus Genome Replication","volume":"78","author":"F Almaz\u00e1n","year":"2004","journal-title":"J Virol"},{"key":"pcbi.1010121.ref007","doi-asserted-by":"crossref","first-page":"13848","DOI":"10.1128\/JVI.79.22.13848-13855.2005","article-title":"Assembly of Severe Acute Respiratory Syndrome Coronavirus RNA Packaging Signal into Virus-Like Particles Is Nucleocapsid Dependent","volume":"79","author":"P-K Hsieh","year":"2005","journal-title":"J Virol"},{"key":"pcbi.1010121.ref008","doi-asserted-by":"crossref","first-page":"6620","DOI":"10.1128\/JVI.79.11.6620-6630.2005","article-title":"Selective Replication of Coronavirus Genomes That Express Nucleocapsid Protein","volume":"79","author":"B Schelle","year":"2005","journal-title":"J Virol"},{"key":"pcbi.1010121.ref009","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1016\/j.jmb.2009.09.040","article-title":"Coronavirus N Protein N-Terminal Domain (NTD) Specifically Binds the Transcriptional Regulatory Sequence (TRS) and Melts TRS-cTRS RNA Duplexes","volume":"394","author":"NE Grossoehme","year":"2009","journal-title":"J Mol Biol"},{"key":"pcbi.1010121.ref010","doi-asserted-by":"crossref","first-page":"2169","DOI":"10.1128\/JVI.02011-09","article-title":"Coronavirus Nucleocapsid Protein Facilitates Template Switching and Is Required for Efficient Transcription","volume":"84","author":"S Z\u00fa\u00f1iga","year":"2010","journal-title":"J Virol"},{"key":"pcbi.1010121.ref011","doi-asserted-by":"crossref","first-page":"10276","DOI":"10.1128\/JVI.01287-10","article-title":"An Interaction between the Nucleocapsid Protein and a Component of the Replicase-Transcriptase Complex Is Crucial for the Infectivity of Coronavirus Genomic RNA","volume":"84","author":"KR Hurst","year":"2010","journal-title":"J Virol"},{"key":"pcbi.1010121.ref012","doi-asserted-by":"crossref","first-page":"11575","DOI":"10.1128\/JVI.00569-10","article-title":"The Coronavirus Nucleocapsid Protein Is Dynamically Associated with the Replication-Transcription Complexes","volume":"84","author":"MH Verheije","year":"2010","journal-title":"J Virol"},{"key":"pcbi.1010121.ref013","doi-asserted-by":"crossref","first-page":"4451","DOI":"10.1128\/JVI.03866-13","article-title":"Recognition of the Murine Coronavirus Genomic RNA Packaging Signal Depends on the Second RNA-Binding Domain of the Nucleocapsid Protein","volume":"88","author":"L Kuo","year":"2014","journal-title":"J Virol"},{"key":"pcbi.1010121.ref014","doi-asserted-by":"crossref","first-page":"7063","DOI":"10.1074\/jbc.M111.287763","article-title":"Functional Transcriptional Regulatory Sequence (TRS) RNA Binding and Helix Destabilizing Determinants of Murine Hepatitis Virus (MHV) Nucleocapsid (N) Protein","volume":"287","author":"SC Keane","year":"2012","journal-title":"J Biol Chem"},{"key":"pcbi.1010121.ref015","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1002\/pmic.200401204","article-title":"Biochemical and immunological studies of nucleocapsid proteins of severe acute respiratory syndrome and 229E human coronaviruses","author":"TK Tang","year":"2005","journal-title":"Proteomics"},{"key":"pcbi.1010121.ref016","doi-asserted-by":"crossref","first-page":"17134","DOI":"10.1074\/jbc.M602107200","article-title":"Crystal Structure of the Severe Acute Respiratory Syndrome (SARS) Coronavirus Nucleocapsid Protein Dimerization Domain Reveals Evolutionary Linkage between Corona- and Arteriviridae","volume":"281","author":"I-M Yu","year":"2006","journal-title":"J Biol Chem"},{"key":"pcbi.1010121.ref017","doi-asserted-by":"crossref","first-page":"1075","DOI":"10.1016\/j.jmb.2007.02.069","article-title":"Structure of the SARS Coronavirus Nucleocapsid Protein RNA-binding Dimerization Domain Suggests a Mechanism for Helical Packaging of Viral RNA","volume":"368","author":"C-Y Chen","year":"2007","journal-title":"J Mol Biol"},{"key":"pcbi.1010121.ref018","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1016\/j.jmb.2007.11.093","article-title":"Solution Structure of the C-terminal Dimerization Domain of SARS Coronavirus Nucleocapsid Protein Solved by the SAIL-NMR Method","volume":"380","author":"M Takeda","year":"2008","journal-title":"J Mol Biol"},{"key":"pcbi.1010121.ref019","doi-asserted-by":"crossref","first-page":"2255","DOI":"10.1128\/JVI.02001-08","article-title":"Multiple Nucleic Acid Binding Sites and Intrinsic Disorder of Severe Acute Respiratory Syndrome Coronavirus Nucleocapsid Protein: Implications for Ribonucleocapsid Protein Packaging","volume":"83","author":"C-K Chang","year":"2009","journal-title":"J Virol"},{"key":"pcbi.1010121.ref020","doi-asserted-by":"crossref","first-page":"e65045","DOI":"10.1371\/journal.pone.0065045","article-title":"Transient Oligomerization of the SARS-CoV N Protein\u2013Implication for Virus Ribonucleoprotein Packaging","volume":"8","author":"C Chang","year":"2013","journal-title":"PLoS One"},{"key":"pcbi.1010121.ref021","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.antiviral.2013.12.009","article-title":"The SARS coronavirus nucleocapsid protein\u2014Forms and functions","volume":"103","author":"CK Chang","year":"2014","journal-title":"Antiviral Res"},{"key":"pcbi.1010121.ref022","doi-asserted-by":"crossref","first-page":"e105938","DOI":"10.15252\/embj.2020105938","article-title":"Structures of the SARS -CoV-2 nucleocapsid and their perspectives for drug design","volume":"39","author":"Y Peng","year":"2020","journal-title":"EMBO J"},{"key":"pcbi.1010121.ref023","doi-asserted-by":"crossref","first-page":"e1009100","DOI":"10.1371\/journal.ppat.1009100","article-title":"Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein","volume":"16","author":"DC Dinesh","year":"2020","journal-title":"PLOS Pathog."},{"key":"pcbi.1010121.ref024","doi-asserted-by":"crossref","first-page":"1228","DOI":"10.1016\/j.apsb.2020.04.009","article-title":"Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites","volume":"10","author":"S Kang","year":"2020","journal-title":"Acta Pharm Sin B"},{"key":"pcbi.1010121.ref025","doi-asserted-by":"crossref","first-page":"11827","DOI":"10.1021\/bi0609319","article-title":"Carboxyl Terminus of Severe Acute Respiratory Syndrome Coronavirus Nucleocapsid Protein: Self-Association Analysis and Nucleic Acid Binding Characterization \u2020","volume":"45","author":"H Luo","year":"2006","journal-title":"Biochemistry"},{"key":"pcbi.1010121.ref026","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1016\/j.febslet.2012.11.016","article-title":"Oligomerization of the carboxyl terminal domain of the human coronavirus 229E nucleocapsid protein","volume":"587","author":"Y-S Lo","year":"2013","journal-title":"FEBS Lett"},{"key":"pcbi.1010121.ref027","doi-asserted-by":"crossref","first-page":"1890","DOI":"10.1002\/pro.3909","article-title":"Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein","volume":"29","author":"Q Ye","year":"2020","journal-title":"Protein Sci"},{"key":"pcbi.1010121.ref028","doi-asserted-by":"crossref","first-page":"1092","DOI":"10.1016\/j.molcel.2020.11.025","article-title":"Phosphoregulation of Phase Separation by the SARS-CoV-2 N Protein Suggests a Biophysical Basis for its Dual Functions","volume":"80","author":"CR Carlson","year":"2020","journal-title":"Mol Cell"},{"key":"pcbi.1010121.ref029","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-020-19843-1","article-title":"Nucleocapsid protein of SARS-CoV-2 phase separates into RNA-rich polymerase-containing condensates","volume":"11","author":"A Savastano","year":"2020","journal-title":"Nat Commun"},{"key":"pcbi.1010121.ref030","doi-asserted-by":"crossref","first-page":"e106478","DOI":"10.15252\/embj.2020106478","article-title":"SARS-CoV-2 nucleocapsid protein phase-separates with RNA and with human hnRNPs","volume":"39","author":"TM Perdikari","year":"2020","journal-title":"EMBO J"},{"key":"pcbi.1010121.ref031","first-page":"1","article-title":"Nucleocapsid mutations R203K\/G204R increase the infectivity, fitness and virulence of SARS-CoV-2","volume":"29","author":"H Wu","year":"2021","journal-title":"Cell Host Microbe"},{"key":"pcbi.1010121.ref032","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1038\/s41467-020-20768-y","article-title":"The SARS-CoV-2 nucleocapsid phosphoprotein forms mutually exclusive condensates with RNA and the membrane-associated M protein","volume":"12","author":"S Lu","year":"2021","journal-title":"Nat Commun"},{"key":"pcbi.1010121.ref033","doi-asserted-by":"crossref","first-page":"11103","DOI":"10.1021\/bi049194b","article-title":"Low stability of nucleocapsid protein in SARS virus","volume":"43","author":"Y Wang","year":"2004","journal-title":"Biochemistry"},{"key":"pcbi.1010121.ref034","doi-asserted-by":"crossref","first-page":"4152","DOI":"10.1111\/j.1742-4658.2008.06564.x","article-title":"Phosphorylation of the arginine\/serine dipeptide-rich motif of the severe acute respiratory syndrome coronavirus nucleocapsid protein modulates its multimerization, translation inhibitory activity and cellular localization","volume":"275","author":"TY Peng","year":"2008","journal-title":"FEBS J"},{"key":"pcbi.1010121.ref035","doi-asserted-by":"crossref","first-page":"102681","DOI":"10.1016\/j.isci.2021.102681","article-title":"Characterization of SARS-CoV-2 nucleocapsid protein reveals multiple functional consequences of the C-terminal domain","volume":"24","author":"C Wu","year":"2021","journal-title":"iScience"},{"key":"pcbi.1010121.ref036","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1016\/j.bbrc.2020.04.136","article-title":"Biochemical characterization of SARS-CoV-2 nucleocapsid protein","volume":"527","author":"W Zeng","year":"2020","journal-title":"Biochem Biophys Res Commun"},{"key":"pcbi.1010121.ref037","doi-asserted-by":"crossref","first-page":"102523","DOI":"10.1016\/j.isci.2021.102523","article-title":"Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids","volume":"24","author":"H Zhao","year":"2021","journal-title":"iScience"},{"key":"pcbi.1010121.ref038","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1016\/j.bpj.2017.06.042","article-title":"An Efficient Method for Estimating the Hydrodynamic Radius of Disordered Protein Conformations","volume":"113","author":"M Nygaard","year":"2017","journal-title":"Biophys J"},{"key":"pcbi.1010121.ref039","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1007\/978-1-0716-0524-0_21","article-title":"Computing, analyzing, and comparing the radius of gyration and hydrodynamic radius in conformational ensembles of intrinsically disordered proteins","volume":"2141","author":"MC Ahmed","year":"2020","journal-title":"Methods Mol Biol"},{"key":"pcbi.1010121.ref040","doi-asserted-by":"crossref","first-page":"4773","DOI":"10.1128\/jvi.70.7.4773-4777.1996","article-title":"The transmissible gastroenteritis coronavirus contains a spherical core shell consisting of M and N proteins","volume":"70","author":"C Risco","year":"1996","journal-title":"J Virol"},{"key":"pcbi.1010121.ref041","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1073\/pnas.0805270106","article-title":"Cryo-electron tomography of mouse hepatitis virus: Insights into the structure of the coronavirion","volume":"106","author":"M B\u00e1rcena","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1010121.ref042","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1007\/s13238-016-0352-8","article-title":"Electron microscopy studies of the coronavirus ribonucleoprotein complex","volume":"8","author":"M Gui","year":"2017","journal-title":"Protein Cell"},{"key":"pcbi.1010121.ref043","first-page":"730","article-title":"Molecular Architecture of the SARS-CoV-2","volume":"183","author":"H Yao","year":"2020","journal-title":"Virus. Cell"},{"key":"pcbi.1010121.ref044","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1099\/0022-1317-39-3-545","article-title":"Ribonucleoprotein-like structures from coronavirus particles","volume":"39","author":"MR Macnaughton","year":"1978","journal-title":"J Gen Virol"},{"key":"pcbi.1010121.ref045","doi-asserted-by":"crossref","first-page":"1129","DOI":"10.1261\/rna.039057.113","article-title":"Crystal structure of Schmallenberg orthobunyavirus nucleoprotein-RNA complex reveals a novel RNA sequestration mechanism","volume":"19","author":"H Dong","year":"2013","journal-title":"RNA"},{"key":"pcbi.1010121.ref046","doi-asserted-by":"crossref","first-page":"1583","DOI":"10.1111\/cmi.12457","article-title":"Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions","volume":"17","author":"K Zhang","year":"2015","journal-title":"Cell Microbiol"},{"key":"pcbi.1010121.ref047","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1016\/j.sbi.2012.01.010","article-title":"Coarse-grained molecular simulations of large biomolecules","volume":"22","author":"S. Takada","year":"2012","journal-title":"Curr Opin Struct Biol"},{"key":"pcbi.1010121.ref048","first-page":"1","article-title":"Unraveling low-resolution structural data of large biomolecules by constructing atomic models with experiment-targeted parallel cascade selection simulations","volume":"6","author":"J Peng","year":"2016","journal-title":"Sci Rep"},{"key":"pcbi.1010121.ref049","doi-asserted-by":"crossref","first-page":"15757","DOI":"10.1073\/pnas.1004569107","article-title":"Multidomain assembled states of Hck tyrosine kinase in solution","volume":"107","author":"S Yang","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1010121.ref050","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1007\/s11373-005-9035-9","article-title":"Modular organization of SARS coronavirus nucleocapsid protein","volume":"13","author":"C Chang","year":"2006","journal-title":"J Biomed Sci"},{"key":"pcbi.1010121.ref051","doi-asserted-by":"crossref","first-page":"466","DOI":"10.1016\/j.ijbiomac.2022.01.121","article-title":"Insights into the specificity for the interaction of the promiscuous SARS-CoV-2 nucleocapsid protein N-terminal domain with deoxyribonucleic acids","volume":"203","author":"IP Caruso","year":"2022","journal-title":"Int J Biol Macromol"},{"key":"pcbi.1010121.ref052","doi-asserted-by":"crossref","first-page":"15351","DOI":"10.1021\/bi051122c","article-title":"SR-rich motif plays a pivotal role in recombinant SARS coronavirus nucleocapsid protein multimerization","volume":"44","author":"H Luo","year":"2005","journal-title":"Biochemistry"},{"key":"pcbi.1010121.ref053","doi-asserted-by":"crossref","first-page":"5885","DOI":"10.1038\/s41467-020-19619-7","article-title":"SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography","volume":"11","author":"S Klein","year":"2020","journal-title":"Nat Commun"},{"key":"pcbi.1010121.ref054","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pbio.3001425","article-title":"SARS-CoV-2 nucleocapsid protein forms condensates with viral genomic RNA","volume":"19","author":"A Jack","year":"2021","journal-title":"PLoS Biol"},{"key":"pcbi.1010121.ref055","doi-asserted-by":"crossref","first-page":"13669","DOI":"10.1128\/JVI.78.24.13669-13677.2004","article-title":"Oligomerization of Hantavirus N Protein: C-Terminal \u03b1-Helices Interact To Form a Shared Hydrophobic Space","volume":"78","author":"P Kaukinen","year":"2004","journal-title":"J Virol"},{"key":"pcbi.1010121.ref056","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.abm4034","article-title":"The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a","volume":"8","author":"LM Bessa","year":"2022","journal-title":"Sci Adv"},{"key":"pcbi.1010121.ref057","doi-asserted-by":"crossref","first-page":"d2304","DOI":"10.1136\/bmj.d2304","article-title":"How to obtain the P value from a confidence interval","volume":"343","author":"DG Altman","year":"2011","journal-title":"BMJ"},{"key":"pcbi.1010121.ref058","first-page":"624","article-title":"Four-dimensional cryo-electron microscopy at quasi-atomic resolution: IMAGIC 4D","author":"M van Heel","year":"2012","journal-title":"American Cancer Society"},{"key":"pcbi.1010121.ref059","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/j.jsb.2016.04.010","article-title":"Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy","volume":"195","author":"JM de la Rosa-Trev\u00edn","year":"2016","journal-title":"J Struct Biol"},{"key":"pcbi.1010121.ref060","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1016\/j.jsb.2013.09.015","article-title":"Xmipp 3.0: An improved software suite for image processing in electron microscopy","volume":"184","author":"JM De la Rosa-Trev\u00edn","year":"2013","journal-title":"J Struct Biol"},{"key":"pcbi.1010121.ref061","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1016\/j.jsb.2012.09.006","article-title":"RELION: Implementation of a Bayesian approach to cryo-EM structure determination","volume":"180","author":"SHW Scheres","year":"2012","journal-title":"J Struct Biol"},{"key":"pcbi.1010121.ref062","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.jsb.2006.05.009","article-title":"EMAN2: An extensible image processing suite for electron microscopy","volume":"157","author":"G Tang","year":"2007","journal-title":"J Struct Biol"},{"key":"pcbi.1010121.ref063","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1007\/978-1-0716-1406-8_13","article-title":"Image Processing in Cryo-Electron Microscopy of Single Particles: The Power of Combining Methods","author":"COS Sorzano","year":"2021","journal-title":"Methods in Molecular Biology"},{"key":"pcbi.1010121.ref064","doi-asserted-by":"crossref","first-page":"1979","DOI":"10.1021\/ct2001045","article-title":"CafeMol: A coarse-grained biomolecular simulator for simulating proteins at work","volume":"7","author":"H Kenzaki","year":"2011","journal-title":"J Chem Theory Comput"},{"key":"pcbi.1010121.ref065","doi-asserted-by":"crossref","first-page":"2981","DOI":"10.1093\/bioinformatics\/btu426","article-title":"YASARA View\u2014molecular graphics for all devices\u2014from smartphones to workstations","volume":"30","author":"E Krieger","year":"2014","journal-title":"Bioinformatics"},{"key":"pcbi.1010121.ref066","doi-asserted-by":"crossref","first-page":"2695","DOI":"10.1093\/bioinformatics\/btl461","article-title":"Bio3d: An R package for the comparative analysis of protein structures","volume":"22","author":"BJ Grant","year":"2006","journal-title":"Bioinformatics"},{"key":"pcbi.1010121.ref067","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera\u2014A visualization system for exploratory research and analysis","volume":"25","author":"EF Pettersen","year":"2004","journal-title":"J Comput Chem"},{"key":"pcbi.1010121.ref068","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1038\/nmeth.2089","article-title":"NIH Image to ImageJ: 25 years of image analysis","author":"CA Schneider","year":"2012","journal-title":"Nature Methods"},{"key":"pcbi.1010121.ref069","doi-asserted-by":"crossref","first-page":"1460","DOI":"10.1002\/jcc.20906","article-title":"Fast procedure for reconstruction of full-atom protein models from reduced representations","volume":"29","author":"P Rotkiewicz","year":"2008","journal-title":"J Comput Chem"},{"key":"pcbi.1010121.ref070","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1016\/S0969-2126(01)00648-7","article-title":"Modeling tricks and fitting techniques for multiresolution structures","author":"W Wriggers","year":"2001","journal-title":"Structure"},{"key":"pcbi.1010121.ref071","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: Visual molecular dynamics","volume":"14","author":"W Humphrey","year":"1996","journal-title":"J Mol Graph"},{"key":"pcbi.1010121.ref072","doi-asserted-by":"crossref","first-page":"3257","DOI":"10.1021\/ct300400x","article-title":"Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone \u03c6, \u03c8 and side-chain \u03c71 and \u03c72 Dihedral Angles","volume":"8","author":"RB Best","year":"2012","journal-title":"J Chem Theory Comput"},{"key":"pcbi.1010121.ref073","doi-asserted-by":"crossref","first-page":"044130","DOI":"10.1063\/5.0014475","article-title":"Scalable molecular dynamics on CPU and GPU architectures with NAMD","volume":"153","author":"JC Phillips","year":"2020","journal-title":"J Chem Phys"},{"key":"pcbi.1010121.ref074","doi-asserted-by":"crossref","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle mesh Ewald: An N \u00b7log (N) method for Ewald sums in large systems","volume":"98","author":"T Darden","year":"1993","journal-title":"J Chem Phys"},{"key":"pcbi.1010121.ref075","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1016\/0021-9991(77)90098-5","article-title":"Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes","volume":"23","author":"JP Ryckaert","year":"1977","journal-title":"J Comput Phys"},{"key":"pcbi.1010121.ref076","doi-asserted-by":"crossref","first-page":"952","DOI":"10.1002\/jcc.540130805","article-title":"Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models","volume":"13","author":"S Miyamoto","year":"1992","journal-title":"J Comput Chem"},{"key":"pcbi.1010121.ref077","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1016\/j.ymeth.2009.04.005","article-title":"Molecular dynamics flexible fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography","volume":"49","author":"LG Trabuco","year":"2009","journal-title":"Methods"},{"key":"pcbi.1010121.ref078","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1006\/jmbi.1999.3091","article-title":"Protein secondary structure prediction based on position-specific scoring matrices","volume":"292","author":"DT Jones","year":"1999","journal-title":"J Mol Biol"},{"key":"pcbi.1010121.ref079","doi-asserted-by":"crossref","first-page":"2157","DOI":"10.1002\/jcc.21224","article-title":"PACKMOL: A package for building initial configurations for molecular dynamics simulations","volume":"30","author":"L Mart\u00ednez","year":"2009","journal-title":"J Comput Chem"},{"key":"pcbi.1010121.ref080","doi-asserted-by":"crossref","first-page":"3696","DOI":"10.1021\/acs.jctc.5b00255","article-title":"ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB","volume":"11","author":"JA Maier","year":"2015","journal-title":"J Chem Theory Comput"},{"key":"pcbi.1010121.ref081","volume-title":"AmberTools20","author":"D.A. Case","year":"2020"},{"key":"pcbi.1010121.ref082","doi-asserted-by":"crossref","first-page":"3878","DOI":"10.1021\/ct400314y","article-title":"Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald","volume":"9","author":"R Salomon-Ferrer","year":"2013","journal-title":"J Chem Theory Comput"},{"key":"pcbi.1010121.ref083","doi-asserted-by":"crossref","first-page":"1542","DOI":"10.1021\/ct200909j","article-title":"Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born","volume":"8","author":"AW G\u00f6tz","year":"2012","journal-title":"J Chem Theory Comput"},{"key":"pcbi.1010121.ref084","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1016\/j.cpc.2012.09.022","article-title":"SPFP: Speed without compromise\u2014A mixed precision model for GPU accelerated molecular dynamics simulations","volume":"184","author":"S Le Grand","year":"2013","journal-title":"Comput Phys Commun"},{"key":"pcbi.1010121.ref085","volume-title":"RStudio: Integrated Development for R. RStudio","author":"RStudio Team","year":"2020"},{"key":"pcbi.1010121.ref086","doi-asserted-by":"crossref","unstructured":"Ester M, Kriegel H-P, Sander J, Xu X. A Density-Based Algorithm for Discovering Clusters in Large Spatial Databases with Noise. Proceedings of the Second International Conference on Knowledge Discovery and Data Mining. AAAI Press; 1996. pp. 226\u2013231. doi: 10.1016\/B978-044452701-1.00067\u20133","DOI":"10.1016\/B978-044452701-1.00067-3"},{"key":"pcbi.1010121.ref087","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v091.i01","article-title":"Dbscan: Fast density-based clustering with R","volume":"91","author":"M Hahsler","year":"2019","journal-title":"J Stat Softw"},{"key":"pcbi.1010121.ref088","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1016\/j.jsb.2005.05.009","article-title":"Fourier shell correlation threshold criteria","volume":"151","author":"M Van Heel","year":"2005","journal-title":"J Struct Biol"},{"key":"pcbi.1010121.ref089","doi-asserted-by":"crossref","first-page":"W636","DOI":"10.1093\/nar\/gkz268","article-title":"The EMBL-EBI search and sequence analysis tools APIs in 2019","volume":"47","author":"F Madeira","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1010121.ref090","doi-asserted-by":"crossref","first-page":"e108","DOI":"10.1002\/cpbi.108","article-title":"Protein Sequence Analysis Using the MPI Bioinformatics Toolkit","volume":"72","author":"F Gabler","year":"2020","journal-title":"Curr Protoc Bioinforma"},{"key":"pcbi.1010121.ref091","doi-asserted-by":"crossref","first-page":"2237","DOI":"10.1016\/j.jmb.2017.12.007","article-title":"A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core","volume":"430","author":"L Zimmermann","year":"2018","journal-title":"J Mol Biol"},{"key":"pcbi.1010121.ref092","article-title":"2dSS: a web server for protein secondary structure visualization","author":"D. P. Lotun","year":"2019","journal-title":"bioRxiv"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1010121","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,5,24]],"date-time":"2022-05-24T00:00:00Z","timestamp":1653350400000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1010121","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,5]],"date-time":"2023-02-05T01:51:48Z","timestamp":1675561908000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1010121"}},"subtitle":[],"editor":[{"given":"Alexey","family":"Onufriev","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,5,12]]},"references-count":92,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2022,5,12]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1010121","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1010121","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,5,12]]}}}