The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA

The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA-binding protein critical for viral genome packaging, yet the molecular details that underlie this process are poorly understood. Here we combine single-molecule spectroscopy with all-atom simulations to uncover the molecular details that con...

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Published inNature communications Vol. 12; no. 1; p. 1936
Main Authors Cubuk, Jasmine, Alston, Jhullian J., Incicco, J. Jeremías, Singh, Sukrit, Stuchell-Brereton, Melissa D., Ward, Michael D., Zimmerman, Maxwell I., Vithani, Neha, Griffith, Daniel, Wagoner, Jason A., Bowman, Gregory R., Hall, Kathleen B., Soranno, Andrea, Holehouse, Alex S.
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 29.03.2021
Nature Publishing Group
Nature Portfolio
Subjects
631/114/2397
631/57/2265
631/57/2269
Binding Sites
Broken symmetry
Coronavirus Nucleocapsid Proteins - chemistry
Coronavirus Nucleocapsid Proteins - metabolism
COVID-19 - virology
Dimerization
Genomes
Humanities and Social Sciences
Liquid phases
Molecular Dynamics Simulation
multidisciplinary
N protein
Nucleocapsids
Packaging
Phase separation
Phosphoproteins - chemistry
Phosphoproteins - metabolism
Polymers
Protein Conformation
Protein Domains
Proteins
Ribonucleic acid
RNA
RNA, Viral - chemistry
RNA, Viral - metabolism
RNA-binding protein
SARS-CoV-2 - chemistry
SARS-CoV-2 - metabolism
Science
Science (multidisciplinary)
Severe acute respiratory syndrome
Severe acute respiratory syndrome coronavirus 2
Spectroscopy
Spectrum analysis
Online AccessGet full text

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Abstract The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA-binding protein critical for viral genome packaging, yet the molecular details that underlie this process are poorly understood. Here we combine single-molecule spectroscopy with all-atom simulations to uncover the molecular details that contribute to N protein function. N protein contains three dynamic disordered regions that house putative transiently-helical binding motifs. The two folded domains interact minimally such that full-length N protein is a flexible and multivalent RNA-binding protein. N protein also undergoes liquid-liquid phase separation when mixed with RNA, and polymer theory predicts that the same multivalent interactions that drive phase separation also engender RNA compaction. We offer a simple symmetry-breaking model that provides a plausible route through which single-genome condensation preferentially occurs over phase separation, suggesting that phase separation offers a convenient macroscopic readout of a key nanoscopic interaction. SARS-CoV-2 nucleocapsid (N) protein is responsible for viral genome packaging. Here the authors employ single-molecule spectroscopy with all-atom simulations to provide the molecular details of N protein and show that it undergoes phase separation with RNA.
AbstractList The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA-binding protein critical for viral genome packaging, yet the molecular details that underlie this process are poorly understood. Here we combine single-molecule spectroscopy with all-atom simulations to uncover the molecular details that contribute to N protein function. N protein contains three dynamic disordered regions that house putative transiently-helical binding motifs. The two folded domains interact minimally such that full-length N protein is a flexible and multivalent RNA-binding protein. N protein also undergoes liquid-liquid phase separation when mixed with RNA, and polymer theory predicts that the same multivalent interactions that drive phase separation also engender RNA compaction. We offer a simple symmetry-breaking model that provides a plausible route through which single-genome condensation preferentially occurs over phase separation, suggesting that phase separation offers a convenient macroscopic readout of a key nanoscopic interaction.
The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA-binding protein critical for viral genome packaging, yet the molecular details that underlie this process are poorly understood. Here we combine single-molecule spectroscopy with all-atom simulations to uncover the molecular details that contribute to N protein function. N protein contains three dynamic disordered regions that house putative transiently-helical binding motifs. The two folded domains interact minimally such that full-length N protein is a flexible and multivalent RNA-binding protein. N protein also undergoes liquid-liquid phase separation when mixed with RNA, and polymer theory predicts that the same multivalent interactions that drive phase separation also engender RNA compaction. We offer a simple symmetry-breaking model that provides a plausible route through which single-genome condensation preferentially occurs over phase separation, suggesting that phase separation offers a convenient macroscopic readout of a key nanoscopic interaction.SARS-CoV-2 nucleocapsid (N) protein is responsible for viral genome packaging. Here the authors employ single-molecule spectroscopy with all-atom simulations to provide the molecular details of N protein and show that it undergoes phase separation with RNA.
The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA-binding protein critical for viral genome packaging, yet the molecular details that underlie this process are poorly understood. Here we combine single-molecule spectroscopy with all-atom simulations to uncover the molecular details that contribute to N protein function. N protein contains three dynamic disordered regions that house putative transiently-helical binding motifs. The two folded domains interact minimally such that full-length N protein is a flexible and multivalent RNA-binding protein. N protein also undergoes liquid-liquid phase separation when mixed with RNA, and polymer theory predicts that the same multivalent interactions that drive phase separation also engender RNA compaction. We offer a simple symmetry-breaking model that provides a plausible route through which single-genome condensation preferentially occurs over phase separation, suggesting that phase separation offers a convenient macroscopic readout of a key nanoscopic interaction. SARS-CoV-2 nucleocapsid (N) protein is responsible for viral genome packaging. Here the authors employ single-molecule spectroscopy with all-atom simulations to provide the molecular details of N protein and show that it undergoes phase separation with RNA.
SARS-CoV-2 nucleocapsid (N) protein is responsible for viral genome packaging. Here the authors employ single-molecule spectroscopy with all-atom simulations to provide the molecular details of N protein and show that it undergoes phase separation with RNA.
ArticleNumber 1936
Author Holehouse, Alex S.
Ward, Michael D.
Hall, Kathleen B.
Incicco, J. Jeremías
Alston, Jhullian J.
Vithani, Neha
Stuchell-Brereton, Melissa D.
Wagoner, Jason A.
Soranno, Andrea
Singh, Sukrit
Zimmerman, Maxwell I.
Griffith, Daniel
Bowman, Gregory R.
Cubuk, Jasmine
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  orcidid: 0000-0001-6915-8242
  surname: Cubuk
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  organization: Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis
– sequence: 2
  givenname: Jhullian J.
  orcidid: 0000-0001-8227-6892
  surname: Alston
  fullname: Alston, Jhullian J.
  organization: Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis
– sequence: 3
  givenname: J. Jeremías
  surname: Incicco
  fullname: Incicco, J. Jeremías
  organization: Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis
– sequence: 4
  givenname: Sukrit
  orcidid: 0000-0003-1914-4955
  surname: Singh
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  organization: Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis
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  givenname: Melissa D.
  surname: Stuchell-Brereton
  fullname: Stuchell-Brereton, Melissa D.
  organization: Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis
– sequence: 6
  givenname: Michael D.
  surname: Ward
  fullname: Ward, Michael D.
  organization: Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis
– sequence: 7
  givenname: Maxwell I.
  surname: Zimmerman
  fullname: Zimmerman, Maxwell I.
  organization: Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis
– sequence: 8
  givenname: Neha
  surname: Vithani
  fullname: Vithani, Neha
  organization: Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis
– sequence: 9
  givenname: Daniel
  orcidid: 0000-0002-9633-9601
  surname: Griffith
  fullname: Griffith, Daniel
  organization: Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis
– sequence: 10
  givenname: Jason A.
  surname: Wagoner
  fullname: Wagoner, Jason A.
  organization: Laufer Center for Physical and Quantitative Biology, Stony Brook University
– sequence: 11
  givenname: Gregory R.
  surname: Bowman
  fullname: Bowman, Gregory R.
  organization: Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis
– sequence: 12
  givenname: Kathleen B.
  surname: Hall
  fullname: Hall, Kathleen B.
  organization: Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine
– sequence: 13
  givenname: Andrea
  orcidid: 0000-0001-8394-7993
  surname: Soranno
  fullname: Soranno, Andrea
  email: soranno@wustl.edu
  organization: Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis
– sequence: 14
  givenname: Alex S.
  orcidid: 0000-0002-4155-5729
  surname: Holehouse
  fullname: Holehouse, Alex S.
  email: alex.holehouse@wustl.edu
  organization: Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis
BackLink https://www.ncbi.nlm.nih.gov/pubmed/33782395$$D View this record in MEDLINE/PubMed
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Snippet The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA-binding protein critical for viral genome packaging, yet the molecular details that underlie this...
SARS-CoV-2 nucleocapsid (N) protein is responsible for viral genome packaging. Here the authors employ single-molecule spectroscopy with all-atom simulations...
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StartPage 1936
SubjectTerms 631/114/2397
631/57/2265
631/57/2269
Binding Sites
Broken symmetry
Coronavirus Nucleocapsid Proteins - chemistry
Coronavirus Nucleocapsid Proteins - metabolism
COVID-19 - virology
Dimerization
Genomes
Humanities and Social Sciences
Liquid phases
Molecular Dynamics Simulation
multidisciplinary
N protein
Nucleocapsids
Packaging
Phase separation
Phosphoproteins - chemistry
Phosphoproteins - metabolism
Polymers
Protein Conformation
Protein Domains
Proteins
Ribonucleic acid
RNA
RNA, Viral - chemistry
RNA, Viral - metabolism
RNA-binding protein
SARS-CoV-2 - chemistry
SARS-CoV-2 - metabolism
Science
Science (multidisciplinary)
Severe acute respiratory syndrome
Severe acute respiratory syndrome coronavirus 2
Spectroscopy
Spectrum analysis
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Title The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA
URI https://link.springer.com/article/10.1038/s41467-021-21953-3
https://www.ncbi.nlm.nih.gov/pubmed/33782395
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https://search.proquest.com/docview/2507146973
https://pubmed.ncbi.nlm.nih.gov/PMC8007728
https://doaj.org/article/dd6a306bbe1846f28cbf4f152c659197
Volume 12
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