publication . Article . 2016

Modeling Effects of RNA on Capsid Assembly Pathways via Coarse-Grained Stochastic Simulation.

Russell Schwartz; Lu Xie; Gregory R. Smith;
Open Access English
  • Published: 01 May 2016 Journal: PLoS ONE, volume 11, issue 5 (issn: 1932-6203, Copyright policy)
  • Publisher: Public Library of Science (PLoS)
Abstract
The environment of a living cell is vastly different from that of an in vitro reaction system, an issue that presents great challenges to the use of in vitro models, or computer simulations based on them, for understanding biochemistry in vivo. Virus capsids make an excellent model system for such questions because they typically have few distinct components, making them amenable to in vitro and modeling studies, yet their assembly can involve complex networks of possible reactions that cannot be resolved in detail by any current experimental technology. We previously fit kinetic simulation parameters to bulk in vitro assembly data to yield a close match between...
Subjects
free text keywords: Research Article, Biology and Life Sciences, Microbiology, Virology, Viral Replication, Viral Packaging, Biochemistry, Biochemical Simulations, Computational Biology, Research and Analysis Methods, Simulation and Modeling, Physical Sciences, Physics, Condensed Matter Physics, Nucleation, Materials Science, Materials by Structure, Oligomers, Chemistry, Polymer Chemistry, Macromolecules, Polymers, Thermodynamics, Free Energy, Electromagnetic Radiation, Light, Light Scattering, Scattering, lcsh:Medicine, lcsh:R, lcsh:Science, lcsh:Q, Bioinformatics, Reaction system, Nucleic acid, RNA, Model system, Biological system, Stochastic simulation, Kinetic rate, Living cell, Biology, Complex network
Funded by
NIH| Inferring in vivo Capsid Assembly Kinetics from in vitro by Stochastic Simulation
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01AI076318-03
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
,
NIH| Heterogeneous Cancer Progression from Microarray Data
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01CA140214-02
  • Funding stream: NATIONAL CANCER INSTITUTE
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65 references, page 1 of 5

1 Zlotnick A. To build a virus capsid. An equilibrium model of the self assembly of polyhedral protein complexes. J. Mol. Biol. 1994:241: 59–67. 8051707 [OpenAIRE] [PubMed]

2 Zlotnick A, Johnson JM, Endres D. A theoretical model successfully identifies features of hepatitis B virus capsid assembly. Biochemistry. 1999:38: 14644–14652. 10545189 [PubMed]

3 Moisant P, Neeman H, Zlotnick A. Exploring the paths of (virus) a ssembly. Biophys. J. 2010:99: 1350–1357. 10.1016/j.bpj.2010.06.030 20816046 [OpenAIRE] [PubMed] [DOI]

4 Tsiang M, Niedziela-Majka A, Hung M, Jin D, Hu E, Yant S, et al A trimer of dimers is the basic building block for human immunodeficiency virus-1 capsid assembly. Biochemistry. 2012:51: 4416–4428. 22564075 [PubMed]

5 Hagan MF, Elrad OM. Understanding the concentration dependence of viral capsid assembly kinetics—the origin of the lag time and identifying the critical nucleus size. Biophys. J. 2010:98: 1065–1074. 10.1016/j.bpj.2009.11.023 20303864 [OpenAIRE] [PubMed] [DOI]

6 Morozov AY, Bruinsma RF, Rudnick J. Assembly of viruses and the pseudo-law of mass action. J. Chem. Phys. 2009:131: 155101–1–155101–17.

7 Schwartz RS, Shor PW, Prevelige PE, Berger BA. Local rule simulation of the kinetics of virus capsid self-assembly. Biophys. J. 1998:75: 2626–2636. 9826587 [OpenAIRE] [PubMed]

8 Rapaport D, Johnson J, Skolnick J. Supramolecular self-assembly: Molecular dynamics modeling of polyhedral shell formation. Commun. Comput. Phys. 1999:122: 231–235.

9 Hagan MF, Chandler D. Dynamic pathways for viral capsid assembly. Biop hys. J. 2006:91: 42–54. 16565055 [OpenAIRE] [PubMed]

10 Nguyen HD, Reddy VS, Brooks CL. Deciphering the kinetic mechanism of spontaneous self- assembly of icosahedral capsids. Nano Lett. 2007:7: 338–344. 17297998 [PubMed]

11 Johnston IG, Louis AA, Doye JPK. Modelling the self-assembly of virus capisds. J. Phys.-Condens. Mat. 2010:22: 104101.

12 Krishna V, Ayton GS, Voth GA. Role of protein interactions in defining HIV-1 viral capsid shape and stability: a coarse-grained analysis. Biophys. J. 2010:98: 18–26. 10.1016/j.bpj.2009.09.049 20085716 [OpenAIRE] [PubMed] [DOI]

13 Baschek JE, Klein HCR, Schwarz US. Stochastic dynamics of virus capsid formation: direct versus hierarchical self-assembly. BMC Biophys. 2012:5:22–1–22–18. [OpenAIRE]

14 Grime JMA and Voth GA. Early stages of the HIV-1 capsid protein lattice formation. Biophys. J. 2012: 103(8): 1774–1783. 10.1016/j.bpj.2012.09.007 23083721 [OpenAIRE] [PubMed] [DOI]

15 Chen B and Tycko R. Simulated self-assembly of the HIV-1 capsid: protein shape and native contacts are sufficient for two-dimensional lattice formation. Biophys. J. 2011: 100(12): 3035–3044. 10.1016/j.bpj.2011.05.025 21689538 [OpenAIRE] [PubMed] [DOI]

65 references, page 1 of 5
Abstract
The environment of a living cell is vastly different from that of an in vitro reaction system, an issue that presents great challenges to the use of in vitro models, or computer simulations based on them, for understanding biochemistry in vivo. Virus capsids make an excellent model system for such questions because they typically have few distinct components, making them amenable to in vitro and modeling studies, yet their assembly can involve complex networks of possible reactions that cannot be resolved in detail by any current experimental technology. We previously fit kinetic simulation parameters to bulk in vitro assembly data to yield a close match between...
Subjects
free text keywords: Research Article, Biology and Life Sciences, Microbiology, Virology, Viral Replication, Viral Packaging, Biochemistry, Biochemical Simulations, Computational Biology, Research and Analysis Methods, Simulation and Modeling, Physical Sciences, Physics, Condensed Matter Physics, Nucleation, Materials Science, Materials by Structure, Oligomers, Chemistry, Polymer Chemistry, Macromolecules, Polymers, Thermodynamics, Free Energy, Electromagnetic Radiation, Light, Light Scattering, Scattering, lcsh:Medicine, lcsh:R, lcsh:Science, lcsh:Q, Bioinformatics, Reaction system, Nucleic acid, RNA, Model system, Biological system, Stochastic simulation, Kinetic rate, Living cell, Biology, Complex network
Funded by
NIH| Inferring in vivo Capsid Assembly Kinetics from in vitro by Stochastic Simulation
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01AI076318-03
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
,
NIH| Heterogeneous Cancer Progression from Microarray Data
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01CA140214-02
  • Funding stream: NATIONAL CANCER INSTITUTE
Download fromView all 3 versions
PLoS ONE
Article . 2016
PLoS ONE
Article . 2016
Provider: Crossref
PLoS ONE
Article
Provider: UnpayWall
65 references, page 1 of 5

1 Zlotnick A. To build a virus capsid. An equilibrium model of the self assembly of polyhedral protein complexes. J. Mol. Biol. 1994:241: 59–67. 8051707 [OpenAIRE] [PubMed]

2 Zlotnick A, Johnson JM, Endres D. A theoretical model successfully identifies features of hepatitis B virus capsid assembly. Biochemistry. 1999:38: 14644–14652. 10545189 [PubMed]

3 Moisant P, Neeman H, Zlotnick A. Exploring the paths of (virus) a ssembly. Biophys. J. 2010:99: 1350–1357. 10.1016/j.bpj.2010.06.030 20816046 [OpenAIRE] [PubMed] [DOI]

4 Tsiang M, Niedziela-Majka A, Hung M, Jin D, Hu E, Yant S, et al A trimer of dimers is the basic building block for human immunodeficiency virus-1 capsid assembly. Biochemistry. 2012:51: 4416–4428. 22564075 [PubMed]

5 Hagan MF, Elrad OM. Understanding the concentration dependence of viral capsid assembly kinetics—the origin of the lag time and identifying the critical nucleus size. Biophys. J. 2010:98: 1065–1074. 10.1016/j.bpj.2009.11.023 20303864 [OpenAIRE] [PubMed] [DOI]

6 Morozov AY, Bruinsma RF, Rudnick J. Assembly of viruses and the pseudo-law of mass action. J. Chem. Phys. 2009:131: 155101–1–155101–17.

7 Schwartz RS, Shor PW, Prevelige PE, Berger BA. Local rule simulation of the kinetics of virus capsid self-assembly. Biophys. J. 1998:75: 2626–2636. 9826587 [OpenAIRE] [PubMed]

8 Rapaport D, Johnson J, Skolnick J. Supramolecular self-assembly: Molecular dynamics modeling of polyhedral shell formation. Commun. Comput. Phys. 1999:122: 231–235.

9 Hagan MF, Chandler D. Dynamic pathways for viral capsid assembly. Biop hys. J. 2006:91: 42–54. 16565055 [OpenAIRE] [PubMed]

10 Nguyen HD, Reddy VS, Brooks CL. Deciphering the kinetic mechanism of spontaneous self- assembly of icosahedral capsids. Nano Lett. 2007:7: 338–344. 17297998 [PubMed]

11 Johnston IG, Louis AA, Doye JPK. Modelling the self-assembly of virus capisds. J. Phys.-Condens. Mat. 2010:22: 104101.

12 Krishna V, Ayton GS, Voth GA. Role of protein interactions in defining HIV-1 viral capsid shape and stability: a coarse-grained analysis. Biophys. J. 2010:98: 18–26. 10.1016/j.bpj.2009.09.049 20085716 [OpenAIRE] [PubMed] [DOI]

13 Baschek JE, Klein HCR, Schwarz US. Stochastic dynamics of virus capsid formation: direct versus hierarchical self-assembly. BMC Biophys. 2012:5:22–1–22–18. [OpenAIRE]

14 Grime JMA and Voth GA. Early stages of the HIV-1 capsid protein lattice formation. Biophys. J. 2012: 103(8): 1774–1783. 10.1016/j.bpj.2012.09.007 23083721 [OpenAIRE] [PubMed] [DOI]

15 Chen B and Tycko R. Simulated self-assembly of the HIV-1 capsid: protein shape and native contacts are sufficient for two-dimensional lattice formation. Biophys. J. 2011: 100(12): 3035–3044. 10.1016/j.bpj.2011.05.025 21689538 [OpenAIRE] [PubMed] [DOI]

65 references, page 1 of 5
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