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Structure and energetics guide dynamic behaviour in a T = 3 icosahedral virus capsid.

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العنوان: Structure and energetics guide dynamic behaviour in a T = 3 icosahedral virus capsid.
المؤلفون: Shrivastav G; Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India. Electronic address: gourav.vfaculty@iitd.ac.in., Borkotoky S; Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India., Dey D; Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India., Singh B; Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India., Malhotra N; Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India., Azad K; Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India., Jayaram B; Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India., Agarwal M; Computer Services Centre, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India. Electronic address: zmanish@cc.iitd.ac.in., Banerjee M; Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India. Electronic address: mbanerjee@bioschool.iitd.ac.in.
المصدر: Biophysical chemistry [Biophys Chem] 2024 Feb; Vol. 305, pp. 107152. Date of Electronic Publication: 2023 Dec 08.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Elsevier Science B.V Country of Publication: Netherlands NLM ID: 0403171 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1873-4200 (Electronic) Linking ISSN: 03014622 NLM ISO Abbreviation: Biophys Chem Subsets: MEDLINE
أسماء مطبوعة: Publication: Amsterdam : Elsevier Science B.V
Original Publication: Amsterdam, North-Holland Pub. Co.
مواضيع طبية MeSH: Capsid*/chemistry , Capsid*/metabolism , Interleukin Receptor Common gamma Subunit*/analysis , Interleukin Receptor Common gamma Subunit*/metabolism, Capsid Proteins/analysis ; Capsid Proteins/metabolism ; RNA/metabolism ; Water/metabolism
مستخلص: Although virus capsids appear as rigid, symmetric particles in experimentally determined structures; biochemical studies suggest a significant degree of structural flexibility in the particles. We carried out all-atom simulations on the icosahedral capsid of an insect virus, Flock House Virus, which show intriguing differences in the degree of flexibility of quasi-equivalent capsid subunits consistent with previously described biological behaviour. The flexibility of all the β and γ subunits of the protein and RNA fragments is analysed and compared. Both γ A subunit and RNA fragment exhibit higher flexibility than the γ B and γ C subunits. The capsid shell is permeable to the bidirectional movement of water molecules, and the movement is heavily influenced by the geometry of the capsid shell along specific symmetry axes. In comparison to the symmetry axes along I5 and I3, the I2 axis exhibits a slightly higher water content. This enriched water environment along I2 could play a pivotal role in facilitating the structural transitions necessary for RNA release, shedding some light on the intricate and dynamic processes underlying the viral life cycle. Our study suggests that the physical characterization of whole virus capsids is the key to identifying biologically relevant transition states in the virus life cycle and understanding the basis of virus infectivity.
Competing Interests: Declaration of Competing Interest The authors declare no conflict of interest.
(Copyright © 2023 Elsevier B.V. All rights reserved.)
فهرسة مساهمة: Keywords: Molecular dynamics simulation; Non-enveloped; Symmetry axes; Virus capsid; Water tunnels
المشرفين على المادة: 0 (Interleukin Receptor Common gamma Subunit)
0 (Capsid Proteins)
63231-63-0 (RNA)
059QF0KO0R (Water)
تواريخ الأحداث: Date Created: 20231219 Date Completed: 20240103 Latest Revision: 20240105
رمز التحديث: 20240105
DOI: 10.1016/j.bpc.2023.107152
PMID: 38113782
قاعدة البيانات: MEDLINE
الوصف
تدمد:1873-4200
DOI:10.1016/j.bpc.2023.107152