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

TY - JOUR

T1 - Structure and energetics guide dynamic behaviour in a T = 3 icosahedral virus capsid

AU - Shrivastav, Gourav

AU - Borkotoky, Subhomoi

AU - Dey, Debajit

AU - Singh, Bhumika

AU - Malhotra, Nidhi

AU - Azad, Kimi

AU - Jayaram, B

AU - Agarwal, Manish

AU - Banerjee, Manidipa

N1 - Copyright © 2023 Elsevier B.V. All rights reserved.

PY - 2024/2

Y1 - 2024/2

N2 - 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 γA subunit and RNA fragment exhibit higher flexibility than the γB and γC 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.

AB - 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 γA subunit and RNA fragment exhibit higher flexibility than the γB and γC 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.

KW - Capsid/chemistry

KW - Interleukin Receptor Common gamma Subunit/analysis

KW - Capsid Proteins/analysis

KW - RNA/metabolism

KW - Water/metabolism

U2 - 10.1016/j.bpc.2023.107152

DO - 10.1016/j.bpc.2023.107152

M3 - Article

C2 - 38113782

SN - 0301-4622

VL - 305

JO - Biophysical Chemistry

JF - Biophysical Chemistry

M1 - 107152

ER -