Long‐time scale simulations of virus‐like particles from three human‐norovirus strains

The dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long‐time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coa...

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Bibliographic Details
Published in:Journal of computational chemistry 2023-06, Vol.44 (16), p.1470-1483
Main Authors: Lipska, Agnieszka G., Sieradzan, Adam K., Czaplewski, Cezary, Lipińska, Andrea D., Ocetkiewicz, Krzysztof M., Proficz, Jerzy, Czarnul, Paweł, Krawczyk, Henryk, Liwo, Adam
Format: Article
Language:English
Subjects:
Antigens
Blood Group Antigens - metabolism
Blood groups
coarse‐graining
Gastroenteritis
human norovirus
Humans
Molecular dynamics
Norovirus - metabolism
Protein Binding
UNRES
vaccines
Viruses
virus‐like particles
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Summary:The dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long‐time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse‐grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that sits in the VLP shell) and the P2 subdomain (that protrudes outside) of the major VP1 protein, this resulting in a correlated wagging motion of the P2 subdomains with respect to the VLP surface. The fluctuations of the P2 subdomain were found to be more pronounced and the P2 domain made a greater angle with the normal to the VLP surface for the GII.2 strain, which could explain the inability of this strain to bind the histo‐blood group antigens (HBGAs). Illustration of the dominant motion of the outer P2 domain of the VP1 protein of human norovirus (upper left), correlation between this domain motion, units clustered into two groups with intragroup‐correlated and intergroup‐anticorrelated motion (upper right), and extent of fluctuations (bottom), which is the largest for the GII.2 strain that does not bind to the histo‐blood group antigens, obtained by molecular dynamics simulations with the UNRES coarse‐grained model for three strains of human norovirus.
ISSN:0192-8651
1096-987X
DOI:10.1002/jcc.27087