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UNRES-GPU for Physics-Based Coarse-Grained Simulations of Protein Systems at Biological Time- and Size-Scales
Abstract
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).
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- Publication version
- Accepted or Published Version
- DOI:
- Digital Object Identifier (open in new tab) 10.1093/bioinformatics/btad391
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- Category:
- Articles
- Type:
- artykuły w czasopismach
- Published in:
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BIOINFORMATICS
no. 39,
ISSN: 1367-4803 - Language:
- English
- Publication year:
- 2023
- Bibliographic description:
- Ocetkiewicz K., Czaplewski C., Krawczyk H., Lipska A., Liwo J., Proficz J., Sieradzan A., Czarnul P.: UNRES-GPU for Physics-Based Coarse-Grained Simulations of Protein Systems at Biological Time- and Size-Scales// BIOINFORMATICS -, (2023),
- DOI:
- Digital Object Identifier (open in new tab) 10.1093/bioinformatics/btad391
- Sources of funding:
- Verified by:
- Gdańsk University of Technology
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