MS2 bacteriophage capsid studied using all-atom molecular dynamics

Abstract

The all-atom model of an MS2 bacteriophage particle without its genome (the capsid) was built using high-resolution cryo-electron microscopy (EM) measurements for initial conformation. The structural characteristics of the capsid and the dynamics of the surrounding solution were examined using molecular dynamics simulation. The model demonstrates the overall preservation of the cryo-EM structure of the capsid at physiological conditions (room temperature and ions composition). The formation of a dense anion layer near the inner surface and a diffuse cation layer near the outer surface of the capsid was detected. The flow of water molecules and ions across the capsid through its pores were quantified, which was considerable for water and substantial for ions.

Gold—Polyoxoborates Nanocomposite Prohibits Adsorption of Bacteriophages on Inner Surfaces of Polypropylene Labware and Protects Samples from Bacterial and Yeast Infections

“…The MS2 bacteriophage, belonging to Fiersviridae , has an icosahedral structure, and its genetic material is (+)ssRNA. It has a diameter of about 27 nm and has one of the smallest known viral genomes so far (3569 nucleotides) [ 45 ]. MS2 is often regarded as a good model for studies on eukaryotic (also pathogenic) viruses [ 46 , 47 , 48 ].…”

All-atom molecular dynamics study of hepatitis B virus containing pregenome RNA in solution

“…Many AA-MD simulations of viruses have been conducted 15 . For example, small viruses such as small satellite tobacco mosaic viruses, 16 satellite tobacco necrosis virus, 17 and porcine circoviruses type 2 [18][19][20] , MS2 bacteriophage 21 , but also larger viruses such as polioviruses 22 , hepatitis B viruses (HBV), 23,24 and immunodeficiency virus 25,26 , have been investigated. Hadden et al 23 investigated the physical properties of an HBV without RNA, that is, with an empty capsid, in an aqueous electrolyte solution.…”

All-atom molecular dynamics study of hepatitis B virus containing pregenome RNA in solution

“…Many AA-MD simulations of viruses have been conducted 15 . For example, small viruses such as small satellite tobacco mosaic viruses, 16 satellite tobacco necrosis virus, 17 and porcine circoviruses type 2 [18][19][20] , MS2 bacteriophage 21 , but also larger viruses such as polioviruses 22 , hepatitis B viruses (HBV), 23,24 and immunodeficiency virus 25,26 , have been investigated. Hadden et al 23 investigated the physical properties of an HBV without RNA, that is, with an empty capsid, in an aqueous electrolyte solution.…”