Details of charge distribution in stable viral capsid

Tarasova, Elvira; Farafonov, Vladimir; Taiji, Makoto; Nerukh, Dmitry

doi:10.1016/j.molliq.2018.06.019

Cited by 14 publications

(9 citation statements)

References 22 publications

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“…1.3 times). This is different compared to PCV2, where twofold increase is observed [8]. A small peak at 12.6 nm is formed by the ions located in pores impregnated in the wall or located near the wall at concave regions, while the larger peak at 14.2 nm is made of ions near the convex regions and ions in the solution several water layers away from the surface.…”

Section: Ions Distributionmentioning

confidence: 70%

MS2 bacteriophage capsid studied using all-atom molecular dynamics

Farafonov

Nerukh

2019

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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.

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Section: Ions Distributionmentioning

confidence: 70%

MS2 bacteriophage capsid studied using all-atom molecular dynamics

Farafonov

Nerukh

2019

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“…Since DNA has negatively charged phosphate groups this looks rather plausible for the negatively charged chloride. It was also found that the concentration of chloride inside the virion exceeded that outside and its outer surface is dominated by the positively charged sodium [63]. Sodium and chloride diffuse inside the capsid through special protein channels more slowly than water does.…”

Section: Different Enzymesmentioning

confidence: 99%

Chlorine-binding structures: role and organization in different proteins

Makogonenko¹,

Hrabovskyi²,

Bereznytskyj³

et al. 2021

Ukr.Biochem.J

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The review focuses on chloride-binding structures in the proteins of bacteria, plants, viruses and animals. The structure and amino acid composition of the chloride-binding site and its role in the functioning of structural, regulatory, transport, receptor, channel proteins, transcription factors and enzymes are considered. Data on the important role of chloride-binding structures and chloride anions in the polymerization of fibrin are presented.

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“…Investigating the physicochemical properties of virus capsids may necessitate knowledge of their electronic charge distributions (49) and atomistic modeling (50,51). Charges of various atoms in the capsids of PDB-derived PSFs are treated as ‘point’ charges; however, because atomic charges are distributed throughout neighboring atomic positions, a point charge representation can lead to erroneous charge density calculations.…”

Section: Physical Properties Calculatormentioning

confidence: 99%

IRAM: virus capsid database and analysis resource

et al. 2019

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IRAM is an online, open access, comprehensive database and analysis resource for virus capsids. The database includes over 200 000 hierarchically organized capsid-associated nucleotide and amino acid sequences, as well as 193 capsids structures of high resolution (1–5 Å). Each capsid’s structure includes a data file for capsid domain (PDB), capsid symmetry unit (PDB) and capsid structure information (PSF); these contain capsid structural information that is necessary to run further computational studies. Physicochemical properties analysis is implemented for calculating capsid total charge at given radii and for calculating charge distributions. This resource includes BLASTn and BLASTp tools, which can be applied to compare nucleotide and amino acid sequences. The diverse functionality of IRAM is valuable to researchers because it integrates different aspects of virus capsids via a user-friendly interface. Such data are critical for studying capsid evolution and patterns of conservation. The IRAM database can also provide initial necessary information for the design of synthetic capsids for various biotechnological applications.

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Details of charge distribution in stable viral capsid

Cited by 14 publications

References 22 publications

MS2 bacteriophage capsid studied using all-atom molecular dynamics

MS2 bacteriophage capsid studied using all-atom molecular dynamics

Chlorine-binding structures: role and organization in different proteins

IRAM: virus capsid database and analysis resource

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