Complete virus capsid at all-atom resolution: Simulations using molecular dynamics and hybrid molecular dynamics/hydrodynamics methods reveal semipermeable membrane function

Tarasova, Elvira; Korotkin, Ivan; Farafonov, Volodymyr; Karabasov, Sergey A.; Nerukh, Dmitry

doi:10.1016/j.molliq.2017.06.124

Cited by 27 publications

(33 citation statements)

References 22 publications

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“…The algorithm similar to our previous work [7], which is grounded on the work of Andoh et al [1], was used. Because royalsocietypublishing.org/journal/rsfs Interface Focus 9: 20180081 the MS2 capsid shape is much closer to a spherical layer than that of PCV2 capsid, the boundary between the interior and the outside solution can be defined simply as the certain distance from the COM.…”

Section: Water and Ion Flow Through The Capsidmentioning

confidence: 99%

MS2 bacteriophage capsid studied using all-atom molecular dynamics

Farafonov

Nerukh

2019

Interface Focus.

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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: Water and Ion Flow Through The Capsidmentioning

confidence: 99%

MS2 bacteriophage capsid studied using all-atom molecular dynamics

Farafonov

Nerukh

2019

Interface Focus.

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“…The preparation of the system and the protocols of the MD simulation are given in our previous publications [1,6]. A protein subunit of PCV2 capsid has been taken from Protein Data Bank (PDB) [16] and reconstructed into full empty capsid with the program VIPERdb [17].…”

Section: Methodsmentioning

confidence: 99%

“…We performed energy minimisation, after that we executed 1ns MD simulation of the systems with positions of all atoms of the capsid being restrained. During the preparation for the productive run the temperature was gradually increased from 200K to 300K [1,6]. Finally, productive MD simulation was carried out for 10ns at 300K.…”

Section: Methodsmentioning

confidence: 99%

“…Recently MD simulations are effectively used for studying the structure, dynamics and properties of whole viruses, in particular viral capsids, which protect the viral genome. These investigations provided details of virus and solution properties that are currently impossible to obtain experimentally, such as permeability of water molecules and ions through the capsid wall [1][2][3][4], water molecule diffusion [4][5], capsid's stability [1][2]6], the structure of viral fragments which are missed from experimental data [6][7][8], the mechanical properties of the virus particle [9], the swelling of viral capsids [10][11][12], and others.…”

Section: Introductionmentioning

confidence: 99%

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Details of charge distribution in stable viral capsid

Tarasova

Farafonov

Taiji

et al. 2018

Journal of Molecular Liquids

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We present the results of Molecular Dynamics simulations of a viral capsid with the aim to analyse ion distribution on the capsid's surface that defines its stability. Two systems were modelled, a stable capsid with neutralising number of ions and an unstable capsid with low number of ions. For the ion distribution analysis the capsid's structure was identical and fixed in both simulations. It was then released for the stability analysis. The ion distribution demonstrated two types of the local regions on the inner surface of the capsid's wall: highly occupied with chloride ions in both systems despite a largely uniform electrostatic potential everywhere on the surface, and the regions that loose almost all chloride ions in the unstable capsid. The latter regions are located close to the cracks that are formed when the capsid is destabilised and thus could initiate the collapse of the capsid.

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“…As time has progressed, all-atom simulations of intact capsids have become increasingly accessible. Notably, such work has included characterization of the stress-response of the southern bean mosaic virus (SBMV) capsid [109], validation of multi-scale modeling approaches based on the Sesbania mosaic virus (SeMV) capsid [110], derivation of a complete atomic model for the rabbit hemorrhagic disease virus (RHDV) capsid [111], and examination of the interplay between solvent and ions and the porcine circovirus type 2 (PCV2) capsid [112, 113]. …”

Section: Capsidsmentioning

confidence: 99%

All-atom virus simulations

Hadden

Perilla

2018

Current Opinion in Virology

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The constant threat of viral disease can be combated by the development of novel vaccines and therapeutics designed to disrupt key features of virus structure or infection cycle processes. Such development relies on high-resolution characterization of viruses and their dynamical behaviors, which are often challenging to obtain solely by experiment. In response, all-atom molecular dynamics simulations are widely leveraged to study the structural components of viruses, leading to some of the largest simulation endeavors undertaken to date. The present work reviews exemplary all-atom simulation work on viruses, as well as progress toward simulating entire virions.

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Complete virus capsid at all-atom resolution: Simulations using molecular dynamics and hybrid molecular dynamics/hydrodynamics methods reveal semipermeable membrane function

Cited by 27 publications

References 22 publications

MS2 bacteriophage capsid studied using all-atom molecular dynamics

MS2 bacteriophage capsid studied using all-atom molecular dynamics

Details of charge distribution in stable viral capsid

All-atom virus simulations

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