Ion Channels in Southern Bean Mosaic Virus Capsid

Silva, Abelardo M.; Cachau, Raúl E.; Goldstein, Daniel J.

doi:10.1016/s0006-3495(87)83249-6

Cited by 26 publications

(15 citation statements)

References 16 publications

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“…During the equilibration phase and also during force-probe simulations, no water permeated the capsid. This observation is in accordance with the results of Silva et al (54), who reported a high energy barrier of E ¼ 300 kcal/mol for water at the gate along the fivefold symmetry axis. No other position on the protein shell exhibited a gate for possible water or ion permeation, which is in good agreement with the lack of water flux in our simulations.…”

Section: Water Permeation Friction and Surface Effectssupporting

confidence: 93%

Mechanical Properties of the Icosahedral Shell of Southern Bean Mosaic Virus: A Molecular Dynamics Study

Zink

Grubmüller

2009

Biophysical Journal

118

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The mechanical properties of viral shells are crucial for viral assembly and infection. To study their distribution and heterogeneity on the viral surface, we performed atomistic force-probe molecular dynamics simulations of the complete shell of southern bean mosaic virus, a prototypical T = 3 virus, in explicit solvent. The simulation system comprised more than 4,500,000 atoms. To facilitate direct comparison with atomic-force microscopy (AFM) measurements, a Lennard-Jones sphere was used as a model of the AFM tip, and was pushed with different velocities toward the capsid protein at 19 different positions on the viral surface. A detailed picture of the spatial distribution of elastic constants and yielding forces was obtained that can explain corresponding heterogeneities observed in previous AFM experiments. Our simulations reveal three different deformation regimes: a prelinear regime of outer surface atom rearrangements, a linear regime of elastic capsid deformation, and a rearrangement regime that describes irreversible structural changes and the transition from elastic to plastic deformation. For both yielding forces and elastic constants, a logarithmic velocity dependency is evident over nearly two decades, the explanation for which requires including nonequilibrium effects within the established theory of enforced barrier crossing.

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Section: Water Permeation Friction and Surface Effectssupporting

confidence: 93%

Mechanical Properties of the Icosahedral Shell of Southern Bean Mosaic Virus: A Molecular Dynamics Study

Zink

Grubmüller

2009

Biophysical Journal

118

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“…The magnitudes of the energies calculated using the simple Langevin-dipole representation of water are much more reasonable than the many hundreds of kcal/M calculated in an earlier model of the 4SBV channelog [82] which did not include water. However, the profile is not satisfactory quantitatively, for it implies impossibly slow ion exchange for a ring of carbonyl oxygens.…”

Section: Free Energy Profile For a Viral Channelog Whose Selectivity supporting

confidence: 48%

“…1 based upon the crystallographic data for 4SBV [82,83]. The left and right views are both from the external perspective but differ in that they show the positions of the H atoms in the selectivity filter when these have been rotated maximally away from the channel axis (left) and maximally towards it (right).…”

Section: A Speculative Structure J?)r the Acetylcholine Receptor Channelmentioning

confidence: 99%

Structure and function of channels and channelogs as studied by computational chemistry

Eisenman

Álvarez

1991

J. Membrain Biol.

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“…The specific domains that form these channels remain to be defined. A pore structure has been proposed to exist at the center of pentameric subunits (at fivefold axes) in the protein shell of icosahedral viruses (20). However, we do not think that this pore structure forms the channels described here.…”

Section: Discussionmentioning

confidence: 74%

Characterization of the ion channels formed by poliovirus in planar lipid membranes

Tosteson

Chow

1997

J Virol

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The steps in poliovirus infection leading to viral entry and uncoating are not well understood. Current evidence suggests that the virus first binds to a plasma membrane-bound receptor present in viable cells, leading to a conformational rearrangement of the viral proteins such that the virus crosses the membrane and releases the genomic RNA. The studies described in this report were undertaken to determine if poliovirus (160S) as well as one of the subviral particles (135S) could interact with membranes lacking poliovirus receptors in an effort to begin to understand the process of uncoating of the virus. We report that both forms of viral particles, 160S and 135S, interact with lipid membranes and induce the formation of ion-permeable channels in a manner that does not require acid pH. The channels induced by the viral particles 160S have a voltage-dependent conductance which depends on the ionic composition of the medium. Our findings raise the possibility that viral entry into cells may be mediated by direct interaction of viral surface proteins with membrane lipids.Poliovirus is a prototypical member of the Picornaviridae family. The plus-stranded RNA genome of this nonenveloped virus is tightly packed within an icosahedrally symmetric spherical shell which is composed of 60 copies of each of four proteins (VP1 to VP4). The myristoylated VP4 and the aminoterminal sequences of the other three capsid proteins are located on the inner surface of the poliovirus virion (8).Infection of cells by poliovirus starts as the virus particle attaches to the receptor at the cell membrane (2, 6). Receptor binding leads to a conformational transition that results in altered particles which lack VP4 and sediment with a coefficient of 135S (compared to 16 0S for the intact virion) (3a, 6, 9). This alteration in sedimentation behavior is further accompanied by the relocation and exposure of most of the aminoterminal regions of VP1 from the inner to the outer surface of the virion shell. Exposure of the amino-terminal regions of VP1 confers membrane binding properties to the 135S particles, which has been observed by Fricks and Hogle (5), using a liposome flotation method. However, the subsequent stages of penetration and uncoating remain poorly defined.For viral replication to take place, the viral RNA must traverse the plasma membrane and be uncoated and released to the cytosol. Several hypotheses have been put forth to explain viral entry and uncoating, ranging from receptor-mediated endocytosis of the whole virion, to direct penetration of the plasma membrane by the 160S particle (hereafter referred to as simply 160S), to entry of the subviral particle 135S by either of those mechanisms (references 1 and 13 and references therein). Binding and anchoring of the viral particle to a membrane are required steps in any of these hypotheses.In this report, we present evidence that domains of the native virion (160S) and the receptor-altered viral particle (135S) bind and interact with lipid bilayers to form ion-permeable channels...

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Ion Channels in Southern Bean Mosaic Virus Capsid

Cited by 26 publications

References 16 publications

Mechanical Properties of the Icosahedral Shell of Southern Bean Mosaic Virus: A Molecular Dynamics Study

Mechanical Properties of the Icosahedral Shell of Southern Bean Mosaic Virus: A Molecular Dynamics Study

Structure and function of channels and channelogs as studied by computational chemistry

Characterization of the ion channels formed by poliovirus in planar lipid membranes

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