Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids

Abstract

Electrostatic properties of cowpea chlorotic mottle virus (CCMV) and cucumber mosaic virus (CMV) were investigated using numerical solutions to the Poisson-Boltzmann equation. Experimentally, it has been shown that CCMV particles swell in the absence of divalent cations when the pH is raised from 5 to 7. CMV, although structurally homologous, does not undergo this transition. An analysis of the calculated electrostatic potential confirms that a strong electrostatic repulsion at the calcium binding sites in the CCMV capsid is most likely the driving force for the capsid swelling process during the release of calcium. The binding interaction between the encapsulated genome material (RNA) inside of the capsid and the inner capsid shell is weakened during the swelling transition. This probably aids in the RNA release process, but it is unlikely that the RNA is released through capsid openings due to unfavorable electrostatic interaction between the RNA and capsid inner shell residues at these openings. Calculations of the calcium binding energies show that Ca 2+ can bind both to the native and swollen forms of the CCMV virion. Favorable binding to the swollen form suggests that Ca 2+ ions can induce the capsid contraction and stabilize the native form.

Multiscale analytic continuation approach to nanosystem simulation: Applications to virus electrostatics

“…This latter electrostatic distribution promotes RNA release from the capsid core. The physical picture is in agreement with previous results on CCMV, 55,56 but PBms took less computation time. The APBS-generated isosurfaces shown in this paper, though similar, are not identical to those reported by Konecny et al 55 This is attributable to differences in grid size, boundary conditions, ions accessibility, and ionic strength used for our APBS calculations.…”

Energies and pressures in viruses: contribution of nonspecific electrostatic interactions

“…A completely numerical PB approaches are also possible. These start with a determination of the spatial distribution of capsid charge based on the capsid amino acid content and the atomic coordinates determined from X-ray studies 28 . The PB equation is then solved on a three-dimensional grid using advanced numerical routines 28 .…”

“…These start with a determination of the spatial distribution of capsid charge based on the capsid amino acid content and the atomic coordinates determined from X-ray studies 28 . The PB equation is then solved on a three-dimensional grid using advanced numerical routines 28 . Such approaches are, however, less transparent concerning the scaling of energies with various parameters of the system, e.g.…”

Electrostatic interactions in biological DNA-related systems

“…CCMV-virus) require proper levels of divalent cations for their stability: the capsids swell without Ca 2+ and at elevated pH levels. [407][408][409] Many ss-RNA viruses compact their genomes using strongly basic flexible protein arms on the inner side of capsid proteins that provoke adsorption of flexible ss-RNA genome. [410][411][412][413] All these facts underline the importance of ES forces for DNA/RNA packaging and capsid self-assembly, producing a growing number of theoretical studies on this hot topic in the last years.…”