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How simple can a model of an empty viral capsid be? Charge distributions in viral capsids

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Abstract

We investigate and quantify salient features of the charge distributions on viral capsids. Our analysis combines the experimentally determined capsid geometry with simple models for ionization of amino acids, thus yielding a detailed description of spatial distribution for positive and negative charges across the capsid wall. The obtained data is processed in order to extract the mean radii of distributions, surface charge densities, as well as dipole moment densities. The results are evaluated and examined in light of previously proposed models of capsid charge distributions, which are shown to have to some extent limited value when applied to real viruses.

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Notes

  1. Outer and inner surfaces, respectively.

  2. The T = pseudo 3 icosahedral capsids do not obey the Caspar–Klug principle of quasi-equivalence because the basic unit is composed of three different (but morphologically similar) proteins.

  3. In all such plots, the following legend is used for different virus types: single-stranded genome (circles), double-stranded genome (squares), bacteriophages (diamonds; both ss and ds genome), and T = p3 ssRNA viruses (triangles).

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Acknowledgements

One of us (A.L.B.) thanks A. Ljubetič for introducing him to the Tcl scripting language in VMD.

A.L.B. acknowledges support from the Slovene Agency for Research and Development under a young researcher grant. A.Š. acknowledges support from the Ministry of Science, Education, and Sports of the Republic of Croatia (Grant No. 035-0352828-2837). R.P. acknowledges support from the Slovene Agency for Research and Development through research program P1-0055 and research project J1-4297.

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Authors and Affiliations

  1. Department of Theoretical Physics, Jožef Stefan Institute, 1000, Ljubljana, Slovenia

    Anže Lošdorfer Božič & Rudolf Podgornik

  2. Institute of Physics, 10001, Zagreb, Croatia

    Antonio Šiber

  3. Department of Physics, Faculty of Mathematics and Physics, 1000, Ljubljana, Slovenia

    Rudolf Podgornik

Authors
  1. Anže Lošdorfer Božič
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  2. Antonio Šiber
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  3. Rudolf Podgornik
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Correspondence to Anže Lošdorfer Božič.

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Lošdorfer Božič, A., Šiber, A. & Podgornik, R. How simple can a model of an empty viral capsid be? Charge distributions in viral capsids. J Biol Phys 38, 657–671 (2012). https://doi.org/10.1007/s10867-012-9278-4

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  • DOI: https://doi.org/10.1007/s10867-012-9278-4

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