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Alkalinization of Icosahedral Non-enveloped Viral Capsid Interior Through Proton Channeling

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Physical Virology

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 1215))

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Abstract

Small icosahedral viruses have a compact capsid that apparently lacks holes through which solvents can be exchanged with the external milieu. However, due to the steric hindrance of amino acids, upon folding, capsid proteins form narrow cavities in which water and ions can be trapped. These occluded solvent molecules can form lines of water, called water wires, representing an arrangement with special features for proton conduction. In this chapter, we review the physico-chemical principles that permit proton conduction through protein cavities. We also describe how a combination of these elements found in an insect viral capsid can allow the virus to sense alkaline environments. Through this analysis, we stress the need to combine experimental and theoretical techniques when modeling complex biological systems.

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Notes

  1. 1.

    This definition applies for dilute solutions. The general formula is as follows: pH = −log (aH+), where aH+ is the activity of H+ (or effective H+ concentration).

  2. 2.

    A similar limitation to these experimental models is found in theoretical simulations when the solvent is treated implicitly (isotropous and homogeneous), an approximation known as the “solvent effect” [24, 25].

  3. 3.

    At neutral pH, [H+] = 10−7. This is equivalent to 10−7 mol H+ per liter (L) of H2O, that is, 1H+ per approx. 1.66 × 10−17 L. Finally, 1.66 × 10−17 L of liquid water corresponds to ≈5.5 × 108 water molecules.

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Acknowledgements

We thank Dieter Blaas, Medical University of Vienna, Vienna Biocenter, A-1030, Austria, for critical reading and useful comments of the manuscript. MMB is a member of the CONICET research staff, Argentina, and she thanks a permit from the CONICET and UNS to do sabbatical stage at DMAG’s lab, Instituto Biofisika (CSIC, UPV/EHU). MMB thanks a traveling grant from the CYTED (216RT0506). This work was partially supported by a grant to DMAG from the Ministerio de Ciencia e Innovación (BFU2012-36241), and Gobierno Vasco (Elkartek KK-2017/00008), Spain.

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Branda, M.M., Guérin, D.M.A. (2019). Alkalinization of Icosahedral Non-enveloped Viral Capsid Interior Through Proton Channeling. In: Greber, U. (eds) Physical Virology. Advances in Experimental Medicine and Biology, vol 1215. Springer, Cham. https://doi.org/10.1007/978-3-030-14741-9_9

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