Using wide biological pores to cap and contain the COVID-19 spike protein

08 September 2021, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Geometric analysis shows that the spike (S) protein in the COVID-19 virus (SARS-Cov-2) can fully or partially enter into the channel of a wide biological pore like perforin (PFN) or streptolysin (SLO) when the latter is anchored in a bilayer lipid membrane. The PFN channel is a β barrel formed from multiple monomers, for example a ~14 nm diameter channel is formed from 22 monomers. Coincidentally the wide canopy of S (which has three identical chains) has an enclosing diameter of ~14 nm. While inside the channel peripheral residues in the canopy may bind with residues on the pore side of the barrel. If there are no adverse cross-reactions this would effectively prevent S from interacting with a target cell. Calculations with data obtained from PDB and other sources show that there are ~12 peripheral residue triples in S within a circle of diameter ~14 nm that can potentially bind with 22 exposed residues in each barrel monomer. The revised Miyazawa-Jernighan matrix is used to calculate the binding energy of canopy-PFN barrel residue pairs. The results show a large number of binding pairs over distances of up to 38 Å into the pore. This geometric view of capture and containment points to the possibility of using biological pores to neutralize SARS-Cov-2 in its many variant forms. Some necessary conditions that must be satisfied for such neutralization to occur are noted.

Keywords

spike protein
biological pore
perforin
beta barrel
SARS-Cov-2

Supplementary materials

Title
Description
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Title
6VXX data file
Description
Residue coordinates and other information extracted from PDB for spike protein of SARS-Cov-2 (PDB id: 6VXX)
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Title
Symmetrized Miyazawa-Jernighan matrix
Description
Revised MJ matrix and its symmetrized version (upper triangle in former reflected across diagonal into lower triangle)
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