Electron breakthrough for COVID-19 omicron variant

7-Feb-2022. Wilson P. Ralston, BioKinetix Research

On 26-Nov-2021 the World Health Organization named a new variant of the SARS-CoV-2 virus that causes COVID-19 disease. The variant was named omicron (the Greek letter O). It was reported to have many mutations some of which might increase the spread of the virus.
Here a structure is presented for the omicron spike protein variant based on a recently deposited sequence in the PubMed protein database[1]. Like the delta variant[2] it is based on an electron-gated ion channel model similar to the L-type calcium channel oscillator model described in Sect. 8-7 (Figs. 8-4.,8-5.,8-6.) of my book[3]. The omicron spike protein structure presented here reveals two important differences with the delta variant. 1) The model has a smaller time constant in Domain 2, allowing omicron to replicate faster, and likely making it more contagious. 2) Omicron has 20 more amino acid residues than delta on S1 in Domain 2. This reduces the deep binding cavities for S1 and S2 helices, thus providing less area for contact with host receptor molecules and reduced potential binding force in the Domain 2 region. This likely makes omicron less deadly than delta.
The deadly nature of COVID-19 and its variants is determined by the amino acid sequence of the spike protein, how it contacts the host molecule it infects, how strong it binds with receptor molecules and how fast it replicates. About 30-100 spike proteins protrude from the surface of each virus particle. The particle has a reported diameter of about 0.1 microns in the dry state. The diameter can be up to 0.3 microns or more when it picks-up water and other substances. It needs water and ions in the ion channel to replicate.

A 3-D electron-gated structure for the omicron spike protein ion channel was developed and is presented in Fig. 23A and Fig. 23B.
It reveals why omicron is less deadly than the delta variant; it has 20 extra amino acid residues on S1 in Domain 2 (shown in Red in Fig. 23A). This reduces the contact distance for binding to a host molecule and potential binding force. Replication of the virus particle is controlled by the electron tunneling time constants for inactivation (Table 23-1. Domain 2 and 4). This can only occur when the particle picks up water and other substances. In the dry state replication stops. The fast 60 ms time constant in Domain 1 might be for replicating the 30-100 spike proteins that surround the virus particle - or it might be charged. Finally, all the models need Arg/Lys NH3 energy amplification to function[4]. This is a fundamental breakthrough that reduces the noise by 23-24 fold. The Noise temperature is reduced to 13K. This amplification mechanism is nature's supreme trick to make life possible. It violates the 2nd law of thermodynamics by reducing entropy[4].

References:
1. NCBI Accession 7T9L_A., release Dec 29, 2021; deposition: Dec 19, 2021
    SARS-CoV-2 Omicron variant: ACE2 Binding, Cryo-EM Structure of Spike Protein-ACE2 Complex
    and Antibody Evasion. Journal: unpublished. Authors: Mannar, D., Saville, J.W., Zhu, X.,
    Srivastava, S.S., Berezuk,A.M., Tuttle, K.S., Marquez, C., Sekirov, I., and Suoramaniam, S.
2. Ralston, W.P., (Aug-2021). Electron breakthrough for COVID-19 delta variant.
    www.biokinetix.org/covid-19-delta-electron.html
3. Ralston, W.P., (2005) Electron-gated ion channels : with amplification by NH3 inversion resonance.
    SciTech Publishing, Inc. Raleigh, NC
4. Ralston, W.P., (1-27-2022). The Arg/Lys NH3 energy amplifier.
    www.biokinetix.org/nh3-energy-amplifier.html

COVID-19 omicron Spike structure Fig.23A,B </a