An extremely high contagiousness of SARS CoV-2 indicates that the virus developed the ability to deceive the innate immune system. The virus could have included in its outer protein domains some motifs that are structurally similar to those that the potential victim's immune system has learned to ignore. The similarity of the primary structures of the viral and human proteins can provoke an autoimmune process. Using an open-access protein database Uniprot, we have compared the SARS CoV-2 proteome with those of other organisms. In the SARS CoV-2 spike (S) protein molecule, we have localized more than two dozen hepta- and octamers homologous to human proteins. They are scattered along the entire length of the S protein molecule, while some of them fuse into sequences of considerable length. Except for one, all these n-mers project from the virus particle and therefore can be involved in providing mimicry and misleading the immune system. All hepta- and octamers of the envelope (E) protein, homologous to human proteins, are located in the viral transmembrane domain and form a 28-mer protein E14-41. The involvement of the protein E in provoking an autoimmune response (after the destruction of the virus particle) seems to be highly likely. Some SARS CoV-2 nonstructural proteins may also be involved in this process, namely ORF3a, ORF7a, ORF7b, ORF8, and ORF9b. It is possible that ORF7b is involved in the dysfunction of olfactory receptors, and the S protein in the dysfunction of taste perception.
Xenin is a regulatory peptide first isolated from the human gastric mucosa. Using an open-access protein database MEDLINE (33 million molecules; 11 billion amino acid residues) and our original computer program, we conducted a search for the xenin motifs in the primary structure of proteins across almost the entire taxonomic range of evolution. Motifs with 40% homology to human xenin are already present in prokaryotes. Homology reaches 84-96% in single-cell algae and plants, becoming complete since bony fishes. We suppose that this regulatory peptide is more ancient and significant than is usually thought.
No abstract
BACKGROUND AND GOAL. In the chain of events “(a) codon/transcription/translation → (b) primary protein structure → (c) post-translational modification of amino acids”, the middle link (b) has been paid little attention. We sought to find out if the adjacency of amino acids in the protein structure obeys any rules. METHOD. We have pooled the data on the primary protein structure from proteomes of more than 700,000 biological species (32,462,157 proteins and 11,117,062,854 amino acid residues) into a universal proteome (a data bank) and determined the frequency of occurrence (F) of 20 proteinogenic amino acids, 400 dimers, 8000 trimers, 160,000 tetramers, and 3,200,000 pentamers. RESULTS AND DISCUSSION. The average length of the protein molecule comprises 342.46 ± 0.06 amino acid residues. In the universal proteome, we found all pentamers except WCMMW. In the remaining 3,199,999 pentamers, F ranged from 1 to 739,321. The pentamers with different amino acids at the same position differ significantly in the frequency of occurrence. The pentamers with the same amino acids at the different positions are statistically indistinguishable in the frequency of occurrence. In the overwhelming majority of pentamers, the observed frequency of occurrence (Fpenta observed) is significantly different from the expected frequency of occurrence (Fpenta expected) obtained by multiplying Famino acid observed of all five amino acids constituting the pentamer. In a protein molecule, amino acids do not have properties that "permit" or "forbid" the appearance of certain amino acids in neighboring positions of the polypeptide chain. The same rule applies to di-, tri-, and tetramers. In the oligomeres, of which the proteins consist, Fobserved depends less on the amino acids that make them up and more on some unknown factor. This factor, by natural selection of codons in the DNA molecule, creates for almost every amino acid in the protein a statistically significant deviation of the observed frequency of occurrence from the expected one. CONCLUSION. The order of codons in DNA (and amino acid residues in a protein) is independent of neighboring codons (and amino acids), however, is non-reductionist and is controlled by a yet unknown factor.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.