Secondary Chemical Bonding between Insoluble Calcium Oxalate and Carbonyl Oxygen Atoms of GLY and VAL Residues Triggers the Formation of Aβ Aggregates and Their Deposition in the Brain

Neurological Sequelae of COVID-19: A Biochemical Perspective

Exogenous factors can induce protein expression and modify the proteome which sustains for a certain period of time. The proteins of SARS-CoV-2 are high in valine plus glycine, which possess potent affinity to divalent cations such as calcium. Calcium buildup changes the protein expression profile by enabling the efficient synthesis of proteins rich in amino acids with calcium affinity. Subsequent formation of insoluble and stiff calcium oxalate and aggregates confers cellular stress and causes cell senescence. This scenario accounts for sequelae seen in some patients following recovery from COVID-19.

Why Omicron Variant of SARS-CoV-2 is Less Fatal?

The article published by Nie et al. addressed one of the two key questions regarding the Omicron variant of SARS‐CoV‐2, while the underpinning for the less deadly nature of the variant remains unexplained. The proteins of the Omicron variant have numerous mutations, notably several substitutions of other amino acids by lysine residues. Glycine and valine attract calcium and enhance the formation of stressful, insoluble, and stiff calcium oxalate. Lysine residues in proteins build up chloride via ionic bonds which solubilizes insoluble and rigid divalent salts. The aforementioned mutations have weakened the lethalness of the Omicron variant perhaps via a biochemical mechanism. Despite net gain in favorable mutations versus deleterious mutations, the overall valine plus glycine content is still high in the proteins of Omicron variant of SARS‐CoV‐2, which remains a public health concern.

Epigenetic Modifications and Neurodegenerative Disorders: A Biochemical Perspective

Methylations in living cells are methyl groups attached to amino acids, DNA, RNA, and so on. However, their biochemical roles have not been fully defined. A theory has been postulated that methylation leads to hyperconjugation, and the electron-donating feature weakens a nearby chemical bond, which increases the bond length of C⁴-N⁴ of 5-methylcytosine, therefore weakening the C⁴-N⁴ bond and resulting in stronger protonation or hydrogen bonding of the N⁴ nitrogen atom. Protonation can give rise to the generation of mutagenic and carcinogenic strong acids such as HCl, which are also capable of solubilizing stressful, insoluble, and stiff salts. Insoluble and rigid salts such as calcium oxalate and/or calcium phosphate were recently proposed as a primary cause of some neurodegenerative disorders. Protonation of nitrogen atoms in 5-methylcytosine enhances the interaction with negatively charged phosphate groups and contributes to the formation of compact heterochromatin. The electronegativity of the oxygen atoms in the modifications of 5-hydroxymethylcytosine or 5-formylcytosine can shorten the lengths of adjacent bonds with no increase of cation affinity in N⁴. The carboxyl group in 5-carboxylcytosine is a weak acid capable of antagonizing mutagenic HCl and modestly helping solubilize insoluble salts. Electron delocalization of the methyl group in N4-methylcytosine results in a lower affinity of N⁴ to cations. The positive charge at N³ in the resonance structure of 3-methylcytosine is lessened by the electron-donating attribute of the methyl group attached to the N³ atom, consequently reducing acid formation. The electron delocalization of three methyl groups decreases the positive charge in the amino nitrogen in the side group of lysine 4 in histone H3, weakening interactions with phosphate groups and consequently activating gene expression. The carbonyl oxygen in 8-oxo-7,8-dihydroguanine draws protons and accumulates HCl, accounting for its moderate mutation propensity and potential capacity to solubilize stiff salts. The biochemical insight will further our understanding on the crosstalk of genetics and epigenetics in the etiology of neurodegenerative diseases.

Single-stranded DNA generated by high temperature accepts protons and builds up mutagenic and carcinogenic strong acids

Malignancies are caused by genetic or environmental factors. Esophageal carcinoma can be triggered by consumption of hot food and beverages. Here we propose that high temperature is one of the culprits and it leads to DNA denaturation. Subsequently the exposed hydrogen bonding acceptors in single stranded DNA attract protons which enhance the formation of mutagenic and carcinogenic strong acids such as HCl. Faster mutation of single-stranded DNA viruses than that of double-stranded DNA viruses lends support to this theory.