The Physical Basis for pH Sensitivity in Biomolecular Structure and Function, With Application to the Spike Protein of SARS-CoV-2

Abstract

Since pH sensitivity has a fundamental role in biology, much effort has been committed to establishing physical models to rationalize and predict pH dependence from molecular structures. Two of the key challenges are to accurately calculate ionizable group solvation and hydration and then to apply this modeling to all conformations relevant to the process in question. Explicit solvent methods coupled to molecular dynamics simulation are increasingly complementing lower resolution implicit solvent techniques, but equally, the scale of biological data acquisition leaves a role for high-throughput modeling. Additionally, determination of ranges of structures for a system allows sampling of key stages in solvation. In a review of the area, it is emphasized that pH sensors in biology beyond the most obvious candidate (histidine side chain, with an unshifted pKa near neutral pH) should be considered; that modeling can benefit from other concepts in bioinformatics, in particular modulation of interactions and function in families of homologs; and that it can also be beneficial to incorporate as many experimental structures as possible, to mitigate against small variations in conformation and to analyze larger, functional, conformational changes. These aspects are then demonstrated with new work on the spike protein of SARS-CoV-2, looking at the pH dependence of variants, including prediction of a change in the balance of locked, closed, and open forms at neutral pH for the Omicron variant spike protein.

Computational investigation of mechanisms for pH modulation of human chloride channels

“…It appears that pH-dependence is modulated by the commonly occurring mechanism of buried (from solvent, surrounded by amino acids, Fig. 5B) histidine sidechain that becomes less stable as pH falls around its normal (solvent exposed) pKa value (Warwicker, 2022).…”

“…Mutagenesis screens for sites of pH-dependence in biological processes can be complicated by the degree to which conformational and interface changes couple to the pH-dependence (Warwicker, 2022). At the centre though will be groups changing protonation state over the process, and thus user-friendly visualisation of reliable predictions for such groups will be useful in guiding experimental design.…”

“…Glutamic acid modulated pH-dependence at around neutral pH implies a substantial pKa shift (pKa) from the normal pKa value (4.4). Such a scale of pKa for amino acid sidechain carboxylates can be observed in enzyme active sites and other systems (Warwicker, 2022). Mechanistically, the large and energetically unfavourable pKa is achieved through maintaining a relatively rigid conformation in an environment that is at least partially buried from solvent water that would hydrate and stabilise the ionised form.…”

Computational Investigation of Mechanisms for pH Modulation of Human Chloride Channels

“…Glutamic acid modulated pH dependence around neutral pH implies a substantial pKa shift (∆pKa) from the normal pKa value (4.4). Such a scale of ∆pKa for amino acid sidechain carboxylates can be observed in enzyme active sites and other systems [18]. Mechanistically, the large and energetically unfavourable ∆pKa is achieved through maintaining a relatively rigid conformation in an environment that is at least partially buried from solvent water that would hydrate and stabilise the ionised form.…”

Recent developments of sequence-based prediction of protein–protein interactions

“…However, AlphaPulldown requires structural templates for each query protein, and we still need to know which protein pairs will interact without depending on the presence or absence of protein structures or structural templates. Furthermore, proteins are dynamic and can change their conformations, for example, under different pH conditions (Warwicker 2022 ). Therefore, the data-driven methods for predicting PPIs, especially sequence-based PPI predictions, which allow exhaustive PPI searches, will continue to be important.…”