The role of disulfide bonds in a Solanum tuberosum saposin-like protein investigated using molecular dynamics

Abstract

The Solanum tuberosum plant specific insert (StPSI) has a defensive role in potato plants, with the requirements of acidic pH and anionic lipids. The StPSI contains a set of three highly conserved disulfide bonds that bridge the protein's helical domains. Removal of these bonds leads to enhanced membrane interactions. This work examined the effects of their sequential removal, both individually and in combination, using all-atom molecular dynamics to elucidate the role of disulfide linkages in maintaining overall protein tertiary structure. The tertiary structure was found to remain stable at both acidic (active) and neutral (inactive) pH despite the removal of disulfide linkages. The findings include how the dimer structure is stabilized and the impact on secondary structure on a residue-basis as a function of disulfide bond removal. The StPSI possesses an extensive network of inter-monomer hydrophobic interactions and intra-monomer hydrogen bonds, which is likely the key to the stability of the StPSI by stabilizing local secondary structure and the tertiary saposin-fold, leading to a robust association between monomers, regardless of the disulfide bond state. Removal of disulfide bonds did not significantly impact secondary structure, nor lead to quaternary structural changes. Instead, disulfide bond removal induces regions of amino acids with relatively higher or lower variation in secondary structure, relative to when all the disulfide bonds are intact. Although disulfide bonds are not required to preserve overall secondary structure, they may have an important role in maintaining a less plastic structure within plant cells in order to regulate membrane affinity or targeting.

14C-Isotope Use to Quantify Covalent Reactions between Flavor Compounds and β-Lactoglobulin

“…Thus, changes in the protein structure as a function of pH and denaturation could make these sites available to react with the isothiocyanate. Aldehyde-lysine and amine-carbonyl group formation are considered common causes of flavor alterations in high-protein products. , …”

“…Aldehyde-lysine and amine-carbonyl group formation are considered common causes of flavor alterations in high-protein products. 20,21 In summary, a C 14 methodology has been developed for the quantification of covalent bond formation between BLG and selected flavor compounds. Of the flavor compounds studied, PEITC showed the highest reactivity with up to ca.…”

Recent advances and challenges in the interaction between myofibrillar proteins and flavor substances

“…These interactions are usually irreversible. The binding of sulfur compounds to proteins can also be classified as covalent interactions ( 9 , 41 ). Anantharamkrishnan et al ( 11 ) showed that covalent bonds were formed between β-lactoglobulin and aldehydes, mercaptans and furans containing functional groups, resulting in Schiff base, Michael addition and disulfide bonds.…”

Structural and biochemical characterization of Arabidopsis alcohol dehydrogenases reveals distinct functional properties but similar redox sensitivity

“…Nevertheless, Cys plays a key role in enzyme function and protein structure stabilization (Paulsen & Carroll, 2013; Poole, 2015). Cys can form structural disulfide bonds that are fundamental for the proper folding of a wide range of proteins (Dupuis et al., 2020; Marshall et al., 2010; Trivedi et al., 2009). When located in the active site of an enzyme, Cys residues can fulfill a catalytic function by forming covalent bonds with the substrate, as observed for thioredoxins, glutaredoxins, peroxiredoxins, and glyceraldehyde‐3‐phosphate dehydrogenases (Zaffagnini, Fermani, et al., 2019).…”