Impact of glycosylation on stability, structure and unfolding of soybean agglutinin (SBA): an insight from thermal perturbation molecular dynamics simulations

Abstract

Glycosylation has been recognized as one of the most prevalent and complex post-translational modifications of proteins involving numerous enzymes and substrates. Its effect on the protein conformational transitions is not clearly understood yet. In this study, we have examined the effect of glycosylation on protein stability using molecular dynamics simulation of legume lectin soybean agglutinin (SBA). Its glycosylated moiety consists of high mannose type N-linked glycan (Man9GlcNAc2). To unveil the structural perturbations during thermal unfolding of these two forms, we have studied and compared them to the experimental results. From the perspective of dynamics, our simulations revealed that the nonglycosylated monomeric form is less stable than corresponding glycosylated form at normal and elevated temperatures. Moreover, at elevated temperature thermal destabilization is more prominent in solvent exposed loops, turns and ends of distinct β sheets. SBA maintains it folded structure due to some important saltbridges, hydrogen bonds and hydrophobic interactions within the protein. The reducing terminal GlcNAc residues interact with the protein residues VAL161, PRO182 and SER225 via hydrophobic and via hydrogen bonding with ASN 9 and ASN 75. Our simulations also revealed that single glycosylation (ASN75) has no significant effect on corresponding cis peptide angle orientation. This atomistic description might have important implications for understanding the functionality and stability of Soybean agglutinin.

Mass Spectrometric Analysis of N-Glycoforms of Soybean Allergenic Glycoproteins Separated by SDS-PAGE

“…Band 8 is assigned to the acidic A3 polypeptide, band 9 to a mixture of the acidic A1, A2, and A4 polypeptides, and band 14 to the basic B1, B2, B3, and B4 components of glycinin. ,, Band 3 is proposed as γ-congcinin, band 4 as the sucrose binding protein, band 5 as β-amylase, and band 11 as whey fraction . Gly m lectin is very close to Gly m Bd 30K in terms of MW, and both of them are located in band 10. ,, Band 12 is Gly m Bd 28 K. , Bands 13 and 15 may be oleosin and some proglycinin A2B1. , It is worth noting that most of these bands contain some known major allergenic proteins, including Gly m Bd 30K, Gly m lectin, Gly m Bd 28K, Gly m 5 consisting of α, α′, β, and β′ subunits of the 7S proteins, and Gly m 6 consisting of A1, A2, A3, A4, B1, B2, B3, and B4 subunits of 11S proteins. These soybean allergens can be retrieved in some food allergen databases, such as the database of the IUIS Allergen Nomenclature Sub-Committee, the Structural Database of Allergenic Proteins (SDAP), and Allergome.…”

“…51 Gly m lectin is very close to Gly m Bd 30K in terms of MW, and both of them are located in band 10. 49,52,53 Band 12 is Gly m Bd 28 K. 31,32 Bands 13 and 15 may be oleosin and some proglycinin A2B1. 46,49 It is worth noting that most of these bands contain some known major allergenic proteins, including Gly m Bd 30K, Gly m lectin, Gly m Bd 28K, Gly m 5 consisting of α, α′, β, and β′ subunits of the 7S proteins, and Gly m 6 consisting of A1, A2, A3, A4, B1, B2, B3, and B4 subunits of 11S proteins.…”

Molecular Cloning and Characteristics of a Lectin from the Bivalve Glycymeris yessoensis

“…It is known that the most common post-translational modification is protein glycosylation, which not only affects stability, structure, and folding but also controls the main biological pathways, ranging from protein transfer and cell adhesion to the host–pathogen interaction [ 39 ].…”

Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics

“…In summary, we see that glycosylation slightly decreases the rigidity of NA, makes the NA structure more compact, and stabilizes the NA head (Figure 2). Other work has shown that glycans can stabilize the protein structure 23,25,62 (Figure SI2), not cause any change in stability, 28,29,63 or destabilize the structure. 64 Similar to what we see, some previous work also shows that glycosylation effects on stability may not be consistent throughout the protein of interest and may change depending on which sequon is examined.…”