Dynamics simulation of soybean agglutinin (SBA) dimer reveals the impact of glycosylation on its enhanced structural stability. (16th June 2016)

• Record Type: Journal Article
• Authors: Halder, Swagata; Surolia, Avadhesha; Mukhopadhyay, Chaitali
• Is Part Of: Carbohydrate research. Volume 428(2016)
• Page Start: 8
• Page End: 17
• Publication Date: 2016-06-16
• Subjects: Soybean agglutinin (SBA) dimer -- Glycosylation -- Molecular dynamics -- Secondary structure -- Vibrational entropy -- Contact map; Carbohydrates -- Periodicals; Chemistry, Organic -- Periodicals; Biochemistry -- Periodicals; Carbohydrates -- Periodicals; Chimie organique -- Périodiques; Glucides -- Périodiques; Biochemistry; Carbohydrates; Chemistry, Organic; Periodicals; Electronic journals; 507.78
• DOI: 10.1016/j.carres.2016.04.009
• Languages: English
• ISSNs: 0008-6215

Abstract

Highlights: Effect of glycosylation on hydrogen bond energy. Survival time analysis of interfacial hydrogen bonds in unfolding temperatures. Configurational entropy analysis of soybean agglutinin. Secondary structure analysis of SBA dimer at its unfolding temperature. Calculation of binding free energy. Graphical Abstract: Abstract: The legume lectins are widely used as a model system for studying protein–carbohydrate and protein–protein interactions. They exhibit a fascinating quaternary structure variation. Recently, it has become clear that lectins exist as oligomers. Soybean agglutinin is a tetrameric legume lectin, each of whose subunits are glycosylated. In the present study we explore the main origin for the stability of soybean agglutinin dimer. In order to understand the role of glycosylation on the dimeric interface, we have carried out normal (298K), high temperatures (380K, 500K) long explicit solvent molecular dynamics (MD) simulations and compared the structural and conformational changes between the glycosylated and non-glycosylated dimers. The study reveals that the high degree of stability at normal temperature is mostly contributed by interfacial ionic interactions (~200 kcal/mol) between polar residues like Lys, Arg, Asp, Thr, Ser, Asn and Gln (62%). It maintains its overall folded conformation due to high subunit interactions at the non-canonical interface. Mainly five important hydrogen bonds between CO of one β sheet of one subunit with the N-H of other β strand of the other subunit help to maintain the structural integrity. Ten inter subunit salt-bridge interactions between Arg 185–Asṕ192, Lys 163–Asṕ169, Asp 169–Lyś 163 and Asp 192–Arǵ 185 at non-canonical interface appear to be important to maintain the three dimensional structure of SBA dimer. Moreover, our simulation results revealed that increase in vibrational entropy could decrease the free energy and contribute to the glycan-induced stabilization by ~45 kcal/mol at normal temperature.