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Dynamics simulation of soybean agglutinin (SBA) dimer reveals the impact of glycosylation on its enhanced structural stability

Halder, Swagata and Surolia, Avadhesha and Mukhopadhyay, Chaitali (2016) Dynamics simulation of soybean agglutinin (SBA) dimer reveals the impact of glycosylation on its enhanced structural stability. In: CARBOHYDRATE RESEARCH, 428 . pp. 8-17.

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Official URL: http://dx.doi.org/10.1016/j.carres.2016.04.009


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 sub-units 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 (similar to 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 C=O of one beta sheet of one subunit with the N-H of other beta strand of the other subunit help to maintain the structural integrity. Ten inter subunit salt-bridge interactions between Arg 185-Asp192, Lys 163-Asp169, Asp 169-Lys 163 and Asp 192-Arg 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 similar to 45 kcal/mol at normal temperature. (C) 2016 Elsevier Ltd. All rights reserved.

Item Type: Journal Article
Additional Information: Copy right for this article belongs to the ELSEVIER SCI LTD, THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND
Keywords: Soybean agglutinin (SBA) dimer; Glycosylation; Molecular dynamics; Secondary structure; Vibrational entropy; Contact map
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 16 Jun 2016 07:51
Last Modified: 16 Jun 2016 07:51
URI: http://eprints.iisc.ac.in/id/eprint/53994

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