Dynamics simulation of soybean agglutinin (SBA) dimer reveals the impact of glycosylation on its enhanced structural stability.
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.
Department of Chemistry, University of Calcutta, 92, A. P. C. Road, Kolkata 700 009, India.
Swagata
S
Halder
Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India. Electronic address: surolia@mbu.iisc.ernet.in.
Avadhesha
A
Surolia
Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India. Electronic address: chaitalicu@yahoo.com.
Chaitali
C
Mukhopadhyay
D006031:Glycosylation; D006860:Hydrogen Bonding; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D037121:Plant Lectins / Q000737:chemistry*; D017510:Protein Folding; D055503:Protein Multimerization; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D030262:Soybean Proteins / Q000737:chemistry*; D013816:Thermodynamics; D010835:Phytohemagglutinins
D037121:Plant Lectins; D030262:Soybean Proteins; C028824:soybean lectin; D010835:Phytohemagglutinins
Contact map; Glycosylation; Molecular dynamics; Secondary structure; Soybean agglutinin (SBA) dimer; Vibrational entropy