Binding diversity of the two binding sites of ricin B lectin.
Ricin B is a galactose-binding protein, which contains two binding sites. We have compared the binding properties of the two binding sites of ricin B chain toward different mono- and disaccharide ligands. The free energies of binding are calculated using the free energy perturbation simulation (thermodynamic integration method) and linear interaction energy approach using CHARMM force field. The second binding site of the protein was found to be weaker compared to the first. The details of the hydrogen-bonding scheme suggested the origin of the epimeric specificity of the protein. The reason for the weaker binding capacity of the second binding site has been addressed.
Ganguly
Debabani
D
Department of Chemistry, University of Calcutta, 92. A. P. C. Road, Kolkata-700 009, India.
Mukhopadhyay
Chaitali
C
D001665:Binding Sites; D001704:Biopolymers / Q000737:chemistry / Q000378:metabolism; D004187:Disaccharides / Q000378:metabolism; D008024:Ligands; D008958:Models, Molecular; D009005:Monosaccharides / Q000378:metabolism; D012276:Ricin / Q000737:chemistry / Q000378:metabolism*; D013816:Thermodynamics
D001704:Biopolymers; D004187:Disaccharides; D008024:Ligands; D009005:Monosaccharides; D012276:Ricin