Binding diversity of the two binding sites of ricin B lectin

作者：Ganguly Debabani; Mukhopadhyay Chaitali^*

来源：Biopolymers, 2006, 83(1): 83-94.

DOI：10.1002/bip.20530

• binding site
• free energy perturbation
• linear interaction energy
• MD simulation
• ricin B chain

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 di-saccharide 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.

• 出版日期2006-9