Related Experiment Video
Updated: Aug 1, 2026

An Assay for Quantifying Protein-RNA Binding in Bacteria
Published on: June 12, 2019
Binding diversity of the two binding sites of ricin B lectin
Debabani Ganguly1, Chaitali Mukhopadhyay
1Department of Chemistry, University of Calcutta, 92. A. P. C. Road, Kolkata-700 009, India.
Abstract:
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.
Related Concept Videos
Ligand Binding Sites
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Ligand Binding and Linkage
Cooperative Binding of Transcription Regulators
Ligand Binding Sites
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

