"Non-covalent Interactions"

An untitled artistic photo by Shahar Keinan, postdoctoral research associate, chemistry department, Duke University.
Non-covalent interactions hold the key to understanding many biological and technological problems. Very recently, researchers in the Yang Research Group at Duke introduced a new approach that's based solely on the electron density and its derivatives. The approach enables visualization of the intricate balance of interactions that stabilize a ligand in its active site.

This figure shows the results of the Yang group's new method for the V5X ligand in the active site of HDAC8 protein. Blue indicates strong, attractive interactions; green stands for van der Waals; and red indicates strong, non-bonded overlap. The top-left oval insert (A) shows the van der Waals surface between the ligand and the phenyl ring of Phe139. The top-right oval insert (B) shows the hydrogen bond between the ligand and His140. And the lower-right oval insert (C) shows the stabilization of the Zn2+ ion interaction with the protein and ligand. As a whole, the group's new method clearly highlights how a ligand "fits" the geometry of the active site and the many small contributions that add up to determine the interaction energy between the ligand and protein.