Non-covalent Interactions
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"Non-covalent Interactions"

November 10, 2011
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. This image was among the entries in the "Envisioning the Invisible" 2010 Mahato memorial event photo contest, organized by the engineering graduate student council at the Pratt School of Engineering at Duke University. The event, which will be annual, honors Abhijit Mahato, a former Duke engineering graduate student who was tragically murdered in 2008. Further information about the contest and pictures of other winning entries and submissions is available Here. [Research supported by National Science Foundation grants CHE 06-16849 and CHE 10-12357.] (Date of Image: August 2010)

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