Paper Citing NAMD - Abstract
Hurley, Margaret M.; Sellers, Michael S.
Prediction of Protein-Peptide Interactions: Application of the XPairIt API to anthrax lethal factor and substrates
SMART BIOMEDICAL AND PHYSIOLOGICAL SENSOR TECHNOLOGY X, 8719 Art. No. 87190A, 2013
As software and methodology develop, key aspects of molecular interactions such as detailed energetics and flexibility are continuously better represented in docking simulations. In the latest iteration of the XPairIt API and Docking Protocol, we perform a blind dock of a peptide into the cleavage site of the Anthrax lethal factor (LF) metalloprotein. Molecular structures are prepared from RCSB:1JKY and we demonstrate a reasonably accurate docked peptide through analysis of protein motion and, using NCI Plot, visualize and characterize the forces leading to binding. We compare our docked structure to the 1JKY crystal structure and the more recent 1PWV structure, and discuss both captured and overlooked interactions. Our results offer a more detailed look at secondary contact and show that both van der Waals and electrostatic interactions from peptide residues further from the enzyme's catalytic site are significant.
