Prediction of protein-peptide interactions: application of the XPairIt API to anthrax lethal factor and substrates

Margaret M. Hurley; Michael S. Sellers

doi:10.1117/12.2014767

31 May 2013 Prediction of protein-peptide interactions: application of the XPairIt API to anthrax lethal factor and substrates

Margaret M. Hurley, Michael S. Sellers

Author Affiliations +

Proceedings Volume 8719, Smart Biomedical and Physiological Sensor Technology X; 87190A (2013) https://doi.org/10.1117/12.2014767
Event: SPIE Defense, Security, and Sensing, 2013, Baltimore, Maryland, United States

Abstract

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.

Citation Download Citation

Margaret M. Hurley and Michael S. Sellers "Prediction of protein-peptide interactions: application of the XPairIt API to anthrax lethal factor and substrates", Proc. SPIE 8719, Smart Biomedical and Physiological Sensor Technology X, 87190A (31 May 2013); https://doi.org/10.1117/12.2014767

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