UC San Diego

Molecular Dynamic (MD) simulation is a powerful computational tool that can be applied to study biological systems at an atomic scale. Antibody 2D1 was isolated from the 1918 influenza virus surface glycoprotein hemagglutinin (HA) and was also known to cross-neutralize the 2009 pandemic influenza HA. Nevertheless, the detailed mechanism is unclear. We have conducted molecular dynamic (MD) simulations to study the interactions

between Ig-2D1 and the HAs from four different strains including its natural binder 1918HA, the 2009 HA, a seasonal 2006 strain and a 2009HA mutant. We found that in 09HA, a serine to asparagine mutation from the 18HA weakened one of the salt bridges, which leaded to the loss of hydrogen bonds and the formation of a water pocket between 09HA and Ig-2D1. Another system involves the cancer suppressor, full-length p53 protein, and its DNA counter-parts. In this system, we observed that the C-terminals contacted DNA and formed direct salt bridges. This observation supported previous research, which reported that the C-terminals interact with DNA nonspecifically to search for the binding sequence. Each of these observations was possible because MD simulations provide atomistic detail, which facilitates the study of protein-protein and protein-DNA interactions. Additionally, MD simulations can furnish refined results, but the simulation and analysis processes can be daunting. To ease the complications, we utilized the Kepler platform and developed several automated workflows that integrated multiple commands into one central process