A Steered Molecular Dynamics approach to studying interactions between ligands and receptors help computational biologists better understand the entire binding mechanism.

Working as a team in our Special Topics in Bioinformatics course, Team Piscataway (Minje Feng, Simon Gui and Jun Su) modeled the interaction between a monoclonal antibody and a prion peptide. Team Newark (Cristina Rozo, Sasha Oulianova and Nicholas Beckloff) pulled a DNA Molecule through the binding pocket of DNA Poymerase

Team Piscataway computed trajectories moving a prion peptide (yellow tube) away from the binding pocket of Fab 3F4, a monoclonal antibody, using a steered molecular dynamics (SMD) technique.

The C-alpha atom of the antibody’s C-terminus was chosen as the mobile atom in this SMD simulation. The C-alpha atom of the prion’s C-terminus was selected as the fixed atom.

The side chains of Met-P109 and Met-P112 (shown in CPK format) is inserted into a cavity formed by Tyr-H33, Trp-H50, Asp-H52, Asn-H56, Glu-H58 from chain H (lime surface) and Trp-L89, His-L95A, Gly-L91, Tyr-L32, Ile-L34 from chain L (pink surface) [Kanyo et al., 1999]. SMD was run at constant velocity using the NAMD (Not just Another Molecular Dynamics program) [Kale et al., 1999] and trajectories were displayed by VMD (Visual Molecular Dynamics) [Humphrey et. al., 1996]. Sample images from that display were captured as gif files to create this simple animation.

Team Newark pulled a DNA Molecule through the binding pocket of DNA Polymerase. Return later to learn more details!

Page last updated March 9, 2004