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Molecular machines moving along nucleic acids are involved in almost every aspect of genetic processes. I will introduce my computational work on one-cylinder walking engines PcrA and NS3 that are amongst smallest molecular motors, as well as on a multi-cylinder DNA packaging motor essential for viral assembly in bacteriophage phi29. The helicases utilize free energy from ATP hydrolysis to walk along single stranded DNA or RNA and to separate the duplex part. I have performed atomistic molecular dynamics simulations to derive potentials that govern unidirectional translocation of PcrA. The DNA/RNA unwinding activity of NS3 is modeled using mainly experimental data. For the pentameric ring motor that packages phi29 viral genome, I have constructed a mechanochemical model based on single molecule experimental measurements. Our model explains how DNA passes through the motor ring under ‘push-and-roll’, and how five motor subunits coordinate to package the DNA in four substeps each cycle. Combining approaches from detailed simulations ‘bottom up’ and functional modeling ‘top down’, I show a computational strategy that can be used in general to study multi-scale properties of molecular machines.

Tea at 3:45 in Alder Room Host Angela Cheer cheer@math.ucdavis.edu