Simbios Talk by Jin Yu, UC Berkeley, March 11, 2009

Title: Probing the design principle: molecular motor scooting along DNA

Molecular motors translocating nucleic acids are involved in almost every aspect of DNA/RNA metabolisms and tied closely to evolution. In this talk I will introduce my computational studies on two types of these systems. One type is of a simplest geometry containing only one ATP binding site, for which I will discuss a small helicase stepping along single strand DNA with alternating domain mobilities, and an additional case as the translocation is coupled to base pair unwinding in the DNA/RNA duplex. The other type assembles with multiple subunits and coordinates multiple catalytic sites, for which I will discuss a DNA packaging motor forcing the DNA into viral capsid by "push-and-roll". With approaches from atomistic simulation "bottom-up" and functional modeling "top-down", I will show how one can probe the evolutionary "design" principles of these nano-engines by integrating information at multiple levels. The principles manifested may benefit future drug design and molecular engineering.