William Scott's hammerhead ribozyme makes the cover of Chemistry & Biology

William Scott's hammerhead ribozyme makes the cover of Chemistry & Biology
William Scott's hammerhead ribozyme makes the cover of Chemistry & Biology
Monday, April 28, 2008

The cover of the April 2008 issue of Chemistry & Biology features an image created by William Scott, associate professor of chemistry and biochemistry at UC Santa Cruz and the Center for Molecular Biology of RNA. The image depicts the three-dimensional chemical structure of an RNA enzyme—a full-length hammerhead ribozyme.

'This particular enzyme works via acid-base catalysis,' Scott said. The acid in the active site on the ribozyme is depicted in magenta; the base in red. The cleavage reaction takes place in the white region. Bound manganese ions that aid the reaction are depicted as small purple spheres.

Scott pointed out that this is a static image determined from the x-ray crystallography structure, but 'chemistry is an inherently dynamic process. Bonds are breaking and forming.'

To find out how the ribozyme actually works, Scott and his graduate student, Monika Martick, collaborated with researchers at the University of Minnesota, Darrin York, associate professor of chemistry, and Tai-Sung Lee, a senior scientist in his laboratory.

'The York lab does computational simulations of the reaction dynamics that are consistent with both the structure and the known chemistry of the reaction,' Scott said.

They used a computational approach to determine what the base and the acid do as the ribozyme mediates acid-base catalysis. Scott said, 'It turns out that a bound water molecule we observe in the active site functions as a proton-relay mechanism.'