Physical Model of Prokaryotic RNA Polymerase Holoenzyme; 2006 Pingry School S.M.A.R.T. Team Project

Abstract

The Pingry School’s S.M.A.R.T. Team (Students Modeling A Research Topic) has worked with Seth Darst to design and produce an accurate, three-dimensional physical model of prokaryotic RNA polymerase holoenzyme using rapid prototyping technology. Prokaryotic transcription is ensured by a multi-subunit RNA polymerase. To recognize a promoter and begin transcription, the 5-subunit core enzyme must bind to one of several sigma factors; forming the 6-subunit holoenzyme. Each of the different sigma factors helps the cell respond to various stimuli by allowing transcription of genes regulated by different promoters. Discussions with Seth Darst allowed the Pingry S.M.A.R.T. Team to use RP RasMol to design models of RNA polymerase, highlighting aspects of the enzyme’s function and its interaction with antibiotics. These final designs were used to direct rapid prototyping machines to build physical models. Along with the web tutorial created by the students, these physical models are “communication tools” that can be used to enhance the understanding of RNA polymerase and the transcription cycle among the scientific and academic community. By contributing this new tool to Seth Darst’s research team, the students have had the opportunity to experience and participate in “real science” as it is practiced in an active research lab. This work is supported by a grant awarded to Timothy Herman by the NIH NCRR SEPA program.