Group:SMART:2006 Pingry SMART Team

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Revision as of 19:57, 14 July 2009

RNA Polymerase Holoenzyme - Open Promoter Complex (RPo)

SMART Teams (Students Modeling A Research Topic) are teams of high school students and their teachers who work with research scientists to design and construct physical models of proteins or other molecular structures that are being investigated in the scientists’ laboratories. S.M.A.R.T. Teams use state-of-the-art molecular design software and rapid prototyping technologies to produce these unique models.

With the support of the Center for Biomolecular Modeling at the Milwaukee School of Engineering, Pingry has established S.M.A.R.T. Teams since the 2003-2004 academic year. The 2006 Pingry S.M.A.R.T. Team worked with Seth Darst, Rockefeller University.

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. 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.

RNA polymerase (RNAP) is the enzymatic machinery responsible for transcription, a key regulatory step in gene expression. The prokaryotic RNAP is a highly conserved, "crab claw" shaped enzyme with a molecular mass of ~400kD. In order to recognize a promoter to begin transcription, the 5-subunit core enzyme (α,α,β,β’,ω) must bind to one of various sigma (σ) factors; this form of the enzyme is called the holoenzyme. Each of the different σ factors recognize different promoter elements upstream of genes allowing the cell to respond to various environmental cues. Once holoenzyme binds the promoter, DNA downstream of this interaction is brought into the enzyme and melted to expose single-stranded DNA. This stage of transcription initiation is described here using a model of RNA polymerase-open-promoter-complex (RPo).