Physical models designed to demonstrate the folding pathway of FiP35 WW domain as predicted by molecular dynamics (MD) simulations using Anton, an MD dedicated supercomputer: 2011 Pingry School S.M.A.R.T. Team Project

Abstract

The Pingry School's 2010–2011 S.M.A.R.T. (Students Modeling A Research Topic) Team worked with Abba E. Leffler and Willy Wriggers of D.E. Shaw Research (DESRES) to explore the phenomenon of protein folding. Researchers at DESRES utilized molecular dynamics (MD) in combination with the Anton supercomputer to generate simulations of the fastest folding WW domain reported to date, FiP35 (Shaw et al. 2010). Anton's ability to predict trajectories of the atoms that constitute a protein molecule resulted in the discovery of FiP35's tendency to follow a sequential, well‐defined folding pathway. The Pingry S.M.A.R.T. Team used these findings as a basis for the design of a series of 3‐dimensional models, created with Jmol and a rapid prototyping 3‐dimensional printer, which collectively describe the protein's tendency to fold from its high‐energy, denatured state to its low energy, folded state (native conformation) according to a predictable pathway. The team also organized a corresponding Proteopedia article with embedded Jmol applets and information on the FiP35 folding pathway. This level of visualization enabled by MD simulations assists in understanding the structural basis of protein folding. The Pingry School S.M.A.R.T. Team coordinates with Tim Herman and Shannon Colton of the Center for Biomolecular Modeling at the Milwaukee School of Engineering, which receives funding from NIH‐NCRR‐SEPA.