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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
Author(s) -
Alfano Andrew Benton,
Leffler Abba E,
Wriggers Willy,
Herman Tim,
Epifano Alex,
Hickey Jack,
LaCosta Will,
Li Sydney,
Meiring Henry,
Temares Daniell,
Van Besien Alexa,
Zhou Ashley,
De Luke,
O'Mara Deirdre
Publication year - 2011
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.25.1_supplement.909.1
Subject(s) - molecular dynamics , supercomputer , folding (dsp implementation) , domain (mathematical analysis) , computer science , protein folding , visualization , ww domain , physics , crystallography , chemistry , computational chemistry , engineering , artificial intelligence , mathematics , operating system , mechanical engineering , biochemistry , gene , mathematical analysis , nuclear magnetic resonance
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.