Issue Date: July 16, 2012
Simulations Peg Protein Folding
Data from theoretical simulations of the folding of green fluorescent protein (GFP) agree well with previous experimental results on the thermodynamics and kinetics of the protein’s folding (Proc. Natl. Acad. Sci. USA, DOI: 10.1073/pnas.1201808109). GFP is widely used as a fluorescent marker in molecular biology studies, so the new results could aid the design of modified forms of GFPs for a range of applications. Devarajan (Dave) Thirumalai of the University of Maryland notes that his team’s molecular dynamics simulations of GFP’s folding pathways are the first to replicate experimental thermodynamic and kinetic data on such a large protein. GFP has about 240 amino acid residues, whereas similar molecular dynamics simulations had been done only for proteins with fewer than 100 residues, he says. Thirumalai and coworkers used a technique called the Molecular Transfer Model to simulate denaturant-induced GFP folding. The data confirm experimental findings showing that GFP folds initially to an ensemble of intermediate states, which then take one of four possible pathways to reach GFP’s native conformation.
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