Volume 90 Issue 29 | p. 41 | Concentrates
Issue Date: July 16, 2012

Simulations Peg Protein Folding

Molecular dynamics simulations are the first that replicate experimental thermodynamic and kinetic data on such a large protein
Department: Science & Technology
News Channels: Biological SCENE
Keywords: protein folding, green fluorescent protein
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Simulated folding routes along a 3-D energy coordinate indicate how GFP intermediates reach the protein’s natively folded structure (bottom right).
Credit: Proc. Natl. Acad. Sci. USA
A cartoon showing several proteins arranged around a three-dimensional reaction coordinate diagram.
 
Simulated folding routes along a 3-D energy coordinate indicate how GFP intermediates reach the protein’s natively folded structure (bottom right).
Credit: Proc. Natl. Acad. Sci. USA
Simulation shows the path taken by an apparently quite nervous green fluorescent protein intermediate as it folds into the protein’s native structure.
Credit: Courtesy of Dave Thirumalai

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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ISSN 0009-2347
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