From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding

Annual Review of Physical Chemistry
J E Shea, Charles L Brooks

Abstract

Beginning with simplified lattice and continuum "minimalist" models and progressing to detailed atomic models, simulation studies have augmented and directed development of the modern landscape perspective of protein folding. In this review we discuss aspects of detailed atomic simulation methods applied to studies of protein folding free energy surfaces, using biased-sampling free energy methods and temperature-induced protein unfolding. We review studies from each on systems of particular experimental interest and assess the strengths and weaknesses of each approach in the context of "exact" results for both free energies and kinetics of a minimalist model for a beta-barrel protein. We illustrate in detail how each approach is implemented and discuss analysis methods that have been developed as components of these studies. We describe key insights into the relationship between protein topology and the folding mechanism emerging from folding free energy surface calculations. We further describe the determination of detailed "pathways" and models of folding transition states that have resulted from unfolding studies. Our assessment of the two methods suggests that both can provide, often complementary, details of folding mechan...Continue Reading

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Citations

Mar 27, 2002·Journal of Computational Chemistry·Brian N Dominy, Charles L Brooks
Aug 19, 2007·Cell Biochemistry and Biophysics·Philip LeDuc, Russell Schwartz
Nov 11, 2003·Journal of Molecular Biology·John Karanicolas, Charles L Brooks
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Methods Mentioned

BETA
peptide folding
protein folding
peptide-folding
NMR
X

Software Mentioned

CHARMM

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