From A to B: a ride in the free energy surfaces of protein G domains suggests how new folds arise

The Journal of Chemical Physics
Ludovico Sutto, Carlo Camilloni

Abstract

Metamorphic proteins are an extremely intriguing case of protein evolution and a golden opportunity to challenge the current simplified models. In a recent work, we showed that a coarse-grained Gō model can be used to study the thermodynamics of lymphotactin, a naturally occurring metamorphic protein. Here, we extend such model by including the necessary atomic detail to study the effects of the single mutations that artificially bring the GA domain of protein G to fold into the GB domain of the same protein. The results of this all-atom Gō model show how the residual structure of the denatured state is an early indicator of a forthcoming fold and function switch. These findings reconcile the results of previous studies on similar systems highlighting the different role played by secondary and tertiary interactions and suggesting a possible way for new folds to arise.

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Citations

May 9, 2014·The Journal of Chemical Physics·Michael Knott, Robert B Best
Aug 1, 2015·PLoS Computational Biology·César A Ramírez-SarmientoIrina Artsimovitch
Aug 3, 2016·Journal of Molecular Recognition : JMR·Chunnian SongGuangju Chen
Nov 1, 2016·Journal of Chemical Theory and Computation·Nathan A BernhardtUlrich H E Hansmann
Jun 3, 2016·PLoS Computational Biology·Tobias SikosekHue Sun Chan

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Methods Mentioned

BETA
protein folding
NMR

Software Mentioned

PYMOL
GA98
GROMACS
GA95s
SMOG

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