A topological order parameter for describing folding free energy landscapes of proteins

2018 ◽  
Vol 149 (17) ◽  
pp. 175101 ◽  
Author(s):  
Pham Dang Lan ◽  
Maksim Kouza ◽  
Andrzej Kloczkowski ◽  
Mai Suan Li
Keyword(s):  
Free Energy ◽  
Order Parameter ◽  
Topological Order ◽  
Energy Landscapes ◽  
Free Energy Landscapes ◽  
Folding Free Energy

Folding free energy landscapes of β-sheets with non-polarizable and polarizable CHARMM force fields

2018 ◽  
Vol 149 (7) ◽  
pp. 072317 ◽  
Author(s):  
Anthony J. Hazel ◽  
Evan T. Walters ◽  
Christopher N. Rowley ◽  
James C. Gumbart
Keyword(s):  
Free Energy ◽  
Force Fields ◽  
Energy Landscapes ◽  
Free Energy Landscapes ◽  
Β Sheets ◽  
Folding Free Energy

The sensitivity of folding free energy landscapes of trpzips to mutations in the hydrophobic core

2017 ◽  
Vol 19 (34) ◽  
pp. 22813-22825 ◽  
Author(s):  
Madhulika Gupta ◽  
Prabir Khatua ◽  
Charusita Chakravarty ◽  
Sanjoy Bandyopadhyay
Keyword(s):  
Free Energy ◽  
Hydrophobic Core ◽  
Energy Landscapes ◽  
The Core ◽  
Free Energy Landscapes ◽  
The Stability ◽  
Folding Free Energy

The sensitivity of the stability of folded states and free energy landscapes to the differences in the hydrophobic content of the core residues has been studied for the set of 16-residue trpzips, namely, Trpzip4, Trpzip5 and Trpzip6.

FOLDING FREE ENERGY LANDSCAPE OF THE DECAPEPTIDE CHIGNOLIN

2008 ◽  
Vol 22 (31) ◽  
pp. 3087-3098 ◽  
Author(s):  
XIANGHUA DOU ◽  
JIHUA WANG
Keyword(s):  
Free Energy ◽  
Force Field ◽  
Force Fields ◽  
Energy Landscapes ◽  
Native Structure ◽  
Good Template ◽  
Free Energy Landscapes ◽  
Folded Structures ◽  
Dynamics Simulations ◽  
Folding Free Energy

Chignolin is an artificially designed ten-residue (GYDPETGTWG) folded peptide, which is the smallest protein and provides a good template for protein folding. In this work, we completed four explicit water molecular dynamics simulations of Chignolin folding using GROMOS and OPLS-AA force fields from extended initial states without any experiment informations. The four-folding free energy landscapes of the peptide has been drawn. The folded state of Chignolin has been successfully predicated based on the free energy landscapes. The four independent simulations gave similar results. (i) The four free energy landscapes have common characters. They are fairly smooth, barrierless, funnel-like and downhill without intermediate state, which consists with the experiment. (ii) The different extended initial structures converge at similar folded structures with the lowest free energy under GROMOS and OPLS-AA force fields. In the GROMOS force field, the backbone RMSD of the folded structures from the NMR native structure of Chignolin is only 0.114 nm, which is a stable structure in this force field. In the OPLS-AA force field, the similar results have been obtained. In addition, the smallest RMSD structure is in better agreement with the NMR native structure but unlikely stable in the force field.

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