Calibration of force-field dependency in free energy landscapes of peptide conformations by quantum chemical calculations

2002 ◽  
Vol 23 (4) ◽  
pp. 470-476 ◽  
Author(s):  
Satoshi Ono ◽  
Masataka Kuroda ◽  
Junichi Higo ◽  
Nobuyuki Nakajima ◽  
Haruki Nakamura
Keyword(s):  
Free Energy ◽  
Force Field ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Energy Landscapes ◽  
Field Dependency ◽  
Peptide Conformations ◽  
Free Energy Landscapes

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.

scholarly journals Distributions of experimental protein structures on coarse-grained free energy landscapes

2015 ◽  
Vol 143 (24) ◽  
pp. 243153 ◽  
Author(s):  
Kannan Sankar ◽  
Jie Liu ◽  
Yuan Wang ◽  
Robert L. Jernigan
Keyword(s):  
Free Energy ◽  
Protein Structures ◽  
Coarse Grained ◽  
Energy Landscapes ◽  
Free Energy Landscapes

Rapid Perturbation of Free-Energy Landscapes: From In Vitro to In Vivo

2012 ◽  
Vol 18 (21) ◽  
pp. 6420-6427 ◽  
Author(s):  
Hannah Gelman ◽  
Max Platkov ◽  
Martin Gruebele
Keyword(s):  
Free Energy ◽  
Energy Landscapes ◽  
Free Energy Landscapes
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