Critical examination of the inherent-structure-landscape analysis of two-state folding proteins.
Recent studies attracted the attention on the inherent-structure-landscape (ISL) approach as a reduced description of proteins allowing to map their full thermodynamic properties. However, the analysis has been so far limited to a single topology of a two-state folding protein, and the simplifying assumptions of the method have not been examined. In this work, we construct the thermodynamics of four two-state folding proteins of different sizes and secondary structure by molecular dynamics (MD) simulations using the ISL method and critically examine possible limitations of the method. Our results show that the ISL approach correctly describes the thermodynamics function, such as the specific heat, on a qualitative level. Using both analytical and numerical methods, we show that some quantitative limitations cannot be overcome with enhanced sampling or the inclusion of harmonic corrections.
Hagmann
Johannes-Geert
JG
Université de Lyon, Ecole Normale Supérieure de Lyon, Laboratoire de Physique, CNRS, 46 Allée d'Italie, 69364 Lyon, France.
Nakagawa
Naoko
N
Peyrard
Michel
M
D003198:Computer Simulation; D004735:Energy Transfer; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*
D011506:Proteins