Physics – Condensed Matter – Statistical Mechanics
Scientific paper
2009-10-25
Physical Review E: Statistical, Nonlinear, and Soft Matter Physics 6, 80 (2009) 061907-1-11
Physics
Condensed Matter
Statistical Mechanics
published Physical Review E, vol. 80, 061907-1-11 (2009)
Scientific paper
10.1103/PhysRevE.80.061907
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 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 Johannnes-Geert
Nakagawa Naoko
Peyrard Michel
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