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Recent studies attracted the attention on the inherent structure landscape(ISL) approach as a reduced description of proteins allowing to map their fullthermodynamic properties. However, the analysis has been so far limited to asingle topology of a two-state folding protein, and the simplifying assumptionsof the method have not been examined. In this work, we construct thethermodynamics of four two-state folding proteins of different sizes andsecondary structure by MD simulations using the ISL method, and criticallyexamine possible limitations of the method. Our results show that the ISLapproach correctly describes the thermodynamics function, such as the specificheat, on a qualitative level. Using both analytical and numerical methods, weshow that some quantitative limitations cannot be overcome with enhancedsampling or the inclusion of harmonic corrections.

Critical examination of the inherent-structure-landscape analysis of two-state folding proteins