Revisiting the inherent structure landscape analysis of two-state folding proteins

Abstract : 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.
Document type :
Preprints, Working Papers, ...
Complete list of metadatas

https://hal-ens-lyon.archives-ouvertes.fr/ensl-00426353
Contributor : Michel Peyrard <>
Submitted on : Sunday, October 25, 2009 - 8:20:50 AM
Last modification on : Thursday, April 19, 2018 - 2:54:03 PM
Long-term archiving on : Thursday, June 17, 2010 - 5:56:09 PM

Files

paper-pre-corrected.pdf
Files produced by the author(s)

Identifiers

  • HAL Id : ensl-00426353, version 1
  • ARXIV : 0910.4710

Collections

Citation

Johannnes-Geert Hagmann, Naoko Nakagawa, Michel Peyrard. Revisiting the inherent structure landscape analysis of two-state folding proteins. 2009. ⟨ensl-00426353v1⟩

Share

Metrics

Record views

13

Files downloads

2