393 research outputs found
Conformational Temperature Characterizing the Folding of a Protein
The time sequences of the molecular dynamics simulation for the folding
process of a protein is analyzed with the inherent structure landscape which
focuses on configurational dynamics of the system. Time dependent energy and
entropy for inherent structures are introduced and from these quantities a
conformational temperature is defined. The conformational temperature follows
the time evolution of a slow relaxation process and reaches the bath
temperature when the system is equilibrated. We show that the nonequilibrium
system is described by two temperatures, one for fast vibration and the other
for slow configurational relaxation, while the equilibrium system is by one
temperature. The proposed formalism is applicable widely for the systems with
many metastable states
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 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.Comment: published Physical Review E, vol. 80, 061907-1-11 (2009
- …