How many dimensions are required to approximate the potential energy landscape of a model protein?
A scheme to approximate the multidimensional potential energy landscape in terms of a minimal number of degrees of freedom is proposed using a linear transformation of the original atomic Cartesian coordinates. For one particular off-lattice model protein the inherent frustration can only be reproduced satisfactorily when a relatively large number of coordinates are employed. However, when this frustration is removed in a Go-type model, the number of coordinates required is significantly lower, especially around the global potential energy minimum. To aid our interpretation of the results we consider modified disconnectivity graphs where a measure of the structural diversity and a metric relation between the stationary points are incorporated.
Komatsuzaki
Tamiki
T
Nonlinear Science Laboratory, Department of Earth and Planetary Sciences, Faculty of Science, Kobe University, Nada, Kobe 657-8501, Japan. tamiki@kobe-u.ac.jp
Hoshino
Kyoko
K
Matsunaga
Yasuhiro
Y
Rylance
Gareth J
GJ
Johnston
Roy L
RL
Wales
David J
DJ
D003198:Computer Simulation; D004735:Energy Transfer; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D011506:Proteins